Index (biojava-structure 6.0.1 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes All Packages

A

aaScore(char, char) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
AbstractCifFileSupplier<S> - Class in org.biojava.nbio.structure.io.cif: Convert a BioJava object to a CifFile.
AbstractCifFileSupplier() - Constructor for class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier
AbstractCifFileSupplier.WrappedAtom - Class in org.biojava.nbio.structure.io.cif: Wrapped atoms represent individual atoms enriched with model- and chain-level information.
AbstractScoresCache - Class in org.biojava.nbio.structure.align.multiple: Abstact implementation of the ScoresCache with the shared code used in all objects with a variables cache.
AbstractScoresCache() - Constructor for class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
AbstractScoresCache(AbstractScoresCache) - Constructor for class org.biojava.nbio.structure.align.multiple.AbstractScoresCache
AbstractStructureAlignment - Class in org.biojava.nbio.structure.align
AbstractStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.AbstractStructureAlignment
AbstractUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce: Base class for a new structure alignment CLI.
AbstractUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
Ac - org.biojava.nbio.structure.Element
ACTINOID - org.biojava.nbio.structure.ElementType
AD - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues
add(int, int, int, int) - Method in class org.biojava.nbio.structure.align.helper.JointFragments
add(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc: add two atoms ( a + b).
add(AtomContact) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
add(GroupContact) - Method in class org.biojava.nbio.structure.contact.GroupContactSet
add(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList
addAlgorithm(StructureAlignment) - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory: Adds a new StructureAlignment algorithm to the list.
addAll(Collection<AtomContact>) - Method in class org.biojava.nbio.structure.contact.AtomContactSet
addAltLoc(Group) - Method in interface org.biojava.nbio.structure.Group: Add a group that is an alternate location for this group.
addAltLoc(Group) - Method in class org.biojava.nbio.structure.HetatomImpl
addAtom(Atom) - Method in interface org.biojava.nbio.structure.Group: Add an atom to this group.
addAtom(Atom) - Method in class org.biojava.nbio.structure.HetatomImpl: Add an atom to this group.
addAtomAsaC(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa
addAtomAsaU(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa
addAtomContact(AtomContact) - Method in class org.biojava.nbio.structure.contact.GroupContact
addAtoms(Atom[]) - Method in class org.biojava.nbio.structure.contact.Grid: Adds a set of atoms, subsequent call to Grid.getIndicesContacts() or Grid.getAtomContacts() will produce the interatomic contacts.
addAtoms(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.contact.Grid: Adds the i and j atoms and fills the grid.
addAtoms(Atom[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid: Adds a set of atoms, subsequent call to Grid.getIndicesContacts() or Grid.getAtomContacts() will produce the interatomic contacts.
addAtoms(Atom[], BoundingBox, Atom[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid: Adds the i and j atoms and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.
addAxis(Matrix4d, int, CESymmParameters.SymmetryType) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes: Adds a new axis of symmetry to the bottom level of the tree
addBond(Bond) - Method in interface org.biojava.nbio.structure.Atom: Add a bond
addBond(Bond) - Method in class org.biojava.nbio.structure.AtomImpl
addBridge(BetaBridge) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState: Adds a Bridge to the residue.
addChain(Chain) - Method in class org.biojava.nbio.structure.EntityInfo: Add new Chain to this EntityInfo
addChain(Chain) - Method in class org.biojava.nbio.structure.Model
addChain(Chain) - Method in interface org.biojava.nbio.structure.Structure: Add a new chain to the first model
addChain(Chain) - Method in class org.biojava.nbio.structure.StructureImpl: Add a new chain to the first model
addChain(Chain, int) - Method in interface org.biojava.nbio.structure.Structure: Add a new chain to the model specified by the given index
addChain(Chain, int) - Method in class org.biojava.nbio.structure.StructureImpl: Add a new chain to the model specified by the given index
addCharges(Structure) - Static method in class org.biojava.nbio.structure.io.ChargeAdder: Function to add the charges to a given structure.
addChemComp(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary: Add a new component to the dictionary
addCoords(Point3d[]) - Method in class org.biojava.nbio.structure.contact.Grid: Adds a set of coordinates, subsequent call to Grid.getIndicesContacts() will produce the contacts, i.e.
addCoords(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.contact.Grid: Adds the i and j coordinates and fills the grid.
addCoords(Point3d[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid: Adds a set of coordinates, subsequent call to Grid.getIndicesContacts() will produce the contacts, i.e.
addCoords(Point3d[], BoundingBox, Point3d[], BoundingBox) - Method in class org.biojava.nbio.structure.contact.Grid: Adds the i and j coordinates and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.
addEntityInfo(EntityInfo) - Method in interface org.biojava.nbio.structure.Structure: Add an EntityInfo to this Structure
addEntityInfo(EntityInfo) - Method in class org.biojava.nbio.structure.StructureImpl: Add an EntityInfo to this Structure
addExtension(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: define supported file extensions compressed extensions .Z,.gz do not need to be specified they are dealt with automatically.
addExtension(String) - Method in interface org.biojava.nbio.structure.io.StructureIOFile: Associates a file extension with this particular StructureIOFile, indicating that files of that type can be parsed.
addGroup(Group) - Method in interface org.biojava.nbio.structure.Chain: Add a group to the list of ATOM record group of this chain.
addGroup(Group) - Method in class org.biojava.nbio.structure.ChainImpl
addGroupsToStructure(Structure, Collection<Group>, int, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Add a list of groups to a new structure.
addGroupToStructure(Structure, Group, int, Chain, boolean) - Static method in class org.biojava.nbio.structure.StructureTools: Adds a particular group to a structure.
addHelix(Helix) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
addIindex(int) - Method in class org.biojava.nbio.structure.contact.GridCell
addJindex(int) - Method in class org.biojava.nbio.structure.contact.GridCell
addMatrixListener(MatrixListener) - Method in class org.biojava.nbio.structure.align.ce.CECalculator
addMatrixListener(MatrixListener) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
addMember(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster
addMirror(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation
addModel(List<Chain>) - Method in interface org.biojava.nbio.structure.Structure: Add a new model.
addModel(List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl: Add a new model.
addMultipleAlignment(MultipleAlignment) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Add a new MultipleAlignment to the end of the ensemble and set its parent ensemble to this.
addMultipleAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
addNcsEquivalent(StructureInterface, StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Add an interface to the list, possibly defining it as NCS-equivalent to an interface already in the list.
addPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
addPoint(Point3d, double) - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia
addPoint(Point3d, T) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox
addProgressListener(AlignmentProgressListener) - Method in class org.biojava.nbio.structure.align.StructurePairAligner
addResidue(SiftsResidue) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment
addRotation(Rotation) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
addSegment(SiftsSegment) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity
addSeqRes(Chain, String) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils: Add the missing groups to the SeqResGroups.
addSSBond(Bond) - Method in interface org.biojava.nbio.structure.Structure: Add a single disulfide Bond to this structure
addSSBond(Bond) - Method in class org.biojava.nbio.structure.StructureImpl: Adds a single disulfide Bond to this structure
addTransformation(String) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup
AFP - Class in org.biojava.nbio.structure.align.model: A class to represent a FATCAT aligned fragment pair (AFP)
AFP() - Constructor for class org.biojava.nbio.structure.align.model.AFP
afp2Res(AFPChain, int, int[], int) - Static method in class org.biojava.nbio.structure.align.AFPTwister: Set the list of equivalent residues in the two proteins given a list of AFPs WARNING: changes the values for FocusRes1, focusRes2 and FocusResn in afpChain!
AFPAlignmentDisplay - Class in org.biojava.nbio.structure.align.util
AFPAlignmentDisplay() - Constructor for class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
AFPCalculator - Class in org.biojava.nbio.structure.align.fatcat.calc: A class that performs calculations on AFPChains
AFPCalculator() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
AFPChain - Class in org.biojava.nbio.structure.align.model: A bean to contain the core of a structure alignment.
AFPChain(String) - Constructor for class org.biojava.nbio.structure.align.model.AFPChain: Construction of an AFPChain needs the algorithm name, since downstream analysis methods (scores, display, etc) behave differently if the alignment is flexible (created with FatCat).
AFPChain(AFPChain) - Constructor for class org.biojava.nbio.structure.align.model.AFPChain: Copy constructor
AFPChainer - Class in org.biojava.nbio.structure.align.fatcat.calc: a class to chain AFPs to an alignment
AFPChainer() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
AFPChainFlipper - Class in org.biojava.nbio.structure.align.xml
AFPChainFlipper() - Constructor for class org.biojava.nbio.structure.align.xml.AFPChainFlipper
AFPChainScorer - Class in org.biojava.nbio.structure.align.util
AFPChainScorer() - Constructor for class org.biojava.nbio.structure.align.util.AFPChainScorer
AfpChainWriter - Class in org.biojava.nbio.structure.align.model: A class to convert the data in an AfpChain object to various String outputs.
AfpChainWriter() - Constructor for class org.biojava.nbio.structure.align.model.AfpChainWriter
AFPChainXMLConverter - Class in org.biojava.nbio.structure.align.xml
AFPChainXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
AFPChainXMLParser - Class in org.biojava.nbio.structure.align.xml
AFPChainXMLParser() - Constructor for class org.biojava.nbio.structure.align.xml.AFPChainXMLParser
AFPOptimizer - Class in org.biojava.nbio.structure.align.fatcat.calc
AFPOptimizer() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
afpPairConn(int, int, FatCatParameters, AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer: //Key function: calculate the connectivity of AFP pairs //no compatibility criteria is executed //note: afp1 is previous to afp2 in terms of the position //this module must be optimized
AFPPostProcessor - Class in org.biojava.nbio.structure.align.fatcat.calc: does post processing after alignment chaingin
AFPPostProcessor() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
AFPTwister - Class in org.biojava.nbio.structure.align
AFPTwister() - Constructor for class org.biojava.nbio.structure.align.AFPTwister
Ag - org.biojava.nbio.structure.Element
Al - org.biojava.nbio.structure.Element
algorithmName - Static variable in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.CeCPMain
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.CeMain
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.CeSideChainMain
algorithmName - Static variable in class org.biojava.nbio.structure.align.ce.OptimalCECPMain
algorithmName - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCat
algorithmName - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
algorithmName - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
algorithmName - Static variable in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
algorithmName - Static variable in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
algorithmName - Static variable in class org.biojava.nbio.structure.symmetry.internal.CeSymm
ALIGFACTOR - Static variable in class org.biojava.nbio.structure.align.pairwise.Gotoh
AligMatEl - Class in org.biojava.nbio.structure.align.helper
AligMatEl() - Constructor for class org.biojava.nbio.structure.align.helper.AligMatEl
align(List<Atom[]>) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
align(List<Atom[]>) - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner: Run an alignment while specifying the atoms to be aligned.
align(List<Atom[]>, Object) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain
align(List<Atom[]>, Object) - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner: Run an alignment and also send a bean containing the parameters.
align(List<Subunit>, List<Subunit>, SubunitClustererParameters, QsAlignParameters) - Static method in class org.biojava.nbio.structure.align.quaternary.QsAlign
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeMain
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
align(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
align(Atom[], Atom[]) - Method in interface org.biojava.nbio.structure.align.StructureAlignment: Run an alignment while specifying the atoms to be aligned.
align(Atom[], Atom[], boolean, FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.ce.CeCPMain: Aligns ca1 and ca2 using a heuristic to check for CPs.
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.ce.CeMain: Align ca2 onto ca1.
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain: Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid
align(Atom[], Atom[], Object) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner
align(Atom[], Atom[], Object) - Method in interface org.biojava.nbio.structure.align.StructureAlignment: run an alignment and also send a bean containing the parameters.
align(Atom[], Atom[], FatCatParameters, boolean) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
align(Atom[], Atom[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Calculate the protein structure superimposition, between two sets of atoms.
align(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm
align(Structure, String, Structure, String) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Align two chains from the structures.
align(Structure, String, Structure, String, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Aligns two chains from the structures using user provided parameters.
align(Structure, List<Chain>) - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner
align(Structure, Structure) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Calculate the alignment between the two full structures with default parameters
align(Structure, Structure, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner: Calculate the alignment between the two full structures with user provided parameters
align(Structure, Structure, SubunitClustererParameters, QsAlignParameters) - Static method in class org.biojava.nbio.structure.align.quaternary.QsAlign
align_NPE(Matrix, StrucAligParameters) - Static method in class org.biojava.nbio.structure.align.pairwise.AligNPE: Align without penalizing end-gaps.
Alignable - Interface in org.biojava.nbio.structure.align.pairwise
alignFlexible(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
alignmentAsMap(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Creates a Map specifying the alignment as a mapping between residue indices of protein 1 and residue indices of protein 2.
AlignmentProgressListener - Class in org.biojava.nbio.structure.align.pairwise: A class to listen to progress of the structure alignment calculations
AlignmentProgressListener() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
AlignmentResult - Class in org.biojava.nbio.structure.align.pairwise: A class to track the alignment results in a flat file
AlignmentResult() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlignmentResult
AlignmentTools - Class in org.biojava.nbio.structure.align.util: Methods for analyzing and manipulating AFPChains and for other pairwise alignment utilities.
AlignmentTools() - Constructor for class org.biojava.nbio.structure.align.util.AlignmentTools
AlignmentTools.IdentityMap<K> - Class in org.biojava.nbio.structure.align.util: A Map can be viewed as a function from K to V.
alignmentToSIF(Writer, AFPChain, Atom[], Atom[], String, String) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Creates a simple interaction format (SIF) file for an alignment.
alignOptimal(Atom[], Atom[], Object, AFPChain[]) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain: Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
AligNPE - Class in org.biojava.nbio.structure.align.pairwise
AligNPE() - Constructor for class org.biojava.nbio.structure.align.pairwise.AligNPE
alignPermuted(Atom[], Atom[], Object, int) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain: Aligns ca1 with ca2 permuted by cp residues.
alignRigid(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
alignRigid(Atom[], Atom[], FatCatParameters) - Method in class org.biojava.nbio.structure.align.fatcat.FatCat
alignSuperfamily() - Method in class demo.DemoSCOP
AlignUtils - Class in org.biojava.nbio.structure.align.helper: Low level helper methods for CE and FATCAT algorithms.
AlignUtils() - Constructor for class org.biojava.nbio.structure.align.helper.AlignUtils
ALKALI_METAL - org.biojava.nbio.structure.ElementType
ALKALINE_EARTH_METAL - org.biojava.nbio.structure.ElementType
ALL_CURRENT_ENDPOINT - Static variable in class org.biojava.nbio.structure.PDBStatus
ALL_POLYMER_TYPES - Static variable in enum org.biojava.nbio.structure.chem.PolymerType: Convenience Set of all polymer types.
AllChemCompProvider - Class in org.biojava.nbio.structure.chem: A ChemComp provider that downloads and caches the components.cif file from the wwPDB site.
AllChemCompProvider() - Constructor for class org.biojava.nbio.structure.chem.AllChemCompProvider
AltAligComparator - Class in org.biojava.nbio.structure.align.pairwise: A comparator to sort AlternativeAlignments based on their number of equivalent residues and RMSD.
AltAligComparator() - Constructor for class org.biojava.nbio.structure.align.pairwise.AltAligComparator
AlternativeAlignment - Class in org.biojava.nbio.structure.align.pairwise: Implements a class which handles one possible (alternative) solution.
AlternativeAlignment() - Constructor for class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
Am - org.biojava.nbio.structure.Element
AMINO_ACID_MATCHER - Static variable in class org.biojava.nbio.structure.AtomPositionMap: Matches CA atoms of protein groups
AminoAcid - Interface in org.biojava.nbio.structure: A Group that represents an AminoAcid.
AMINOACID - org.biojava.nbio.structure.GroupType: The type for amino acids (L-peptides)
AminoAcidImpl - Class in org.biojava.nbio.structure: AminoAcid inherits most from Hetatom.
AminoAcidImpl() - Constructor for class org.biojava.nbio.structure.AminoAcidImpl: inherits most from Hetero and has just a few extensions.
amount(Atom) - Static method in class org.biojava.nbio.structure.Calc: Gets the length of the vector (2-norm)
analyze() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters: This method is the main function call to extract all step parameters, pairing parameters, and sequence information from the Structure object provided to the constructor.
analyze(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm: Analyze the symmetries of the input Atom array using the DEFAULT parameters.
analyze(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm: Analyze the symmetries of the input Atom array using the provided parameters.
analyzeLevel(Atom[], CESymmParameters) - Static method in class org.biojava.nbio.structure.symmetry.internal.CeSymm: Analyze a single level of symmetry.
angle(Quat4d) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions: Calculate the rotation angle component of the input unit quaternion.
angle(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc: Gets the angle between two vectors
ANGLE - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
angleCheckOk(FragmentPair, FragmentPair, float) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
AngleOrderDetectorPlus - Class in org.biojava.nbio.structure.symmetry.internal: Guesses an order of rotational symmetry from the angle.
AngleOrderDetectorPlus(double) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
AngleOrderDetectorPlus(int) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
AngleOrderDetectorPlus(int, double) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
AngleOrderDetectorPlus(int, double, boolean) - Constructor for class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus: Determine order by finding the order (up to the maxOrder) which has the closest rotation angle to the observed rotation.
antiparallel - org.biojava.nbio.structure.secstruc.BridgeType
ANYTHING_MATCHER - Static variable in class org.biojava.nbio.structure.AtomPositionMap: Matches all atoms
apairs_from_idxlst(JointFragments) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: Set apairs according to a list of (i,j) tuples.
apairs_from_seed(int, int, int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: Set apairs according to a seed position.
applyAlignment(Map<S, T>, Map<T, S>, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Applies an alignment k times.
applyAlignment(Map<T, T>, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Applies an alignment k times.
approach_ap3(Atom[], Atom[], FragmentPair[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner
Ar - org.biojava.nbio.structure.Element
Architecture - org.biojava.nbio.structure.cath.CathCategory
areInSameAxis(int, int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup: Returns true if both given transform ids belong to the same crystallographic axis (a, b or c) For two non-rotation transformations (i.e.
arrayLeftDivide(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element left division, C = A.\B
arrayLeftDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element left division in place, A = A.\B
arrayRightDivide(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element right division, C = A./B
arrayRightDivideEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element right division in place, A = A./B
arrayTimes(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element multiplication, C = A.*B
arrayTimesEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix: Element-by-element multiplication in place, A = A.*B
As - org.biojava.nbio.structure.Element
AsaCalculator - Class in org.biojava.nbio.structure.asa: Class to calculate Accessible Surface Areas based on the rolling ball algorithm by Shrake and Rupley.
AsaCalculator(Point3d[], double, int, int, double) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator: Constructs a new AsaCalculator.
AsaCalculator(Atom[], double, int, int) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator: Constructs a new AsaCalculator.
AsaCalculator(Structure, double, int, int, boolean) - Constructor for class org.biojava.nbio.structure.asa.AsaCalculator: Constructs a new AsaCalculator.
assignment - Variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo
assignSecStruc(Structure, List<SecStrucInfo>) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools
Astral - Class in org.biojava.nbio.structure.scop: Provides programmatic access to ASTRAL representative sets.
Astral(String, Reader) - Constructor for class org.biojava.nbio.structure.scop.Astral: Constructs a new Astral object.
Astral(String, URL) - Constructor for class org.biojava.nbio.structure.scop.Astral: Constructs a new Astral object.
Astral(Astral.AstralSet) - Constructor for class org.biojava.nbio.structure.scop.Astral: Constructs a new Astral object.
Astral.AstralSet - Enum in org.biojava.nbio.structure.scop: An ASTRAL sequence-identity cutoff with an identifier such as:
ASYMMETRIC - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass
At - org.biojava.nbio.structure.Element
Atom - Interface in org.biojava.nbio.structure: A simple interface for an Atom.
ATOM_CA_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.FileParsingParameters: The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
ATOM_PLANE - org.biojava.nbio.structure.BondType
AtomCache - Class in org.biojava.nbio.structure.align.util: A utility class that provides easy access to Structure objects.
AtomCache() - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Default AtomCache constructor.
AtomCache(String) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Creates an instance of an AtomCache that is pointed to the a particular path in the file system.
AtomCache(String, String) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Creates an instance of an AtomCache that is pointed to the a particular path in the file system.
AtomCache(UserConfiguration) - Constructor for class org.biojava.nbio.structure.align.util.AtomCache: Creates a new AtomCache object based on the provided UserConfiguration.
AtomContact - Class in org.biojava.nbio.structure.contact: A pair of atoms that are in contact
AtomContact(Pair<Atom>, double) - Constructor for class org.biojava.nbio.structure.contact.AtomContact
AtomContactSet - Class in org.biojava.nbio.structure.contact: A set of atom-atom contacts to hold the results of intra and inter-chain contact calculations
AtomContactSet(double) - Constructor for class org.biojava.nbio.structure.contact.AtomContactSet
AtomIdentifier - Class in org.biojava.nbio.structure.contact
AtomIdentifier(int, String) - Constructor for class org.biojava.nbio.structure.contact.AtomIdentifier
AtomImpl - Class in org.biojava.nbio.structure: Implementation of an Atom of a PDB file.
AtomImpl() - Constructor for class org.biojava.nbio.structure.AtomImpl
AtomIterator - Class in org.biojava.nbio.structure: an iterator over all atoms of a structure / group.
AtomIterator(Group) - Constructor for class org.biojava.nbio.structure.AtomIterator: Constructs an AtomIterator object.
AtomIterator(Structure) - Constructor for class org.biojava.nbio.structure.AtomIterator: Constructs an AtomIterator object over all models
AtomIterator(Structure, int) - Constructor for class org.biojava.nbio.structure.AtomIterator: Constructs an AtomIterator object over a single model
atomn - org.biojava.nbio.structure.chem.ResidueType
AtomPositionMap - Class in org.biojava.nbio.structure: A map from ResidueNumbers to ATOM record positions in a PDB file.
AtomPositionMap(Atom[]) - Constructor for class org.biojava.nbio.structure.AtomPositionMap: Creates a new AtomPositionMap containing peptide alpha-carbon atoms
AtomPositionMap(Atom[], AtomPositionMap.GroupMatcher) - Constructor for class org.biojava.nbio.structure.AtomPositionMap: Creates a new AtomPositionMap containing only atoms matched by matcher.
AtomPositionMap(Structure) - Constructor for class org.biojava.nbio.structure.AtomPositionMap: Creates a new AtomPositionMap containing representative atoms from a structure.
AtomPositionMap.GroupMatcher - Interface in org.biojava.nbio.structure: Used as a Predicate to indicate whether a particular Atom should be mapped
ATOMRECORD - Static variable in interface org.biojava.nbio.structure.AminoAcid: Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
atoms - Variable in class org.biojava.nbio.structure.HetatomImpl
atomsToPoints(Collection<Atom>) - Static method in class org.biojava.nbio.structure.Calc: Convert an array of atoms into an array of vecmath points
atomsToPoints(Atom[]) - Static method in class org.biojava.nbio.structure.Calc: Convert an array of atoms into an array of vecmath points
Au - org.biojava.nbio.structure.Element
AU - org.biojava.nbio.structure.xtal.TransformType
AugmentedResidueRange - Class in org.biojava.nbio.structure: Created by douglas on 1/23/15.
AugmentedResidueRange(String, String, String, int, AtomPositionMap) - Constructor for class org.biojava.nbio.structure.AugmentedResidueRange
AugmentedResidueRange(String, ResidueNumber, ResidueNumber, int, AtomPositionMap) - Constructor for class org.biojava.nbio.structure.AugmentedResidueRange
Author - Class in org.biojava.nbio.structure: Describes author attributes for author information in a PDB file.
Author() - Constructor for class org.biojava.nbio.structure.Author
AUTO - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
AVGTM_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
Axis(Matrix4d, int, CESymmParameters.SymmetryType, int, int) - Constructor for class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
AxisAligner - Class in org.biojava.nbio.structure.symmetry.axis
AxisAligner() - Constructor for class org.biojava.nbio.structure.symmetry.axis.AxisAligner

B

B - org.biojava.nbio.structure.Element
Ba - org.biojava.nbio.structure.Element
BASE_LIST_DNA - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
BASE_LIST_RNA - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
BASE_MAP - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
BasePairParameters - Class in org.biojava.nbio.structure.basepairs: This module calculates the el Hassan-Calladine Base Pairing and Base-pair Step Parameters for any nucleic acid containing structure that has the information about the core base-pair rings.
BasePairParameters(Structure) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters: This constructor takes a Structure object, finds base pair and base-pair step parameters for double-helical regions within the structure for only canonical DNA pairs.
BasePairParameters(Structure, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters: This constructor takes a Structure object, and whether to use the RNA standard bases.
BasePairParameters(Structure, boolean, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters: This constructor takes a Structure object, whether to use RNA, and whether to remove duplicate sequences.
BasePairParameters(Structure, boolean, boolean, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.BasePairParameters: This constructor takes a Structure object, finds base pair and base-pair step parameters for double-helical regions within the structure.
basePairReferenceFrame(Pair<Group>) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters: This method calculates the central frame (4x4 transformation matrix) of a single base pair.
basicLoad() - Method in class demo.DemoLoadStructure
basicLoad(String) - Method in class demo.DemoDomainsplit
basicLoad(PDBFileReader, String) - Method in class demo.DemoChangeChemCompProvider
BCIF - org.biojava.nbio.structure.io.StructureFiletype
BCIF_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration
BcifFileReader - Class in org.biojava.nbio.structure.io: Parse binary Cif files and provide capabilities to store them locally.
BcifFileReader() - Constructor for class org.biojava.nbio.structure.io.BcifFileReader: Constructs a new BcifFileReader, initializing the extensions member variable.
BcifFileReader(String) - Constructor for class org.biojava.nbio.structure.io.BcifFileReader: Constructs a new BcifFileReader, initializing the extensions member variable.
Be - org.biojava.nbio.structure.Element
bend - org.biojava.nbio.structure.secstruc.SecStrucType
BerkeleyScopInstallation - Class in org.biojava.nbio.structure.scop: SCOPe: The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley (http://scop.berkeley.edu/).
BerkeleyScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.BerkeleyScopInstallation
bestTrace1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTrace1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTrace2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTrace2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTraces1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTraces1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTraces2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTraces2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTraceScore - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTraceScore - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTracesN - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTracesN - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
bestTracesScores - Variable in class org.biojava.nbio.structure.align.ce.CECalculator
bestTracesScores - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
BetaBridge - Class in org.biojava.nbio.structure.secstruc: Container that represents a beta Bridge between two residues.
BetaBridge(int, int, BridgeType) - Constructor for class org.biojava.nbio.structure.secstruc.BetaBridge
BETTER_PERFORMANCE_MORE_MEMORY - org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior: use a built-in HashMap for faster access to memory, at the price of more memory consumption
Bi - org.biojava.nbio.structure.Element
BIO - org.biojava.nbio.structure.align.client.StructureName.Source
BIO_NAME_PATTERN - Static variable in class org.biojava.nbio.structure.BioAssemblyIdentifier
BioAssemblyIdentifier - Class in org.biojava.nbio.structure
BioAssemblyIdentifier(String) - Constructor for class org.biojava.nbio.structure.BioAssemblyIdentifier
BioAssemblyIdentifier(String, int) - Constructor for class org.biojava.nbio.structure.BioAssemblyIdentifier
BioAssemblyIdentifier(PdbId, int) - Constructor for class org.biojava.nbio.structure.BioAssemblyIdentifier
BioAssemblyInfo - Class in org.biojava.nbio.structure.quaternary: Representation of a Biological Assembly annotation as provided by the PDB.
BioAssemblyInfo() - Constructor for class org.biojava.nbio.structure.quaternary.BioAssemblyInfo: Empty constructor
BioAssemblyTools - Class in org.biojava.nbio.structure.quaternary
BioAssemblyTools() - Constructor for class org.biojava.nbio.structure.quaternary.BioAssemblyTools
BIOJAVA_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo: Secondary strucuture calculated and assigned by DSSP of BioJava
BioJavaStructureAlignment - Class in org.biojava.nbio.structure.align: Wrapper for the BioJava Structure Alignment Implementation
BioJavaStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.BioJavaStructureAlignment
BIOL_ASSEMBLY_IDENTIFIER - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
BiologicalAssemblyBuilder - Class in org.biojava.nbio.structure.quaternary: Reconstructs the quaternary structure of a protein from an asymmetric unit
BiologicalAssemblyBuilder() - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
BiologicalAssemblyTransformation - Class in org.biojava.nbio.structure.quaternary: The transformation needed for generation of biological assemblies from the contents of a PDB/mmCIF file.
BiologicalAssemblyTransformation() - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Default Constructor
BiologicalAssemblyTransformation(BiologicalAssemblyTransformation) - Constructor for class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Copy Constructor
Bk - org.biojava.nbio.structure.Element
blankOutBreakFlag(AFPChain, Atom[], int, int, CECalculator, boolean[][], int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
blankOutCEOrig(Atom[], int, int, CECalculator, Matrix, int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
blankOutPreviousAlignment(AFPChain, Atom[], int, int, CECalculator, Matrix, int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools
BlastClustReader - Class in org.biojava.nbio.structure.symmetry.utils
BlastClustReader(int) - Constructor for class org.biojava.nbio.structure.symmetry.utils.BlastClustReader
Block - Interface in org.biojava.nbio.structure.align.multiple: A Block is a Data Structure that stores aligned positions of a MultipleAlignment with the condition that residues are in a sequential order.
BlockImpl - Class in org.biojava.nbio.structure.align.multiple: General implementation of a Block that supports any type of sequential alignment with gaps.
BlockImpl(BlockImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl: Copy constructor.
BlockImpl(BlockSet) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockImpl: Constructor.
blockInfo(AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer: get the afp list and residue list for each block
BlockSet - Interface in org.biojava.nbio.structure.align.multiple: A BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment.
BlockSetImpl - Class in org.biojava.nbio.structure.align.multiple: A general implementation of a BlockSet to store a flexible part of a multiple alignment.
BlockSetImpl(BlockSetImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl: Copy constructor.
BlockSetImpl(MultipleAlignment) - Constructor for class org.biojava.nbio.structure.align.multiple.BlockSetImpl: Constructor.
Bond - Interface in org.biojava.nbio.structure: A simple bond -- it stores information about two atoms as well as information about its bond order.
BOND_TYPES_TO_PARSE - Static variable in class org.biojava.nbio.structure.io.BondMaker: The types of bonds that are read from struct_conn (type specified in field conn_type_id)
BondImpl - Class in org.biojava.nbio.structure: A simple bond -- it stores information about two atoms as well as information about its bond order.
BondImpl(Atom, Atom, int) - Constructor for class org.biojava.nbio.structure.BondImpl: Constructs a new bond from a pair of atoms and the bond order of the bond between them.
BondImpl(Atom, Atom, int, boolean) - Constructor for class org.biojava.nbio.structure.BondImpl: Constructs a new bond from a pair of atoms and the bond order of the bond between them.
BondMaker - Class in org.biojava.nbio.structure.io: Adds polymer bonds for peptides and nucleotides based on distance cutoffs and intra-group (residue) bonds based on data from the Chemical Component Dictionary to the Structure object.
BondMaker(Structure, FileParsingParameters) - Constructor for class org.biojava.nbio.structure.io.BondMaker
BONDS_INITIAL_CAPACITY - Static variable in class org.biojava.nbio.structure.AtomImpl: The inital capacity of the bonds list.
BondType - Enum in org.biojava.nbio.structure: Work in progress - NOT final!
BoundingBox - Class in org.biojava.nbio.structure.contact: A bounding box for short cutting some geometrical calculations.
BoundingBox(double, double, double, double, double, double) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox
BoundingBox(Point3d[]) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox: Constructs a BoundingBox by calculating maxs and mins of given array of atoms.
BoundingBox(BoundingBox) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox
BoundingBox(BoundingBox[]) - Constructor for class org.biojava.nbio.structure.contact.BoundingBox: Given a set of bounding boxes returns a bounding box that bounds all of them.
Br - org.biojava.nbio.structure.Element
BRANCHED - org.biojava.nbio.structure.EntityType: The 'branched' type use mainly to represent carbohydrates.
BravaisLattice - Enum in org.biojava.nbio.structure.xtal: An enum to represent the 7 Bravais lattices
bridge - org.biojava.nbio.structure.secstruc.SecStrucType
BridgeType - Enum in org.biojava.nbio.structure.secstruc: A bridge is formed by two non-overlapping stretches of three residues each (i-1,i,i+1) and (j-1,j,j+1), where i
build() - Static method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping: Builds the mapping by reading SIFTS the tsv file set in SiftsChainToUniprotMapping.DEFAULT_FILE variable.
buildSymmetryGraph(List<AFPChain>, Atom[], boolean) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Converts a set of AFP alignments into a Graph of aligned residues, where each vertex is a residue and each edge means the connection between the two residues in one of the alignments.
buildSymmetryGraph(AFPChain) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools: Converts a self alignment into a directed jGraphT of aligned residues, where each vertex is a residue and each edge means the equivalence between the two residues in the self-alignment.

C

c - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange: first allowed c-term
C - org.biojava.nbio.structure.Element
C_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name for the backbone carbonyl
C1_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone C1' in RNA
C2_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone C2' in RNA
C2_ROTATION - org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod
C2RotationSolver - Class in org.biojava.nbio.structure.symmetry.core
C2RotationSolver(QuatSymmetrySubunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.C2RotationSolver
C3_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone C3' in RNA
C4_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone C4' in RNA
Ca - org.biojava.nbio.structure.Element
CA_AND_SIDE_CHAIN_ANGLE_SCORING - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
CA_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the backbone C-alpha atom.
CA_MIN_DIST - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc: min distance of two CA atoms if H-bonds are allowed to form
CA_SCORING - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
cache(K, V) - Method in class org.biojava.nbio.structure.domain.SerializableCache: This will not cache null values.
cacheFileName - Variable in class org.biojava.nbio.structure.domain.SerializableCache
CAConverter - Class in org.biojava.nbio.structure.io: Converts full atom representations to Calpha only ones.
CAConverter() - Constructor for class org.biojava.nbio.structure.io.CAConverter
calAfpRmsd(int, int[], int, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer: //return the rmsd of the residues from the segments that form the given AFP list //this value can be a measurement (1) for the connectivity of the AFPs
Calc - Class in org.biojava.nbio.structure: Utility operations on Atoms, AminoAcids, Matrices, Point3d, etc.
Calc() - Constructor for class org.biojava.nbio.structure.Calc
calc_rmsd(Atom[], Atom[], int, boolean) - Method in class org.biojava.nbio.structure.align.ce.CECalculator: superimpose and get rmsd
calc_rmsd(Atom[], Atom[], int, boolean, boolean) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced: superimpose and get rmsd
calcAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Calculates ASAs for all interfaces in list, both for the unbound chains and for the complex of the two chains together.
calcAsas(int, int, int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Calculates ASAs for all interfaces in list, both for the unbound chains and for the complex of the two chains together.
calcCenterOfRotation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner
calcGlobalSymmetry(List<Subunit>, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Calculate GLOBAL symmetry results.
calcGlobalSymmetry(Structure, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Calculate GLOBAL symmetry results.
calcGlobalSymmetry(Stoichiometry, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Calculate GLOBAL symmetry results.
calcIdSimilarity(char[], char[], int) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
calcLength(List<ResidueRangeAndLength>) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength: Calculates the combined number of residues of the ResidueRanges in rrs.
calcLocalSymmetries(List<Subunit>, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Returns a List of LOCAL symmetry results.
calcLocalSymmetries(Structure, QuatSymmetryParameters, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Returns a List of LOCAL symmetry results.
calcLocalSymmetries(Stoichiometry, QuatSymmetryParameters) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector: Returns a List of LOCAL symmetry results.
CalcPoint - Class in org.biojava.nbio.structure.geometry: Utility operations on Point3d.
calcRotationAngleInDegrees(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc: Calculates the angle from centerPt to targetPt in degrees.
calcScores(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment: calculates scores for this alignment ( %id )
calcScores(QuatSymmetrySubunits, Matrix4d, List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.QuatSuperpositionScorer: Returns minimum, mean, and maximum RMSD and TM-Score for two superimposed sets of subunits TM score: Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)
calcSimilarity() - Method in class org.biojava.nbio.structure.align.model.AFPChain
calculate(Structure, boolean) - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc: Predicts the secondary structure of this Structure object, using a DSSP implementation.
calculateAsas() - Method in class org.biojava.nbio.structure.asa.AsaCalculator: Calculates the Accessible Surface Areas for the atoms given in constructor and with parameters given.
calculateBlockGap(int[][][]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Method that calculates the number of gaps in each subunit block of an optimal AFP alignment.
calculatedFragmentPairs(List<FragmentPair>) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
calculateDsspSecondaryStructure(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils: Generate the secondary structure for a Biojava structure object.
calculateInterfaces(Structure) - Static method in class org.biojava.nbio.structure.contact.StructureInterfaceList: Calculates the interfaces for a structure using default parameters
calculateMinCP(int[], int, int, int) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain: Finds the alignment index of the residues minCPlength before and after the duplication.
calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus
calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.GraphComponentOrderDetector
calculateOrder(AFPChain, Atom[]) - Method in interface org.biojava.nbio.structure.symmetry.internal.OrderDetector
calculateOrder(AFPChain, Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector
calculateScores(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer: Calculates and puts the RMSD and the average TM-Score of the MultipleAlignment.
calculateSuperpositionByIdx(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
calculateTp(Matrix4d) - Static method in class org.biojava.nbio.structure.basepairs.BasePairParameters: This method calculates pairing and step parameters from 4x4 transformation matrices (used internally) that comes out as a Matrix4d.
calculator - Variable in class org.biojava.nbio.structure.align.ce.CeMain
call() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment
call() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer
CallableStructureAlignment - Class in org.biojava.nbio.structure.align: Simple Callable Class that calculates a pairwise alignment in a different thread, so that multiple pairwise alignments can be run in parallel (examples: all-to-all alignments, DB search alignments).
CallableStructureAlignment() - Constructor for class org.biojava.nbio.structure.align.CallableStructureAlignment: Default constructor.
CallableStructureAlignment(Atom[], Atom[], String, ConfigStrucAligParams) - Constructor for class org.biojava.nbio.structure.align.CallableStructureAlignment: Constructor for all-to-all alignment calculation.
calNS(FatCatParameters, AFPChain) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
calSigAll(FatCatParameters, AFPChain) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva
canonical - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters
CartesianProduct<T> - Class in org.biojava.nbio.structure.quaternary: A cartesian product between two lists A and B is the set of all ordered pairs of the elements of both sets.
CartesianProduct(List<T>, List<T>) - Constructor for class org.biojava.nbio.structure.quaternary.CartesianProduct: Class constructor specifying the two lists of a cartesian product.
CATH - org.biojava.nbio.structure.align.client.StructureName.Source
CATH_DOWNLOAD_ALL_RELEASES_DIR - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
CATH_DOWNLOAD_URL - Static variable in class org.biojava.nbio.structure.cath.CathInstallation
CathCategory - Enum in org.biojava.nbio.structure.cath: The categories found within CATH.
CathDatabase - Interface in org.biojava.nbio.structure.cath: General API for interacting with CATH.
CathDomain - Class in org.biojava.nbio.structure.cath: A class which represents a single CATH domain.
CathDomain() - Constructor for class org.biojava.nbio.structure.cath.CathDomain
CathFactory - Class in org.biojava.nbio.structure.cath: Controls global CathDatabases being used.
CathFragment - Class in org.biojava.nbio.structure.cath
CathFragment() - Constructor for class org.biojava.nbio.structure.cath.CathFragment
CathInstallation - Class in org.biojava.nbio.structure.cath
CathInstallation() - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
CathInstallation(String) - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
CathInstallation(String, boolean, boolean) - Constructor for class org.biojava.nbio.structure.cath.CathInstallation
CathNode - Class in org.biojava.nbio.structure.cath: Represents a node in the CATH hierarchy.
CathNode() - Constructor for class org.biojava.nbio.structure.cath.CathNode
CathSegment - Class in org.biojava.nbio.structure.cath
CathSegment() - Constructor for class org.biojava.nbio.structure.cath.CathSegment
CB_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools: The atom name of the side-chain C-beta atom
Cd - org.biojava.nbio.structure.Element
Ce - org.biojava.nbio.structure.Element
CE_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
CECalculator - Class in org.biojava.nbio.structure.align.ce: This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.
CECalculator(CeParameters) - Constructor for class org.biojava.nbio.structure.align.ce.CECalculator
CeCalculatorEnhanced - Class in org.biojava.nbio.structure.align.ce: This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3), as has been originally developed by I.
CeCalculatorEnhanced(CeParameters) - Constructor for class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
CeCPMain - Class in org.biojava.nbio.structure.align.ce: A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.
CeCPMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPMain
CeCPMain.CPRange - Class in org.biojava.nbio.structure.align.ce: Tiny wrapper for the disallowed regions of an alignment.
CECPParameters - Class in org.biojava.nbio.structure.align.ce: Provides parameters to CeCPMain
CECPParameters() - Constructor for class org.biojava.nbio.structure.align.ce.CECPParameters
CECPParameters.DuplicationHint - Enum in org.biojava.nbio.structure.align.ce
CeCPStartupParams() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
CeCPUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
CeCPUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
CeCPUserArgumentProcessor.CeCPStartupParams - Class in org.biojava.nbio.structure.align.ce
ceil(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable: Return the smallest key in the table >= k.
CELLTRANSL - org.biojava.nbio.structure.xtal.TransformType
CeMain - Class in org.biojava.nbio.structure.align.ce: The main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I.
CeMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeMain
center(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint: Center a cloud of points.
centerAtoms(Atom[]) - Static method in class org.biojava.nbio.structure.Calc: Center the atoms at the Centroid.
centerAtoms(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc: Center the atoms at the Centroid, if the centroid is already know.
centered - Variable in class org.biojava.nbio.structure.geometry.SuperPositionAbstract
centerOfMass(Atom[]) - Static method in class org.biojava.nbio.structure.Calc: Returns the center of mass of the set of atoms.
centroid(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint: Calculate the centroid of the point cloud.
CeParameters - Class in org.biojava.nbio.structure.align.ce: Contains the parameters that can be sent to CE
CeParameters() - Constructor for class org.biojava.nbio.structure.align.ce.CeParameters
CeParameters.ScoringStrategy - Enum in org.biojava.nbio.structure.align.ce
CeSideChainMain - Class in org.biojava.nbio.structure.align.ce
CeSideChainMain() - Constructor for class org.biojava.nbio.structure.align.ce.CeSideChainMain
CeSideChainUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce
CeSideChainUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
CeStartupParams() - Constructor for class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
CeSymm - Class in org.biojava.nbio.structure.symmetry.internal: Identify the symmetries in a structure by running an alignment of the structure against itself disabling the diagonal of the identity alignment.
CeSymmIterative - Class in org.biojava.nbio.structure.symmetry.internal: Iterative version of CeSymm that aims at identifying all symmetry axis of a structure.
CeSymmIterative(CESymmParameters) - Constructor for class org.biojava.nbio.structure.symmetry.internal.CeSymmIterative: For the iterative algorithm to work properly the refinement and optimization options should be turned on, because the alignment has to be consistent at every recursive step.
CESymmParameters - Class in org.biojava.nbio.structure.symmetry.internal: Provides parameters to CeSymm.
CESymmParameters() - Constructor for class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
CESymmParameters(CESymmParameters) - Constructor for class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
CESymmParameters.OrderDetectorMethod - Enum in org.biojava.nbio.structure.symmetry.internal
CESymmParameters.RefineMethod - Enum in org.biojava.nbio.structure.symmetry.internal
CESymmParameters.SymmetryType - Enum in org.biojava.nbio.structure.symmetry.internal: The internal symmetry detection can be divided into two types: CLOSE: includes the circular and dihedral symmetries, and OPEN: includes the helical and protein repeats symmetries.
CeSymmResult - Class in org.biojava.nbio.structure.symmetry.internal: This Class stores all the relevant information of an internal symmetry result obtained with CeSymm.
CeSymmResult() - Constructor for class org.biojava.nbio.structure.symmetry.internal.CeSymmResult
CeUserArgumentProcessor - Class in org.biojava.nbio.structure.align.ce: process the arguments from command line
CeUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
CeUserArgumentProcessor.CeStartupParams - Class in org.biojava.nbio.structure.align.ce
Cf - org.biojava.nbio.structure.Element
Chain - Interface in org.biojava.nbio.structure: Defines the interface for a Chain.
CHAIN_NR_SYMBOL - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
CHAIN_REGEX - Static variable in class org.biojava.nbio.structure.ResidueRange
CHAIN_SPLIT_SYMBOL - Static variable in class org.biojava.nbio.structure.align.util.AtomCache
chainEntrySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
CHAINID_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier: URL parameter specifying a single chain to include; overridden by residues
ChainImpl - Class in org.biojava.nbio.structure: A Chain in a PDB file.
ChainImpl() - Constructor for class org.biojava.nbio.structure.ChainImpl: Constructs a ChainImpl object.
chainName - Variable in class org.biojava.nbio.structure.align.client.StructureName
ChainSignature - Class in org.biojava.nbio.structure.symmetry.misc
ChainSignature(String, int, List<String>) - Constructor for class org.biojava.nbio.structure.symmetry.misc.ChainSignature
ChargeAdder - Class in org.biojava.nbio.structure.io: A class to add appropriate charge information to a structure.
ChargeAdder() - Constructor for class org.biojava.nbio.structure.io.ChargeAdder
checkDoFirstInstall() - Method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider: Checks if the chemical components already have been installed into the PDB directory.
checkFileExists(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
checkFileExists(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory
checkInput(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionAbstract: Check that the input to the superposition algorithms is valid.
checkScaleMatrix(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell: Given a scale matrix parsed from a PDB entry (SCALE1,2,3 records), compares it to our calculated Mtranspose matrix to see if they coincide and returns true if they do.
checkScaleMatrixConsistency(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell: Given a scale matrix parsed from the PDB entry (SCALE1,2,3 records), checks that the matrix is a consistent scale matrix by comparing the cell volume to the inverse of the scale matrix determinant (tolerance of 1/100).
CHEM_COMP_CACHE_DIRECTORY - Static variable in class org.biojava.nbio.structure.chem.DownloadChemCompProvider
chem_comp_type - Variable in enum org.biojava.nbio.structure.chem.ResidueType: String value of the type
chemComp - Variable in class org.biojava.nbio.structure.HetatomImpl
ChemComp - Class in org.biojava.nbio.structure.chem: Properties of a chemical component.
ChemComp() - Constructor for class org.biojava.nbio.structure.chem.ChemComp
ChemCompAtom - Class in org.biojava.nbio.structure.chem: Properties of an atom of a chemical component.
ChemCompAtom() - Constructor for class org.biojava.nbio.structure.chem.ChemCompAtom
ChemCompBond - Class in org.biojava.nbio.structure.chem: Properties of a bond in a chemical component.
ChemCompBond() - Constructor for class org.biojava.nbio.structure.chem.ChemCompBond
ChemCompConsumer - Interface in org.biojava.nbio.structure.io.cif: Create the ChemicalComponentDictionary from CIF data.
ChemCompConsumerImpl - Class in org.biojava.nbio.structure.io.cif: Consumes a CCD file to create the ChemicalComponentDictionary.
ChemCompConsumerImpl() - Constructor for class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
ChemCompConverter - Class in org.biojava.nbio.structure.io.cif: Convert CifFiles to chem comps.
ChemCompConverter() - Constructor for class org.biojava.nbio.structure.io.cif.ChemCompConverter
ChemCompDescriptor - Class in org.biojava.nbio.structure.chem: Properties of the chemical component descriptor.
ChemCompDescriptor() - Constructor for class org.biojava.nbio.structure.chem.ChemCompDescriptor
ChemCompDistribution - Class in demo
ChemCompDistribution() - Constructor for class demo.ChemCompDistribution
ChemCompGroupFactory - Class in org.biojava.nbio.structure.chem
ChemCompGroupFactory() - Constructor for class org.biojava.nbio.structure.chem.ChemCompGroupFactory
ChemCompProvider - Interface in org.biojava.nbio.structure.chem: Interface that is implemented by all classes that can provide ChemComp definitions.
ChemCompTools - Class in org.biojava.nbio.structure.chem
ChemCompTools() - Constructor for class org.biojava.nbio.structure.chem.ChemCompTools
ChemicalComponentDictionary - Class in org.biojava.nbio.structure.chem: A representation of the Chemical Component Dictionary.
ChemicalComponentDictionary() - Constructor for class org.biojava.nbio.structure.chem.ChemicalComponentDictionary
chol() - Method in class org.biojava.nbio.structure.jama.Matrix: Cholesky Decomposition
CholeskyDecomposition - Class in org.biojava.nbio.structure.jama: Cholesky Decomposition.
CholeskyDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.CholeskyDecomposition: Cholesky algorithm for symmetric and positive definite matrix.
CIF - org.biojava.nbio.structure.io.StructureFiletype
CIF_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.BcifFileReader
CIF_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.CifFileReader
CIF_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.BcifFileReader
CIF_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.CifFileReader
CifBean - Interface in org.biojava.nbio.structure.io.cif: Flag for BioJava beans that resemble categories defined by the mmCIF schema.
CifChainSupplierImpl - Class in org.biojava.nbio.structure.io.cif: Convert a chain to a CifFile.
CifChainSupplierImpl() - Constructor for class org.biojava.nbio.structure.io.cif.CifChainSupplierImpl
CifFileConsumer<S> - Interface in org.biojava.nbio.structure.io.cif: Defines a rather generic interface which allows to populate some data structure with data parsed from a CIF file.
CifFileReader - Class in org.biojava.nbio.structure.io: Parse text Cif files and provide capabilities to store them locally.
CifFileReader() - Constructor for class org.biojava.nbio.structure.io.CifFileReader: Constructs a new CifFileReader, initializing the extensions member variable.
CifFileReader(String) - Constructor for class org.biojava.nbio.structure.io.CifFileReader: Constructs a new CifFileReader, initializing the extensions member variable.
CifFileSupplier<S> - Interface in org.biojava.nbio.structure.io.cif: Create a CifFile instance for a given container of structure data.
CifStructureConsumer - Interface in org.biojava.nbio.structure.io.cif: Defines the categories to consume during CIF parsing.
CifStructureConsumerImpl - Class in org.biojava.nbio.structure.io.cif: An implementation of a CifFileConsumer for BioJava.
CifStructureConsumerImpl(FileParsingParameters) - Constructor for class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
CifStructureConverter - Class in org.biojava.nbio.structure.io.cif: Convert BioJava structures to CifFiles and vice versa.
CifStructureConverter() - Constructor for class org.biojava.nbio.structure.io.cif.CifStructureConverter
CifStructureSupplierImpl - Class in org.biojava.nbio.structure.io.cif: Convert a structure to a CifFile.
CifStructureSupplierImpl() - Constructor for class org.biojava.nbio.structure.io.cif.CifStructureSupplierImpl
Cl - org.biojava.nbio.structure.Element
claFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
Class - org.biojava.nbio.structure.cath.CathCategory
Class - org.biojava.nbio.structure.scop.ScopCategory
cleanup(List<Domain>) - Static method in class org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover
cleanUpAltLocs(Structure) - Static method in class org.biojava.nbio.structure.StructureTools: Cleans up the structure's alternate location (altloc) groups.
clear() - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache: Clear the cached scores.
clear() - Method in interface org.biojava.nbio.structure.align.multiple.Block: Clear scores and other properties which depend on the specific alignment.
clear() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
clear() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Clear scores and other properties which depend on the specific alignment.
clear() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
clear() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Clear scores and other properties which depend on the specific alignment.
clear() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Clear scores and other properties which depend on the specific alignment.
clear() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
clear() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
clear() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation: Clears all domains, requiring the file to be reparsed for subsequent accesses
clear() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers
clearAlgorithms() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory: Removes all algorithms from the list
clearAtoms() - Method in interface org.biojava.nbio.structure.Group: Remove all atoms from this group.
clearAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl
clearCache() - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory: Force the in-memory cache to be reset.
clearExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory: clear the supported file extensions
clearListeners() - Method in class org.biojava.nbio.structure.align.StructurePairAligner
CliTools - Class in org.biojava.nbio.structure.align.util: Utilities for autoconfiguring javabeans based on command line arguments.
clone() - Method in class org.biojava.nbio.structure.align.model.AFPChain: Creates and returns a copy of this object.
clone() - Method in interface org.biojava.nbio.structure.align.multiple.Block: Creates and returns an identical copy of this block.
clone() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl
clone() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet: Creates and returns an identical copy of this blockset, including a deep copy of all constituent Blocks.
clone() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl
clone() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment: Creates and returns an identical copy of this alignment, including a deep copy of all constituent BlockSets.
clone() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble: Creates and returns an identical copy of this ensemble, including a deep clone of all constituent alignments.
clone() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl
clone() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl
clone() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair
clone() - Method in class org.biojava.nbio.structure.AminoAcidImpl: returns and identical copy of this Group object .
clone() - Method in class org.biojava.nbio.structure.asa.GroupAsa
clone() - Method in interface org.biojava.nbio.structure.Atom: Return an identical copy of this object .
clone() - Method in class org.biojava.nbio.structure.AtomImpl: returns and identical copy of this object .
clone() - Method in interface org.biojava.nbio.structure.Chain: Returns an identical copy of this Chain.
clone() - Method in class org.biojava.nbio.structure.ChainImpl
clone() - Method in class org.biojava.nbio.structure.ecod.EcodDomain
clone() - Method in interface org.biojava.nbio.structure.Group: Returns and identical copy of this Group object .
clone() - Method in class org.biojava.nbio.structure.GroupIterator: Creates and returns a copy of this object.
clone() - Method in class org.biojava.nbio.structure.HetatomImpl: returns and identical copy of this Group object .
clone() - Method in class org.biojava.nbio.structure.io.SSBondImpl
clone() - Method in class org.biojava.nbio.structure.jama.Matrix: Clone the Matrix object.
clone() - Method in class org.biojava.nbio.structure.NucleotideImpl
clone() - Method in class org.biojava.nbio.structure.PdbId
clone() - Method in class org.biojava.nbio.structure.scop.ScopDescription
clone() - Method in class org.biojava.nbio.structure.scop.ScopDomain
clone() - Method in class org.biojava.nbio.structure.secstruc.HBond
clone() - Method in interface org.biojava.nbio.structure.Structure: Return an identical copy of this Structure object
clone() - Method in class org.biojava.nbio.structure.StructureImpl: Returns an identical copy of this structure .
clone() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters
clone(Object) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache: Subclasses should override clone and use the copy constructor.
cloneAtomArray(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools: Provides an equivalent copy of Atoms in a new array.
cloneAtomsAndBonds(Group) - Method in class org.biojava.nbio.structure.HetatomImpl
cloneGroups(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools: Clone a set of representative Atoms, but returns the parent groups
clonePoint3dArray(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint: Clone an array of points.
close() - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile
CLOSED - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
cluster(List<Subunit>, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.cluster.SubunitClusterer
cluster(List<Domain>, PDPDistanceMatrix) - Static method in class org.biojava.nbio.structure.domain.pdp.ClusterDomains
cluster(AlternativeAlignment[]) - Static method in class org.biojava.nbio.structure.align.ClusterAltAligs
cluster(AlternativeAlignment[], int) - Static method in class org.biojava.nbio.structure.align.ClusterAltAligs
cluster(Structure, SubunitClustererParameters) - Static method in class org.biojava.nbio.structure.cluster.SubunitClusterer
ClusterAltAligs - Class in org.biojava.nbio.structure.align: A class that clusters alternative alignments according to their similarity.
ClusterAltAligs() - Constructor for class org.biojava.nbio.structure.align.ClusterAltAligs
ClusterDomains - Class in org.biojava.nbio.structure.domain.pdp
ClusterDomains() - Constructor for class org.biojava.nbio.structure.domain.pdp.ClusterDomains
Cm - org.biojava.nbio.structure.Element
Co - org.biojava.nbio.structure.Element
coil - org.biojava.nbio.structure.secstruc.SecStrucType
CollectionTools - Class in org.biojava.nbio.structure.align.util: Utilities for working with collections.
CollectionTools() - Constructor for class org.biojava.nbio.structure.align.util.CollectionTools
combine(List<Integer>, List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup
combine(BiologicalAssemblyTransformation, BiologicalAssemblyTransformation) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation: Returns the combination (product) of two biological assembly transformations.
combineWith(List<List<Integer>>) - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup: Combine the ResidueGroup with the alignment block.
combineWith(Stoichiometry) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry: Make a combined Stoichiometry object of this and the other.
comFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation
compare(int[], int[]) - Method in class org.biojava.nbio.structure.align.helper.IdxComparator
compare(AlternativeAlignment, AlternativeAlignment) - Method in class org.biojava.nbio.structure.align.pairwise.AltAligComparator
compare(Segment, Segment) - Method in class org.biojava.nbio.structure.domain.pdp.SegmentComparator
compareTo(PdbPair) - Method in class org.biojava.nbio.structure.align.client.PdbPair
compareTo(StructureName) - Method in class org.biojava.nbio.structure.align.client.StructureName: Orders identifiers lexicographically by PDB ID and then full Identifier
compareTo(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemComp
compareTo(StructureInterface) - Method in class org.biojava.nbio.structure.contact.StructureInterface
compareTo(Domain) - Method in class org.biojava.nbio.structure.domain.pdp.Domain
compareTo(Segment) - Method in class org.biojava.nbio.structure.domain.pdp.Segment
compareTo(PdbId) - Method in class org.biojava.nbio.structure.PdbId
compareTo(BiologicalAssemblyTransformation) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
compareTo(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber: Compare residue numbers by chain, sequence number, and insertion code
compareTo(Site) - Method in class org.biojava.nbio.structure.Site
compareTo(ChainSignature) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature
compareToPositional(ResidueNumber) - Method in class org.biojava.nbio.structure.ResidueNumber: Compare residue numbers by sequence number and insertion code, ignoring the chain
complementBase(char, boolean) - Static method in class org.biojava.nbio.structure.basepairs.BasePairParameters: This method returns the complement of a base.
complete() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup
completeGroup() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup: Starts with an incomplete set of group generators in `permutations` and expands it to include all possible combinations.
COMPONENTS_FILE_LOCATION - Static variable in class org.biojava.nbio.structure.chem.AllChemCompProvider
COMPOSED_OPERATOR_SEPARATOR - Static variable in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder: The character separating operator ids that are composed.
cond() - Method in class org.biojava.nbio.structure.jama.Matrix: Matrix condition (2 norm)
cond() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition: Two norm condition number
ConfigStrucAligParams - Interface in org.biojava.nbio.structure.align.ce
ConfigurationException - Exception in org.biojava.nbio.structure.align.util
ConfigurationException() - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
ConfigurationException(String) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException: Constructs a ConfigurationException object.
ConfigurationException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException
ConfigurationException(Throwable) - Constructor for exception org.biojava.nbio.structure.align.util.ConfigurationException: Constructs a ConfigurationException object.
configureBean(Object, String[]) - Static method in class org.biojava.nbio.structure.align.util.CliTools: Configure a JavaBean based on a set of command line arguments.
constructWithCopy(double[][]) - Static method in class org.biojava.nbio.structure.jama.Matrix: Construct a matrix from a copy of a 2-D array.
consume(Category) - Method in interface org.biojava.nbio.structure.io.cif.MetalBondConsumer
consume(Category) - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl
consumeAtomSite(AtomSite) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeAtomSite(AtomSite) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeAtomSites(AtomSites) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeAtomSites(AtomSites) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeAuditAuthor(AuditAuthor) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeAuditAuthor(AuditAuthor) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeCell(Cell) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeCell(Cell) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.io.cif.ChemCompConsumer: Consume a particular Cif category.
consumeChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
consumeChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeChemComp(ChemComp) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeChemCompAtom(ChemCompAtom) - Method in interface org.biojava.nbio.structure.io.cif.ChemCompConsumer: Consume a particular Cif category.
consumeChemCompAtom(ChemCompAtom) - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
consumeChemCompBond(ChemCompBond) - Method in interface org.biojava.nbio.structure.io.cif.ChemCompConsumer: Consume a particular Cif category.
consumeChemCompBond(ChemCompBond) - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl
consumeChemCompBond(ChemCompBond) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeChemCompBond(ChemCompBond) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeDatabasePDBRemark(DatabasePDBRemark) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeDatabasePDBRemark(DatabasePDBRemark) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeDatabasePDBRev(DatabasePDBRev) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeDatabasePDBRev(DatabasePDBRev) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeDatabasePDBRevRecord(DatabasePDBRevRecord) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeDatabasePDBRevRecord(DatabasePDBRevRecord) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeEntity(Entity) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeEntity(Entity) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeEntityPoly(EntityPoly) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeEntityPoly(EntityPoly) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeEntityPolySeq(EntityPolySeq) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeEntityPolySeq(EntityPolySeq) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeEntitySrcGen(EntitySrcGen) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeEntitySrcGen(EntitySrcGen) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeEntitySrcNat(EntitySrcNat) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeEntitySrcNat(EntitySrcNat) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeEntitySrcSyn(PdbxEntitySrcSyn) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeEntitySrcSyn(PdbxEntitySrcSyn) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeExptl(Exptl) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeExptl(Exptl) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxAuditRevisionHistory(PdbxAuditRevisionHistory) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxAuditRevisionHistory(PdbxAuditRevisionHistory) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxChemCompIdentifier(PdbxChemCompIdentifier) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxChemCompIdentifier(PdbxChemCompIdentifier) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxDatabaseStatus(PdbxDatabaseStatus) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxDatabaseStatus(PdbxDatabaseStatus) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxEntityBranchDescriptor(PdbxEntityBranchDescriptor) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxEntityBranchDescriptor(PdbxEntityBranchDescriptor) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxMolecule(PdbxMolecule) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxMolecule(PdbxMolecule) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxMoleculeFeatures(PdbxMoleculeFeatures) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxMoleculeFeatures(PdbxMoleculeFeatures) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxNonpolyScheme(PdbxNonpolyScheme) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxNonpolyScheme(PdbxNonpolyScheme) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxReferenceEntityLink(PdbxReferenceEntityLink) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxReferenceEntityLink(PdbxReferenceEntityLink) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxReferenceEntityList(PdbxReferenceEntityList) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxReferenceEntityList(PdbxReferenceEntityList) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxReferenceEntityPolyLink(PdbxReferenceEntityPolyLink) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxReferenceEntityPolyLink(PdbxReferenceEntityPolyLink) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxStructAssembly(PdbxStructAssembly) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxStructAssembly(PdbxStructAssembly) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxStructAssemblyGen(PdbxStructAssemblyGen) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxStructAssemblyGen(PdbxStructAssemblyGen) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxStructModResidue(PdbxStructModResidue) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxStructModResidue(PdbxStructModResidue) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumePdbxStructOperList(PdbxStructOperList) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumePdbxStructOperList(PdbxStructOperList) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeRefine(Refine) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeRefine(Refine) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStruct(Struct) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStruct(Struct) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructAsym(StructAsym) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructAsym(StructAsym) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructConf(StructConf) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructConf(StructConf) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructConn(StructConn) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructConn(StructConn) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructConnType(StructConnType) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructConnType(StructConnType) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructKeywords(StructKeywords) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructKeywords(StructKeywords) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructNcsOper(StructNcsOper) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructNcsOper(StructNcsOper) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructRef(StructRef) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructRef(StructRef) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructRefSeq(StructRefSeq) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructRefSeq(StructRefSeq) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructRefSeqDif(StructRefSeqDif) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructRefSeqDif(StructRefSeqDif) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructSheetRange(StructSheetRange) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructSheetRange(StructSheetRange) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructSite(StructSite) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructSite(StructSite) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeStructSiteGen(StructSiteGen) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeStructSiteGen(StructSiteGen) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
consumeSymmetry(Symmetry) - Method in interface org.biojava.nbio.structure.io.cif.CifStructureConsumer: Consume a particular Cif category.
consumeSymmetry(Symmetry) - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl
Contact - Class in org.biojava.nbio.structure.contact: A simple class to store contacts in the form of pairs of indices and a distance associated to them.
Contact(int, int, double) - Constructor for class org.biojava.nbio.structure.contact.Contact
contacts(Point3d[], Point3d[], double) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint
contains(Point3d) - Method in class org.biojava.nbio.structure.contact.BoundingBox: Check if a given point falls within this box
contains(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable: Is the key in the table?
contains(ResidueNumber) - Method in class org.biojava.nbio.structure.AugmentedResidueRange
contains(ResidueNumber, AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange
containsChainId(String, String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
containsKey(Object) - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap
containsUniProtId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
convert(File, File) - Static method in class demo.DemoMmcifToPdbConverter
convertAfpChain(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator: copy data from this class into AFPChain container object.
convertAfpChain(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced: copy data from this class into AFPChain container object.
convertAtomsToSeq(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools
convertPairsToXML(SortedSet<PdbPair>, String) - Static method in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
convertToDoubleArray(Matrix4d) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils: Convert a four-d matrix to a double array.
convertXMLtoPairs(String) - Static method in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
copy() - Method in class org.biojava.nbio.structure.jama.Matrix: Make a deep copy of a matrix
copyLigandsByProximity(Structure, Structure) - Static method in class org.biojava.nbio.structure.SubstructureIdentifier: Supplements the reduced structure with ligands from the full structure based on a distance cutoff.
copyLigandsByProximity(Structure, Structure, double, int, int) - Static method in class org.biojava.nbio.structure.SubstructureIdentifier: Supplements the reduced structure with ligands from the full structure based on a distance cutoff.
CoreSuperimposer - Class in org.biojava.nbio.structure.align.multiple.util: Superimposes the core aligned residues of every structure in a MultipleAlignment onto a reference structure.
CoreSuperimposer() - Constructor for class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer: Default Constructor.
CoreSuperimposer(int) - Constructor for class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer: Constructor using a specified structure as reference.
COVALENT - org.biojava.nbio.structure.BondType
cpFastaToAfpChain(File, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.
cpFastaToAfpChain(String, String, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter
cpFastaToAfpChain(ProteinSequence, ProteinSequence, Structure, int) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter: Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.
cpPoint - Variable in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters: The CP point, specified as a residue index
CPRange() - Constructor for class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
Cr - org.biojava.nbio.structure.Element
createAFPChain(Atom[], Atom[], ResidueNumber[], ResidueNumber[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools: Fundamentally, an alignment is just a list of aligned residues in each protein.
createArtificalStructure(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
createPurelyNonPolyEntities(List<List<Chain>>, List<List<Chain>>, List<EntityInfo>) - Static method in class org.biojava.nbio.structure.io.EntityFinder: Given all chains of all models find entities for the nonpolymers and water chains within them, assigning entity ids, types and descriptions to them.
createVirtualCBAtom(AminoAcid) - Static method in class org.biojava.nbio.structure.Calc: creates a virtual C-beta atom.
CrystalBuilder - Class in org.biojava.nbio.structure.xtal: A class containing methods to find interfaces in a given crystallographic Structure by reconstructing the crystal lattice through application of symmetry operators
CrystalBuilder(Structure) - Constructor for class org.biojava.nbio.structure.xtal.CrystalBuilder
CrystalBuilder(Structure, Map<String, String>, Map<String, Matrix4d>) - Constructor for class org.biojava.nbio.structure.xtal.CrystalBuilder: Special constructor for NCS-aware CrystalBuilder.
CrystalCell - Class in org.biojava.nbio.structure.xtal: A crystal cell's parameters.
CrystalCell() - Constructor for class org.biojava.nbio.structure.xtal.CrystalCell
CrystalCell(double, double, double, double, double, double) - Constructor for class org.biojava.nbio.structure.xtal.CrystalCell
CrystalTransform - Class in org.biojava.nbio.structure.xtal: Representation of a transformation in a crystal: - a transformation id (each of the transformations in a space group, 0 to m) - a crystal translation The transformation matrix in crystal basis is stored, representing the basic transformation together with the crystal translation.
CrystalTransform(CrystalTransform) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform: Copy constructor
CrystalTransform(SpaceGroup) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform: Creates a new CrystalTransform representing the identity transform in cell (0,0,0)
CrystalTransform(SpaceGroup, int) - Constructor for class org.biojava.nbio.structure.xtal.CrystalTransform: Represents the n-th transform
Cs - org.biojava.nbio.structure.Element
Cu - org.biojava.nbio.structure.Element
CUBIC - org.biojava.nbio.structure.xtal.BravaisLattice
CURRENT - org.biojava.nbio.structure.PDBStatus.Status
CUSTOM - org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy: The strategy is defined via an external function, we do not have to do anything.
cut(Atom[], Domain, CutValues, int[][], PDPDistanceMatrix) - Method in class org.biojava.nbio.structure.domain.pdp.Cut
Cut - Class in org.biojava.nbio.structure.domain.pdp
Cut() - Constructor for class org.biojava.nbio.structure.domain.pdp.Cut
CUT_OFF_VALUE - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
CUT_OFF_VALUE1 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
CUT_OFF_VALUE1M - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
CUT_OFF_VALUE1S - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
CUT_OFF_VALUE2 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters
cutDomain(Domain, CutSites, PDPDistanceMatrix) - Method in class org.biojava.nbio.structure.domain.pdp.CutDomain
CutDomain - Class in org.biojava.nbio.structure.domain.pdp
CutDomain(Atom[], PDPDistanceMatrix) - Constructor for class org.biojava.nbio.structure.domain.pdp.CutDomain
CutSites - Class in org.biojava.nbio.structure.domain.pdp
CutSites() - Constructor for class org.biojava.nbio.structure.domain.pdp.CutSites
CutValues - Class in org.biojava.nbio.structure.domain.pdp
CutValues() - Constructor for class org.biojava.nbio.structure.domain.pdp.CutValues
CYCLE - org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy: Cycle through the alphabet (e.g., ...xyzABC...)
cyclicPeptide - org.biojava.nbio.structure.chem.PolymerType: cyclic peptides

D

D - org.biojava.nbio.structure.Element

Deuterium

d2 - Static variable in class org.biojava.nbio.structure.io.FileConvert

d3 - Static variable in class org.biojava.nbio.structure.io.FileConvert

DatabasePDBRevRecord - Class in org.biojava.nbio.structure

Represents revision records for use by PDBHeader.

DatabasePDBRevRecord() - Constructor for class org.biojava.nbio.structure.DatabasePDBRevRecord

DatabasePDBRevRecord(String, String, String) - Constructor for class org.biojava.nbio.structure.DatabasePDBRevRecord

DatabasePDBRevRecord(DatabasePDBRevRecord, int) - Constructor for class org.biojava.nbio.structure.DatabasePDBRevRecord

dateToIsoString(Date) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Covert a Date object to ISO time format.

dBetaPeptideCGammaLinking - org.biojava.nbio.structure.chem.ResidueType

DBL - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

DBRef - Class in org.biojava.nbio.structure

A class to represent database cross references.

DBRef() - Constructor for class org.biojava.nbio.structure.DBRef

debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator

debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer

debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer

debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor

debug - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner

debug - Static variable in class org.biojava.nbio.structure.align.util.AlignmentTools

DEF_NUM_CELLS - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder

DEFAULT - Static variable in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

DEFAULT - Static variable in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior

DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod

DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod

DEFAULT - Static variable in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType

DEFAULT_ALGORITHM_NAME - Static variable in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser

DEFAULT_ASA_SPHERE_POINTS - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList

Default number of points to use when calculating ASAs

DEFAULT_BCIF_FILE_SERVER - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory

The default server to retrieve BinaryCIF files.

DEFAULT_BIOASSEMBLY_STYLE - Static variable in class org.biojava.nbio.structure.align.util.AtomCache

The default output bioassembly style: if true the bioassemblies are multimodel, if false the bioassemblies are flat with renamed chains for symmetry-partners.

DEFAULT_CHEMCOMP_PATHURL_TEMPLATE - Static variable in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

DEFAULT_CLUSTER_CUTOFF - Static variable in class org.biojava.nbio.structure.align.ClusterAltAligs

DEFAULT_CONNECTION_TIMEOUT - Static variable in class org.biojava.nbio.structure.align.util.URLConnectionTools

The default connection timeout in ms - 15 seconds

DEFAULT_CONTACT_CUTOFF - Static variable in class org.biojava.nbio.structure.contact.InterfaceFinder

DEFAULT_CONTACT_OVERLAP_SCORE_CLUSTER_CUTOFF - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList

Any 2 interfaces with contact overlap score larger than this value will be considered to be clustered

DEFAULT_FILE - Static variable in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

DEFAULT_FRAGLEN - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

DEFAULT_GAP_EXTENSION - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters

DEFAULT_GAP_OPEN - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters

DEFAULT_INTERFACE_DISTANCE_CUTOFF - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder

Default maximum distance between two chains to be considered an interface.

DEFAULT_LIGAND_PROXIMITY_CUTOFF - Static variable in class org.biojava.nbio.structure.StructureTools

Threshold for plausible binding of a ligand to the selected substructure

DEFAULT_MAX_PROPELLER - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

DEFAULT_MAX_PROPELLER - Static variable in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

DEFAULT_MAX_SHEAR - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

DEFAULT_MAX_STAGGER - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

DEFAULT_MAX_STAGGER - Static variable in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

DEFAULT_MAX_STRETCH - Static variable in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

DEFAULT_METHOD_NAME - Static variable in class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter

DEFAULT_MIN_COFACTOR_SIZE - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList

Default minimum size of cofactor molecule (non-chain HET atoms) that will be used

DEFAULT_MIN_CP_LENGTH - Static variable in class org.biojava.nbio.structure.align.ce.CECPParameters

DEFAULT_MINIMUM_INTERFACE_AREA - Static variable in class org.biojava.nbio.structure.contact.StructureInterfaceList

Default minimum area for a contact between two chains to be considered a valid interface.

DEFAULT_N_SPHERE_POINTS - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

The default value for number of sphere points to sample.

DEFAULT_NTHREADS - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

DEFAULT_oRmsdThr - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters

DEFAULT_PDB_FILE_SERVER - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory

The default server name, prefixed by the protocol string (http://, https:// or ftp://).

DEFAULT_PROBE_SIZE - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

DEFAULT_RCSB_DATA_API_SERVER - Static variable in class org.biojava.nbio.structure.PDBStatus

DEFAULT_RESOLUTION - Static variable in class org.biojava.nbio.structure.PDBHeader

DEFAULT_RFREE - Static variable in class org.biojava.nbio.structure.PDBHeader

DEFAULT_SCORING_STRATEGY - Static variable in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

DEFAULT_SERVER_URL - Static variable in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

DEFAULT_SUBSTITUTION_MATRIX - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters

DEFAULT_SYMMETRY_THRESHOLD - Static variable in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathFactory

DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathInstallation

DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.ecod.EcodFactory

DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation

DEFAULT_VERSION - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation

delete(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable

Delete the key (and paired value) from table.

deleteColumn(AFPChain, Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Delete an alignment position from the original alignment object.

deleteHighestDistanceColumn(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Find the alignment position with the highest atomic distance between the equivalent atomic positions of the arrays and remove it from the alignment.

deleteStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Attempts to delete all versions of a structure from the local directory.

deleteStructure(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Attempts to delete all versions of a structure from the local directory.

DELTA - Static variable in class org.biojava.nbio.structure.xtal.SpaceGroup

deltaComp(double, double, double) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup

demo - package demo

DemoAsa - Class in demo

DemoAsa() - Constructor for class demo.DemoAsa

DemoAtomCache - Class in demo

Example of how to load PDB files using the AtomCache class.

DemoAtomCache() - Constructor for class demo.DemoAtomCache

DemoBerkeleyScop - Class in demo

A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP

DemoBerkeleyScop() - Constructor for class demo.DemoBerkeleyScop

DemoBioAssemblies - Class in demo

DemoBioAssemblies() - Constructor for class demo.DemoBioAssemblies

DemoCATH - Class in demo

An example for how to access CATH data.

DemoCATH() - Constructor for class demo.DemoCATH

DemoCE - Class in demo

Example of how to run a structure alignment using the CE algorithm.

DemoCE() - Constructor for class demo.DemoCE

DemoCeSymm - Class in demo

Quick demo of how to call CE-Symm programmatically.

DemoCeSymm() - Constructor for class demo.DemoCeSymm

DemoChangeChemCompProvider - Class in demo

This demo shows how to use an alternative ChemCompProvider.

DemoChangeChemCompProvider() - Constructor for class demo.DemoChangeChemCompProvider

DemoCommandLineStartup - Class in demo

DemoCommandLineStartup() - Constructor for class demo.DemoCommandLineStartup

DemoContacts - Class in demo

DemoContacts() - Constructor for class demo.DemoContacts

DemoCrystalInterfaces - Class in demo

DemoCrystalInterfaces() - Constructor for class demo.DemoCrystalInterfaces

DemoDomainsplit - Class in demo

DemoDomainsplit() - Constructor for class demo.DemoDomainsplit

DemoFATCAT - Class in demo

DemoFATCAT() - Constructor for class demo.DemoFATCAT

DemoLoadSecStruc - Class in demo

Demonstration of how to load a Structure with the SS information, either from the PDB file annotation (Author's assignment) or from the DSSP file in the PDB servers (DSSP assignment).

DemoLoadSecStruc() - Constructor for class demo.DemoLoadSecStruc

DemoLoadStructure - Class in demo

Example for how to load protein structures (from PDB files).

DemoLoadStructure() - Constructor for class demo.DemoLoadStructure

DemoMMCIFReader - Class in demo

An example of how to read MMcif files

DemoMMCIFReader() - Constructor for class demo.DemoMMCIFReader

DemoMmcifToPdbConverter - Class in demo

An example of how to convert mmCIF file to PDB file

DemoMmcifToPdbConverter() - Constructor for class demo.DemoMmcifToPdbConverter

DemoMmtfReader - Class in demo

Class to show how to read a Biojava structure using MMTF

DemoMmtfReader() - Constructor for class demo.DemoMmtfReader

DemoMmtfWriter - Class in demo

DemoMmtfWriter() - Constructor for class demo.DemoMmtfWriter

DemoMultipleMC - Class in demo

Demo for running the MultipleMC Algorithm on a protein family.

DemoMultipleMC() - Constructor for class demo.DemoMultipleMC

DemoQsAlign - Class in demo

Demo on how to use programatically QsAlign for the alignment of quaternary structures.

DemoQsAlign() - Constructor for class demo.DemoQsAlign

DemoSCOP - Class in demo

A class demonstrating the use of the SCOP parsing tools

DemoSCOP() - Constructor for class demo.DemoSCOP

DemoSecStrucCalc - Class in demo

Demonstration on how to use the Secondary Structure Prediction (DSSP) implementation in BioJava and obtain different SS representations and outputs.

DemoSecStrucCalc() - Constructor for class demo.DemoSecStrucCalc

DemoSymmetry - Class in demo

A demo on how to use the quaternary symmetry detection algorithms.

DemoSymmetry() - Constructor for class demo.DemoSymmetry

deserialize(File) - Static method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

desFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation

det() - Method in class org.biojava.nbio.structure.jama.LUDecomposition

Determinant

det() - Method in class org.biojava.nbio.structure.jama.Matrix

Matrix determinant

dGammaPeptideCDeltaLinking - org.biojava.nbio.structure.chem.ResidueType

DIFFERENT - org.biojava.nbio.structure.align.quaternary.QsRelation

None of the Subunits of one Structure have an equivalent in the other Structure.

disableCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache

display(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

DISTANCE_INCREMENT - Static variable in class org.biojava.nbio.structure.align.ce.CeParameters

DistanceBox<T> - Class in org.biojava.nbio.structure.symmetry.geometry

DistanceBox(double) - Constructor for class org.biojava.nbio.structure.symmetry.geometry.DistanceBox

Creates a new instance of DistanceBox

distanceIncrement - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

divideInternally(SubunitClustererParameters) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Analyze the internal symmetry of the SubunitCluster and divide its Subunit into the internal repeats (domains) if they are internally symmetric.

divideStructure(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Method that converts the symmetric units of a structure into different structures, so that they can be individually visualized.

dna - org.biojava.nbio.structure.chem.PolymerType

polydeoxyribonucleotide

DNA_ONLY - Static variable in enum org.biojava.nbio.structure.chem.PolymerType

Convenience Set of polymer types classified as DNA.

dna3PrimeTerminus - org.biojava.nbio.structure.chem.ResidueType

dna5PrimeTerminus - org.biojava.nbio.structure.chem.ResidueType

dnaLinking - org.biojava.nbio.structure.chem.ResidueType

dnarna - org.biojava.nbio.structure.chem.PolymerType

polydeoxyribonucleotide/polyribonucleotide hybrid

doChainAfp(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPChainer

// Key function: chain (assembly) the AFPs // a AFP (k) is defined as (i, j, k), with i and j are staring points // AFP extension (eg.

doIter0(int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

doIter0(int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

Domain - Class in org.biojava.nbio.structure.domain.pdp

Domain - org.biojava.nbio.structure.scop.ScopCategory

Domain() - Constructor for class org.biojava.nbio.structure.domain.pdp.Domain

DomainCounter - org.biojava.nbio.structure.cath.CathCategory

domainDescriptionFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation

domainListFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation

DomainProvider - Interface in org.biojava.nbio.structure.domain

Decomposes a structure from the PDB into representative domains

DOMAINS_PATH - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation

domallFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation

doPOST(URL, String) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools

Do a POST to a URL and return the response stream for further processing elsewhere.

doPOST(URL, String, int) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools

Do a POST to a URL and return the response stream for further processing elsewhere.

doPrintConnections() - Method in class org.biojava.nbio.structure.io.FileConvert

Returns if the Connections should be added default is true;

dot(SparseVector) - Method in class org.biojava.nbio.structure.math.SparseVector

Calculates the dot product of this vector a with b

dotProduct(Quat4d, Quat4d) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions

Compute the dot (inner) product of two quaternions.

DOUBLE - org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy

Represent every cluster with two symbols from the alphabet, this forces us to specify number of subunits for every subunit (e.g., AA1AB1AC1...).

DownloadChemCompProvider - Class in org.biojava.nbio.structure.chem

This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site.

DownloadChemCompProvider() - Constructor for class org.biojava.nbio.structure.chem.DownloadChemCompProvider

DownloadChemCompProvider(String) - Constructor for class org.biojava.nbio.structure.chem.DownloadChemCompProvider

downloadClaFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

downloadComFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

downloadDesFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

downloadDomainDescriptionFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation

downloadDomainListFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation

downloadDomallFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation

downloadFile() - Static method in class org.biojava.nbio.structure.chem.AllChemCompProvider

Downloads the components.cif.gz file from the wwPDB site.

downloadFileFromRemote(URL, File) - Method in class org.biojava.nbio.structure.cath.CathInstallation

downloadFileFromRemote(URL, File) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

downloadHieFile() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

downloadNodeListFile() - Method in class org.biojava.nbio.structure.cath.CathInstallation

downloadStructure(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Downloads an MMCIF file from the PDB to the local path

dpeptide - org.biojava.nbio.structure.chem.PolymerType

polypeptide(D)

dPeptideAminoTerminus - org.biojava.nbio.structure.chem.ResidueType

dPeptideCarboxyTerminus - org.biojava.nbio.structure.chem.ResidueType

dPeptideLinking - org.biojava.nbio.structure.chem.ResidueType

dSaccharide - org.biojava.nbio.structure.chem.ResidueType

dSaccharide14and14linking - org.biojava.nbio.structure.chem.ResidueType

dSaccharide14and16linking - org.biojava.nbio.structure.chem.ResidueType

DSSP_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo

Secondary strucuture parsed from a DSSP output file

DSSPParser - Class in org.biojava.nbio.structure.secstruc

Class to parse a DSSP file (output of the DSSP program), that contains the secondary structure assignment of a structure.

DSSPParser() - Constructor for class org.biojava.nbio.structure.secstruc.DSSPParser

duplicateCA2(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools

Utility method for working with circular permutations.

duplicationHint - Variable in class org.biojava.nbio.structure.align.ce.CECPParameters

duplicationHint - Variable in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

Dy - org.biojava.nbio.structure.Element

E

ECOD - org.biojava.nbio.structure.align.client.StructureName.Source

ECOD_RE - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation

ECOD_URL - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation

EcodDatabase - Interface in org.biojava.nbio.structure.ecod

General API for interacting with ECOD.

EcodDomain - Class in org.biojava.nbio.structure.ecod

An EcodDomain contains all the information of the ECOD database: id, classification groups (from higher to lower in the tree: X,H,T,F), PDB code, chain, residue ranges and status (manual or automatic classification).

EcodDomain() - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain

Default constructor with all null properties

EcodDomain(Long, String, Boolean, Integer, Integer, Integer, Integer, String, String, String, String, String, String, String, String, Long, Set<String>) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain

EcodDomain(Long, String, Boolean, Integer, Integer, Integer, Integer, String, String, String, String, String, String, String, String, String, Long, Set<String>) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain

EcodDomain(String) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain

EcodDomain(EcodDomain) - Constructor for class org.biojava.nbio.structure.ecod.EcodDomain

EcodFactory - Class in org.biojava.nbio.structure.ecod

Controls global EcodDatabases being used.

EcodInstallation - Class in org.biojava.nbio.structure.ecod

Provides access to the Evolutionary Classification of Protein Domains (ECOD).

EcodInstallation() - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation

EcodInstallation(String, String) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation

Use EcodFactory to create instances.

EcodInstallation.EcodParser - Class in org.biojava.nbio.structure.ecod

EcodParser(BufferedReader) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser

EcodParser(File) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser

EcodParser(Reader) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser

EcodParser(String) - Constructor for class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser

eig() - Method in class org.biojava.nbio.structure.jama.Matrix

Eigenvalue Decomposition

EigenvalueDecomposition - Class in org.biojava.nbio.structure.jama

Eigenvalues and eigenvectors of a real matrix.

EigenvalueDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.EigenvalueDecomposition

Check for symmetry, then construct the eigenvalue decomposition Structure to access D and V.

ELECTRON_CRYSTALLOGRAPHY - org.biojava.nbio.structure.ExperimentalTechnique

ELECTRON_MICROSCOPY - org.biojava.nbio.structure.ExperimentalTechnique

Element - Enum in org.biojava.nbio.structure

Element is an enumeration of the elements of the periodic table.

ElementType - Enum in org.biojava.nbio.structure

ElementType is an enumeration of the types of elements found in the periodic table.

enableCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache

ENDS - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

ENDSEND - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

ensureClaInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

ensureComInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

ensureDesInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

ensureDomainDescriptionInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation

ensureDomainListInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation

ensureDomainsFileInstalled() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

Blocks until ECOD domains file has been downloaded and parsed.

ensureDomallInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation

ensureHieInstalled() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

ensureNodeListInstalled() - Method in class org.biojava.nbio.structure.cath.CathInstallation

entity_poly_type - Variable in enum org.biojava.nbio.structure.chem.PolymerType

EntityFinder - Class in org.biojava.nbio.structure.io

Heuristical finding of Entities (called Compounds in legacy PDB format) in a given Structure.

EntityFinder() - Constructor for class org.biojava.nbio.structure.io.EntityFinder

EntityInfo - Class in org.biojava.nbio.structure

An object to contain the info from the PDB header for a Molecule.

EntityInfo() - Constructor for class org.biojava.nbio.structure.EntityInfo

EntityInfo(EntityInfo) - Constructor for class org.biojava.nbio.structure.EntityInfo

Constructs a new EntityInfo copying all data from the given one but not setting the Chains

EntityType - Enum in org.biojava.nbio.structure

The type of entity (polymer, non-polymer, water, macrolide) as defined in the mmCIF dictionary:

entityTypeFromString(String) - Static method in enum org.biojava.nbio.structure.EntityType

Creates a new EntityType from a String value.

entrySet() - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap

Always returns the empty set

equals(Object) - Method in class org.biojava.nbio.structure.align.client.PdbPair

equals(Object) - Method in class org.biojava.nbio.structure.align.client.StructureName

equals(Object) - Method in class org.biojava.nbio.structure.align.model.AFPChain

A week equality metric.

equals(Object) - Method in class org.biojava.nbio.structure.Author

equals(Object) - Method in class org.biojava.nbio.structure.chem.ChemComp

equals(Object) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

equals(Object) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier

equals(Object) - Method in class org.biojava.nbio.structure.contact.Pair

equals(Object) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

equals(Object) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

equals(Object) - Method in class org.biojava.nbio.structure.io.SSBondImpl

equals(Object) - Method in class org.biojava.nbio.structure.PdbId

equals(Object) - Method in class org.biojava.nbio.structure.ResidueNumber

equals(Object) - Method in class org.biojava.nbio.structure.ResidueRange

equals(Object) - Method in class org.biojava.nbio.structure.ResidueRangeAndLength

equals(Object) - Method in class org.biojava.nbio.structure.scop.ScopDescription

Compares the fields sunID, category, classificationId, and name for equality

equals(Object) - Method in class org.biojava.nbio.structure.secstruc.BetaBridge

equals(Object) - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc

equals(Object) - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo

equals(Object) - Method in class org.biojava.nbio.structure.Site

equals(Object) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup

equals(Object) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature

equals(Object) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

equals(PDBHeader) - Method in class org.biojava.nbio.structure.PDBHeader

Compare two PDBHeader objects

equalsPositional(Object) - Method in class org.biojava.nbio.structure.ResidueNumber

Check if the seqNum and insertion code are equivalent, ignoring the chain

EQUIVALENT - org.biojava.nbio.structure.align.quaternary.QsRelation

All the Subunits of one Structure have an equivalent in the other Structure.

EQUIVALENT_VERSIONS - Static variable in class org.biojava.nbio.structure.scop.BerkeleyScopInstallation

A map from SCOP version names which the Berkeley server offers as a download to an array of equivalent deprecated SCOP version names.

Er - org.biojava.nbio.structure.Element

Es - org.biojava.nbio.structure.Element

Eu - org.biojava.nbio.structure.Element

execute(Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmIterative

This method uses iteratively CeSymm to calculate all symmetries in the input array of atoms and organize them in a multiple alignment of the repeats.

expandNcsOps(Structure, Map<String, String>, Map<String, Matrix4d>) - Static method in class org.biojava.nbio.structure.xtal.CrystalBuilder

Apply the NCS operators in the given Structure adding new chains as needed.

ExperimentalTechnique - Enum in org.biojava.nbio.structure

An enum to represent the experimental technique of a PDB structure

extended - org.biojava.nbio.structure.secstruc.SecStrucType

extendFragments(Atom[], Atom[], JointFragments[], StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner

extendFragments(Atom[], Atom[], JointFragments, StrucAligParameters) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner

extendHelix(int) - Method in class org.biojava.nbio.structure.symmetry.core.HelixExtender

extractAFPChains(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator

extractFragments(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

extractFragments(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

extractSubunits(Structure, int, double, int) - Static method in class org.biojava.nbio.structure.cluster.SubunitExtractor

Extract the information of each protein Chain in a Structure and converts them into a List of Subunit.

F

F - org.biojava.nbio.structure.Element

F_UNCLASSIFIED - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser

String for unclassified F-groups

Family - org.biojava.nbio.structure.scop.ScopCategory

FastaAFPChainConverter - Class in org.biojava.nbio.structure.io

A collection of static utilities to convert between AFPChains and FastaSequences.

FastaAFPChainConverter() - Constructor for class org.biojava.nbio.structure.io.FastaAFPChainConverter

fastaFileToAfpChain(File, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter

Reads the file fastaFile, expecting exactly two sequences which give a pairwise alignment.

fastaStringToAfpChain(String, String, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter

Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.

FastaStructureParser - Class in org.biojava.nbio.structure.io

Reads a protein sequence from a fasta file and attempts to match it to a 3D structure.

FastaStructureParser(File, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser

FastaStructureParser(InputStream, SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound>, SequenceCreatorInterface<AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser

FastaStructureParser(FastaReader<ProteinSequence, AminoAcidCompound>, AtomCache) - Constructor for class org.biojava.nbio.structure.io.FastaStructureParser

fastaToAfpChain(String, String, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter

TODO Write comment

fastaToAfpChain(Map<String, ProteinSequence>, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter

Uses two sequences each with a corresponding structure to create an AFPChain corresponding to the alignment.

fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>, AminoAcidCompound>, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter

Provided only for convenience.

fastaToAfpChain(ProteinSequence, ProteinSequence, Structure, Structure) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter

Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.

FatCat - Class in org.biojava.nbio.structure.align.fatcat

FatCat() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCat

FatCatAligner - Class in org.biojava.nbio.structure.align.fatcat.calc

A class that does calculations on an AFPChain

FatCatAligner() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner

FatCatFlexible - Class in org.biojava.nbio.structure.align.fatcat

FatCatFlexible() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatFlexible

FatCatParameters - Class in org.biojava.nbio.structure.align.fatcat.calc

FatCatParameters() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

FatCatRigid - Class in org.biojava.nbio.structure.align.fatcat

FatCatRigid() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatRigid

FatCatStartupParams() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

FatCatUserArgumentProcessor - Class in org.biojava.nbio.structure.align.fatcat

FatCatUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor

FatCatUserArgumentProcessor.FatCatStartupParams - Class in org.biojava.nbio.structure.align.fatcat

FCAlignHelper - Class in org.biojava.nbio.structure.align.fatcat.calc

FCAlignHelper(double[][], int, int, double, double) - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper

do an alignment given the provided matrix sij0

Fe - org.biojava.nbio.structure.Element

FETCH_CURRENT - org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior

Fetch the most recent version of the PDB entry.

FETCH_FILES - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

Fetch missing files from the server.

FETCH_IF_OUTDATED - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

Fetch missing files from the server, also fetch if file present but older than the server file.

FETCH_OBSOLETE - org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior

Fetch the obsolete entry from the PDB archives.

FETCH_REMEDIATED - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

Fetch missing files from the server.

FIBER_DIFFRACTION - org.biojava.nbio.structure.ExperimentalTechnique

FILE - org.biojava.nbio.structure.align.client.StructureName.Source

FileConvert - Class in org.biojava.nbio.structure.io

Methods to convert a structure object into different file formats.

FileConvert(Structure) - Constructor for class org.biojava.nbio.structure.io.FileConvert

Constructs a FileConvert object.

FileParsingParameters - Class in org.biojava.nbio.structure.io

A class that configures parameters that can be sent to the PDB file parsers FileParsingParameters.setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms FileParsingParameters.setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed.

FileParsingParameters() - Constructor for class org.biojava.nbio.structure.io.FileParsingParameters

FILESPLIT - Static variable in class org.biojava.nbio.structure.cath.CathInstallation

FILESPLIT - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation

fillAlignedAtomArrays(AFPChain, Atom[], Atom[], Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Fill the aligned Atom arrays with the equivalent residues in the afpChain.

filterByCathCode(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase

Return list of CATH descriptions whose CATH codes (e.g.

filterByCathCode(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

filterByClassificationId(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

Get all scop descriptions that start with a classification ID, e.g.

filterByClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

filterByDescription(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase

Return list of CATH descriptions whose descriptions (name field) starts with the query.

filterByDescription(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

filterByDescription(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

Get all scop descriptions that start with a certain name.

filterByDescription(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

filterByDomainName(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

search through SCOP and filter based on domain name

filterByDomainName(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

filterByHierarchy(String) - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase

Get a list of domains within a particular level of the hierarchy

filterByHierarchy(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

Get a list of domains within a particular level of the hierarchy

filterByNodeName(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase

Return list of CATH domains whose node name (e.g.

filterByNodeName(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

filterDuplicateAFPs(AFPChain, CECalculator, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain

Takes as input an AFPChain where ca2 has been artificially duplicated.

filterDuplicateAFPs(AFPChain, CECalculator, Atom[], Atom[], CECPParameters) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain

filterLigands(List<Group>) - Static method in class org.biojava.nbio.structure.StructureTools

Removes all polymeric and solvent groups from a list of groups

finalizeStructure() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

findGroup(String, String) - Method in interface org.biojava.nbio.structure.Structure

Request a particular group from a structure.

findGroup(String, String) - Method in class org.biojava.nbio.structure.StructureImpl

Request a particular group from a structure.

findGroup(String, String, int) - Method in interface org.biojava.nbio.structure.Structure

Request a particular group from a structure.

findGroup(String, String, int) - Method in class org.biojava.nbio.structure.StructureImpl

Request a particular group from a structure.

findPairs(List<Chain>) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method performs a search for base pairs in the structure.

findPairs(List<Chain>) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This is an implementation for finding non-canonical base pairs when there may be missing or overhanging bases.

findPairs(List<Chain>) - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

This is an alternative implementation of findPair() that looks for anything that would fit the criteria for a base-pair, useful for the context of tertiary structure of RNA.

findPolyEntities(List<List<Chain>>) - Static method in class org.biojava.nbio.structure.io.EntityFinder

Utility method that employs some heuristics to find the EntityInfos for the polymeric chains given in constructor.

finish() - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl

finish() - Method in interface org.biojava.nbio.structure.io.cif.CifFileConsumer

Ultimate setup which can include steps which require several categories to be available and integrate them into the final container.

finish() - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl

finish() - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl

finish(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

first_cut - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues

fixMicroheterogenity(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

This sets all microheterogeneous groups (previously alternate location groups) as separate groups.

flagLoading(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache

flagLoadingFinished(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache

flipAlignment(String) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser

Takes an XML representation of the alignment and flips the positions of name1 and name2

flipChain(AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainFlipper

Flip the position of name1 and name2 (as well as all underlying data) in an AFPChain.

floor(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable

Return the largest key in the table <= k.

FLUORESCENCE_TRANSFER - org.biojava.nbio.structure.ExperimentalTechnique

flush() - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile

flushCache() - Method in class org.biojava.nbio.structure.domain.SerializableCache

Fm - org.biojava.nbio.structure.Element

Fold - org.biojava.nbio.structure.scop.ScopCategory

FORCE_DOWNLOAD - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

For every file, force downloading from the server

FORMAT_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier

URL parameter specifying the file format (PDB or CIF)

formBondsFromStructConn(StructConn) - Method in class org.biojava.nbio.structure.io.BondMaker

formDisulfideBonds(List<SSBondImpl>) - Method in class org.biojava.nbio.structure.io.BondMaker

Creates disulfide bond objects and references in the corresponding Atoms objects, given a list of SSBondImpls parsed from a PDB file.

formLinkRecordBond(PDBTemporaryStorageUtils.LinkRecord) - Method in class org.biojava.nbio.structure.io.BondMaker

Creates bond objects from a LinkRecord as parsed from a PDB file

formMatrix(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint

FORTY_175 - org.biojava.nbio.structure.scop.Astral.AstralSet

FORTY_175A - org.biojava.nbio.structure.scop.Astral.AstralSet

FORTY_175B - org.biojava.nbio.structure.scop.Astral.AstralSet

FORTY_201 - org.biojava.nbio.structure.scop.Astral.AstralSet

FORTY_202 - org.biojava.nbio.structure.scop.Astral.AstralSet

FORTY_203 - org.biojava.nbio.structure.scop.Astral.AstralSet

FOURBAR - org.biojava.nbio.structure.xtal.TransformType

FOURFOLD - org.biojava.nbio.structure.xtal.TransformType

FOURFOLDSCREW - org.biojava.nbio.structure.xtal.TransformType

Fr - org.biojava.nbio.structure.Element

frag_pairwise_compat(FragmentPair[], int, float, int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner

Calculate the pairwise compatibility of fpairs.

FragmentJoiner - Class in org.biojava.nbio.structure.align.pairwise

Joins the initial Fragments together to larger Fragments

FragmentJoiner() - Constructor for class org.biojava.nbio.structure.align.pairwise.FragmentJoiner

FragmentPair - Class in org.biojava.nbio.structure.align.pairwise

a pair of fragments of two protein structures

FragmentPair(int, int, int) - Constructor for class org.biojava.nbio.structure.align.pairwise.FragmentPair

fromAFP(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Converts a refined symmetry AFPChain alignment into the standard representation of symmetry in a MultipleAlignment, that contains the entire Atom array of the strcuture and the symmetric repeats are orgaized in different rows in a single Block.

fromCathCode(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory

fromCharacter(Character) - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType

fromCharacter(Character) - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType

Converts a Character representing a Secondary Structure type into the corresponding enum object.

fromCifFile(CifFile) - Static method in class org.biojava.nbio.structure.io.cif.ChemCompConverter

Convert CifFile to chem comp dictionary.

fromCifFile(CifFile) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert CifFile to Structure without any FileParsingParameters.

fromCifFile(CifFile, FileParsingParameters) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert CifFile to Structure.

fromConciseAlignmentString(String) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

fromInputStream(InputStream) - Static method in class org.biojava.nbio.structure.io.cif.ChemCompConverter

Convert InputStream to chem comp dictionary.

fromInputStream(InputStream) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert InputStream to Structure without any FileParsingParameters.

fromInputStream(InputStream, FileParsingParameters) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert InputStream to Structure.

fromMultiXML(String) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

fromPath(Path) - Static method in class org.biojava.nbio.structure.io.cif.ChemCompConverter

Read data from a file and convert to chem comp dictionary.

fromPath(Path) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Read data from a file and convert to Structure without any FileParsingParameters.

fromPath(Path, FileParsingParameters) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Read data from a file and convert to Structure.

fromStartupParams(StartupParameters) - Static method in class org.biojava.nbio.structure.align.util.UserConfiguration

fromString(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory

fromString(String) - Static method in enum org.biojava.nbio.structure.PDBStatus.Status

fromString(String) - Static method in class org.biojava.nbio.structure.ResidueNumber

Convert a string representation of a residue number to a residue number object.

fromString(String) - Static method in enum org.biojava.nbio.structure.scop.ScopCategory

fromURL(URL) - Static method in class org.biojava.nbio.structure.io.cif.ChemCompConverter

Get data from a URL and convert to chem comp dictionary.

fromURL(URL) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Get data from a URL and convert to Structure without any FileParsingParameters.

fromURL(URL, FileParsingParameters) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Get data from a URL and convert to Structure.

fromXML(String) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

fromXML(String) - Static method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot

fromXML(String) - Static method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper

fromXML(String, String, String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser

new utility method that checks that the order of the pair in the XML alignment is correct and flips the direction if needed

fromXML(String, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser

G

Ga - org.biojava.nbio.structure.Element

GAP_COVERAGE_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.EntityFinder

Gap coverage value (num gaps over length of sequence) for each chain of the match: 2 chains with more gap coverage than this value will not be considered part of the same entity

GapArray - Class in org.biojava.nbio.structure.align.helper

GapArray() - Constructor for class org.biojava.nbio.structure.align.helper.GapArray

gapExtension - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

gapExtension - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

gapOpen - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

gapOpen - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

Gd - org.biojava.nbio.structure.Element

Ge - org.biojava.nbio.structure.Element

get(int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

Gets the interface corresponding to given id.

get(int) - Method in class org.biojava.nbio.structure.math.SparseVector

get a value

get(int, int) - Method in class org.biojava.nbio.structure.jama.Matrix

Get a single element.

get(int, int) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix

access a value at i,j

get(Object) - Method in class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap

get(K) - Method in class org.biojava.nbio.structure.domain.SerializableCache

get(Key) - Method in class org.biojava.nbio.structure.math.SymbolTable

Return the value paired with given key; null if key is not in table.

get(Chain) - Method in class org.biojava.nbio.structure.io.cif.CifChainSupplierImpl

get(Structure) - Method in class org.biojava.nbio.structure.io.cif.CifStructureSupplierImpl

get(S) - Method in interface org.biojava.nbio.structure.io.cif.CifFileSupplier

Convert some model instance describing structure information to a CifFile instance.

get1LetterCode(String) - Static method in class org.biojava.nbio.structure.StructureTools

Convert a three letter amino acid or nucleotide code into a single character code.

get1LetterCodeAmino(String) - Static method in class org.biojava.nbio.structure.StructureTools

Convert three character amino acid codes into single character e.g.

getA() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

getA() - Method in class org.biojava.nbio.structure.xtal.CrystalCell

getAbsoluteMinimumSequenceLength() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.

getAccept1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

getAccept2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

getAcceptedAtomNames() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

By default the parser will read in all atoms (unless using the CAonly switch).

getAccessions() - Method in class org.biojava.nbio.structure.io.FastaStructureParser

Gets the protein accessions mapped from the Fasta file.

getAfpAftIndex() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAfpBefIndex() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAfpChain() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner

getAfpChainLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAfpChainList() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAfpChainTwiBin() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAfpChainTwiList() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAfpChainTwiNum() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAfpDisCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getAfpDisCut0() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getAfpIndex() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAfpSet() - Method in class org.biojava.nbio.structure.align.model.AFPChain

Get the set of AFPs for this alignment.

getAlgebraicFromMatrix(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup

getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor

getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor

getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor

getAlgorithm() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor

getAlgorithm() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor

getAlgorithm() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor

getAlgorithm(String) - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory

getAlgorithmName() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment

getAlgorithmName() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment

getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.CeCPMain

getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.CeMain

getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain

getAlgorithmName() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain

getAlgorithmName() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible

getAlgorithmName() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid

getAlgorithmName() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAlgorithmName() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain

getAlgorithmName() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Returns the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.

getAlgorithmName() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

getAlgorithmName() - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner

Get the name of this Algorithm.

getAlgorithmName() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner

getAlgorithmName() - Method in interface org.biojava.nbio.structure.align.StructureAlignment

Get the name of the Algorithm

getAligMat() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

getAligMat() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

getAligMat(int, int) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

getAlign(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay

Extract the alignment output

getAlign(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay

Sets the following properties: The alignment strings alnseq1, alnseq2, and alnsymb alnbeg1 and 2 alnLength and gapLen

getAlign_se1() - Method in class org.biojava.nbio.structure.align.ce.CECalculator

getAlign_se1() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

getAlign_se2() - Method in class org.biojava.nbio.structure.align.ce.CECalculator

getAlign_se2() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

getAlignedAtoms1(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay

getAlignedAtoms2(AFPChain, Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay

getAlignedAtomsForSubunits1(int) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

getAlignedAtomsForSubunits2(int) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

getAlignedAtomsSubunit(int) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

getAlignedAtomsSubunits() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

getAlignedModel(Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

get an artificial List of chains containing the Atoms and groups.

getAlignedResIndex(Group, Chain) - Method in class org.biojava.nbio.structure.EntityInfo

Given a Group g of Chain c (member of this EntityInfo) return the corresponding position in the alignment of all member sequences (1-based numbering), i.e.

getAlignedStructure(List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Get an artificial Structure containing a different model for every input structure, so that the alignment result can be viewed in Jmol.

getAlignedStructure(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

getAlignedStructure(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Get an artifical Structure containing both chains.

getAlignedStructure(Structure, Structure) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

create an artifical Structure object that contains the two structures superimposed onto each other.

getAlignedSubunits1() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

Return the aligned subunits of the first Subunit group, in the alignment order.

getAlignedSubunits2() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

Return the aligned subunits of the second Subunit group, in the alignment order.

getAlignedUserCollection(String) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter

Takes a protein sequence string with capital and lowercase letters and sets its user collection to record which letters are uppercase (aligned) and which are lowercase (unaligned).

getAlignment() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

The alignment that specifies the residue equivalencies of the equivalent Subunits.

getAlignmentAtoms(Structure) - Method in class org.biojava.nbio.structure.align.StructurePairAligner

Returns the atoms that are being used for the alignment.

getAlignments() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

getAlignments() - Method in class org.biojava.nbio.structure.align.StructurePairAligner

return the alternative alignments that can be found for the two structures

getAlignmentString() - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner

getAlignPairs() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

The file that contains a list of PDB pairs to be aligned

getAlignPos(int[][]) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper

record the aligned pairs in alignList[][0], alignList[][1]; return the number of aligned pairs

getAlignRes() - Method in interface org.biojava.nbio.structure.align.multiple.Block

Returns the double List containing the aligned residues for each structure.

getAlignRes() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

getAlignResCounts() - Method in interface org.biojava.nbio.structure.align.multiple.Block

Returns the number of non null positions (residues) of each structure in the alignment Block.

getAlignResCounts() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

getAlignResCounts() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Returns the number of non null positions (residues) of each structure in the alignment Block Set.

getAlignResCounts() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

getAlignResCounts() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Returns the number of non null positions (residues) of each structure in the alignment.

getAlignResCounts() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

getAlignScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAlignScoreUpdate() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAllAlgorithmNames() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory

getAllAlgorithms() - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory

getAllAtomArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools

Returns and array of all atoms of the chain, including Hydrogens (if present) and all HETATOMs.

getAllAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools

Convert all atoms of the structure (all models) into an Atom array

getAllAtomArray(Structure, int) - Static method in class org.biojava.nbio.structure.StructureTools

Convert all atoms of the structure (specified model) into an Atom array

getAllAtoms() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

getAllChains() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

getAllDomains() - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase

Get all ECOD domains

getAllDomains() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

Get all ECOD domains

getAllGroupsFromSubset(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools

Expand a set of atoms into all groups from the same structure.

getAllGroupsFromSubset(Atom[], GroupType) - Static method in class org.biojava.nbio.structure.StructureTools

Expand a set of atoms into all groups from the same structure.

getAllInterfaces() - Method in class org.biojava.nbio.structure.contact.InterfaceFinder

Find all inter polymer-chain interfaces in the structure.

getAllNonHAtomArray(Chain, boolean) - Static method in class org.biojava.nbio.structure.StructureTools

Returns and array of all non-Hydrogen atoms in the given Chain, optionally including HET atoms or not Waters are not included.

getAllNonHAtomArray(Structure, boolean) - Static method in class org.biojava.nbio.structure.StructureTools

Returns and array of all non-Hydrogen atoms in the given Structure, optionally including HET atoms or not.

getAllNonHAtomArray(Structure, boolean, int) - Static method in class org.biojava.nbio.structure.StructureTools

Returns and array of all non-Hydrogen atoms in the given Structure, optionally including HET atoms or not.

getAllNonHCoordsArray(Chain, boolean) - Static method in class org.biojava.nbio.structure.StructureTools

Returns and array of all non-Hydrogen atoms coordinates in the given Chain, optionally including HET atoms or not Waters are not included.

getAllOxidationStates() - Method in enum org.biojava.nbio.structure.Element

Returns a list of all oxidation states the element is found in.

getAllSpaceGroups() - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser

getAlnbeg1() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAlnbeg2() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAlnLength() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAlnseq1() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAlnseq2() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAlnsymb() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getAlpha() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

A letter that is assigned to this cluster in stoichiometry.

getAlpha() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

getAlpha() - Method in class org.biojava.nbio.structure.xtal.CrystalCell

getAlphabet() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

getAltAligNumber() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

returns the sequential number of this alternative alignment

getAltAtomId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getAltLoc() - Method in interface org.biojava.nbio.structure.Atom

Get alternate Location.

getAltLoc() - Method in class org.biojava.nbio.structure.AtomImpl

getAltLoc1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

getAltLoc2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

getAltLocGroup(Character) - Method in interface org.biojava.nbio.structure.Group

Gets the alternate location group to this group that has the alt-loc character code passed.

getAltLocGroup(Character) - Method in class org.biojava.nbio.structure.HetatomImpl

getAltLocs() - Method in interface org.biojava.nbio.structure.Group

Get the list of other alternate location groups.

getAltLocs() - Method in class org.biojava.nbio.structure.HetatomImpl

getAltShortSymbol() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

Gets the alternative international short name (as sometimes used in PDB), e.g.

getAminoAcid(String) - Static method in class org.biojava.nbio.structure.StandardAminoAcid

get a standard amino acid.

getAminoOneLetter(String) - Static method in class org.biojava.nbio.structure.chem.ChemCompTools

getAminoThreeLetter(Character) - Static method in class org.biojava.nbio.structure.chem.ChemCompTools

getAminoType() - Method in interface org.biojava.nbio.structure.AminoAcid

Returns the name of the AA, in single letter code.

getAminoType() - Method in class org.biojava.nbio.structure.AminoAcidImpl

Returns the name of the AA, in single letter code.

getAngle() - Method in class org.biojava.nbio.structure.align.util.RotationAxis

The rotation angle

getAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

Returns the pitch angle of the helix

getAngle(Matrix3d) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis

Quickly compute the rotation angle from a rotation matrix.

getAngle(Matrix4d) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis

Quickly compute the rotation angle from a rotation matrix.

getAngle(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis

Calculate the rotation angle for a structure

getAngle(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Returns the magnitude of the angle between the first and second blocks of afpChain, measured in degrees.

getAngle(Matrix) - Static method in class org.biojava.nbio.structure.align.util.RotationAxis

Calculate the rotation angle for a given matrix

getAngleDiff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getAngleThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

getArchitectureId() - Method in class org.biojava.nbio.structure.cath.CathDomain

getArchitectureName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getArray() - Method in class org.biojava.nbio.structure.jama.Matrix

Access the internal two-dimensional array.

getArrayCopy() - Method in class org.biojava.nbio.structure.jama.Matrix

Copy the internal two-dimensional array.

getAsaC() - Method in class org.biojava.nbio.structure.asa.GroupAsa

Returns the ASA of the residue in the complexed state

getAsaU() - Method in class org.biojava.nbio.structure.asa.GroupAsa

Returns the ASA of the residue in the uncomplexed state

getAssemblyId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getAssignment() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo

getAsymmetryParameter(double) - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

getAtcc() - Method in class org.biojava.nbio.structure.EntityInfo

getAtom() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom

getAtom(int) - Method in interface org.biojava.nbio.structure.Group

Get at atom by position.

getAtom(int) - Method in class org.biojava.nbio.structure.HetatomImpl

Get at atom by position.

getAtom(String) - Method in interface org.biojava.nbio.structure.Group

Get an atom given its PDB name.

getAtom(String) - Method in class org.biojava.nbio.structure.HetatomImpl

Get an atom given its PDB name.

getAtomA() - Method in interface org.biojava.nbio.structure.Bond

Gets atom 'A' of this bond.

getAtomA() - Method in class org.biojava.nbio.structure.BondImpl

Gets atom 'A' of this bond.

getAtomArray(Atom[], List<Group>, List<Group>) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

getAtomArray(Chain, String[]) - Static method in class org.biojava.nbio.structure.StructureTools

Returns an array of the requested Atoms from the Chain object.

getAtomArray(Structure, String[]) - Static method in class org.biojava.nbio.structure.StructureTools

Returns an array of the requested Atoms from the Structure object.

getAtomArrayAllModels(Structure, String[]) - Static method in class org.biojava.nbio.structure.StructureTools

Returns an array of the requested Atoms from the Structure object.

getAtomArrays() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Returns the array of Atoms for each structure from its parent Ensemble.

getAtomArrays() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Get an array of representative atoms for each structure (CA atoms for proteins).

getAtomArrays() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

getAtomArrays() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

getAtomAsaCs() - Method in class org.biojava.nbio.structure.asa.GroupAsa

getAtomAsaUs() - Method in class org.biojava.nbio.structure.asa.GroupAsa

getAtomB() - Method in interface org.biojava.nbio.structure.Bond

Gets atom 'B' of this bond.

getAtomB() - Method in class org.biojava.nbio.structure.BondImpl

Gets atom 'B' of this bond.

getAtomCAArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools

Returns an Atom array of the C-alpha atoms.

getAtomCAArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools

Return an Atom array of the C-alpha atoms.

getAtomCache() - Static method in class org.biojava.nbio.structure.StructureIO

getAtomCaThreshold() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.

getAtomContacts() - Method in class org.biojava.nbio.structure.contact.Grid

Returns all contacts, i.e.

getAtomContacts() - Method in class org.biojava.nbio.structure.contact.GroupContact

getAtomCoordinateBounds(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools

getAtomForSequencePosition(MultipleAlignment, List<Integer>, int, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Returns the Atom of the specified structure that is aligned in the sequence alignment position specified.

getAtomGroup(int) - Method in interface org.biojava.nbio.structure.Chain

Return the Group at given position, from within Groups with observed density in the chain, i.e.

getAtomGroup(int) - Method in class org.biojava.nbio.structure.ChainImpl

getAtomGroups() - Method in interface org.biojava.nbio.structure.Chain

Return all Groups with observed density in the chain, i.e.

getAtomGroups() - Method in class org.biojava.nbio.structure.ChainImpl

getAtomGroups(GroupType) - Method in interface org.biojava.nbio.structure.Chain

Return a List of all (observed) Groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.

getAtomGroups(GroupType) - Method in class org.biojava.nbio.structure.ChainImpl

getAtomicMass() - Method in enum org.biojava.nbio.structure.Element

Returns the atomic mass for this Element.

getAtomicNumber() - Method in enum org.biojava.nbio.structure.Element

Returns the atomic number of this Element.

getAtomId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getAtomId() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom

getAtomId1() - Method in class org.biojava.nbio.structure.chem.ChemCompBond

getAtomId2() - Method in class org.biojava.nbio.structure.chem.ChemCompBond

getAtomLength() - Method in interface org.biojava.nbio.structure.Chain

Returns the number of Groups with observed density in the chain, i.e.

getAtomLength() - Method in class org.biojava.nbio.structure.ChainImpl

getAtoms() - Method in class org.biojava.nbio.structure.chem.ChemComp

getAtoms() - Method in interface org.biojava.nbio.structure.Group

Get list of atoms.

getAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl

Get list of atoms.

getAtoms() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

getAtoms(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the CA atoms for the provided name.

getAtoms(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache

getAtomsCAInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools

Returns the set of intra-chain contacts for the given chain for C-alpha atoms (including non-standard aminoacids appearing as HETATM groups), i.e.

getAtomSequence() - Method in interface org.biojava.nbio.structure.Chain

Returns the sequence of amino acids as it has been provided in the ATOM records.

getAtomSequence() - Method in class org.biojava.nbio.structure.ChainImpl

getAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface

getAtomsForGroup(Group) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get a list of atoms for a group.

getAtomsInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools

Returns the set of intra-chain contacts for the given chain for all non-H atoms of non-hetatoms, i.e.

getAtomsInContact(Chain, String[], double) - Static method in class org.biojava.nbio.structure.StructureTools

Returns the set of intra-chain contacts for the given chain for given atom names, i.e.

getAtomsInContact(Chain, Chain, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools

Returns the set of inter-chain contacts between the two given chains for all non-H atoms.

getAtomsInContact(Chain, Chain, String[], double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools

Returns the set of inter-chain contacts between the two given chains for the given atom names.

getAtomType1() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

getAtomType2() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

getAuBoundingBox(int) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox

Get the AU BoundingBox for the given cell index (cellIdx=0 would be original AU) The AU BoundingBox is the BoundingBox that bounds all chains belonging to the AU

getAuthorList() - Method in class org.biojava.nbio.structure.JournalArticle

Get the list of Authors of the JournalArticle

getAuthors() - Method in class org.biojava.nbio.structure.PDBHeader

Return the names of the authors as listed in the AUTHORS section of a PDB file.

getAverageResidueDistances(List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.

getAverageResidueDistances(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.

getAverageScore() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

Returns the average similarity score between all pairs of members in the cluster

getAvgTMScore(List<Atom[]>, List<Integer>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

Calculates the average TMScore all the possible pairwise structure comparisons of the given a set of superimposed Atoms and the original structure lengths.

getAvgTMScore(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

Calculates the average TMScore of all the possible pairwise structure comparisons of the given alignment.

getAxes() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

getAxisAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

Returns the AxisAngle of the helix transformation

getAxisAngle() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

getAxisAngle(int, AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler

getAxisAngle(int, AxisAngle4d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler

getAxisAngle(int, AxisAngle4f) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler

getAxisAngle4d() - Method in class org.biojava.nbio.structure.align.util.RotationAxis

Returns the rotation axis and angle in a single javax.vecmath.AxisAngle4d object

getAxisEnds(Atom[]) - Method in class org.biojava.nbio.structure.align.util.RotationAxis

Find a segment of the axis that covers the specified set of atoms.

getAxisFoldType(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

Given a transformId returns the type of axis of rotation: 1 (no rotation), 2, 3, 4 or 6 -fold and for improper rotations: -1, -2, -3, -4 and -6

getAxisTypes() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

getB() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

getB() - Method in class org.biojava.nbio.structure.xtal.CrystalCell

getBackboneAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools

Return an Atom array of the main chain atoms: CA, C, N, O Any group that contains those atoms will be included, be it a standard aminoacid or not

getBadRmsd() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getBaseIdentifier() - Method in class org.biojava.nbio.structure.align.client.StructureName

StructureName wraps another StructureIdentifier.

getBeta() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

getBeta() - Method in class org.biojava.nbio.structure.xtal.CrystalCell

getBinaryOperators() - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver

Returns a list of operators for this assembly.

getBioAssemblies() - Method in class org.biojava.nbio.structure.PDBHeader

Return the map of biological assemblies.

getBiologicalAssemblies(String) - Static method in class org.biojava.nbio.structure.StructureIO

Returns all biological assemblies for the given PDB id, using multiModel=false

getBiologicalAssemblies(String, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns all biological assemblies for given PDB id.

getBiologicalAssemblies(String, boolean) - Static method in class org.biojava.nbio.structure.StructureIO

Returns all biological assemblies for the given PDB id.

getBiologicalAssembly(String) - Static method in class org.biojava.nbio.structure.StructureIO

Returns the first biological assembly that is available for the given PDB id, using multiModel=false

getBiologicalAssembly(String, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the default biological unit (bioassemblyId=1, known in PDB as pdb1.gz).

getBiologicalAssembly(String, boolean) - Static method in class org.biojava.nbio.structure.StructureIO

Returns the first biological assembly that is available for the given PDB id.

getBiologicalAssembly(String, int) - Static method in class org.biojava.nbio.structure.StructureIO

Returns the biological assembly for the given PDB id and bioassembly identifier, using multiModel=false

getBiologicalAssembly(String, int, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the assembly from the biounit annotations found in Structure.getPDBHeader()

getBiologicalAssembly(String, int, boolean) - Static method in class org.biojava.nbio.structure.StructureIO

Returns the biological assembly for the given PDB id and bioassembly identifier.

getBiologicalAssembly(PdbId, int, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the assembly from the biounit annotations found in Structure.getPDBHeader()

getBiologicalMoleculeBounds(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools

getBiologicalMoleculeCentroid(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools

Returns the centroid of the biological molecule.

getBiologicalMoleculeMaximumExtend(Structure, List<BiologicalAssemblyTransformation>) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools

Returns the maximum extend of the biological molecule in the x, y, or z direction.

getBiologicalUnit() - Method in class org.biojava.nbio.structure.EntityInfo

getBioUnitTransformationList(PdbxStructAssembly, int, PdbxStructAssemblyGen, PdbxStructOperList) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder

Returns a list of transformation matrices for the generation of a macromolecular assembly for the specified assembly Id.

getBJSequence() - Method in interface org.biojava.nbio.structure.Chain

Converts the SEQRES groups of a Chain to a Biojava Sequence object.

getBJSequence() - Method in class org.biojava.nbio.structure.ChainImpl

getBlock(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Returns the Block with the specified index of the MultipleAlignment.

getBlock(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

getBlock2Afp() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getBlockForSequencePosition(MultipleAlignment, List<Integer>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Returns the block number of a specified position in the sequence alignment, given the mapping from structure to function.

getBlockGap() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getBlockNrForAlignPos(AFPChain, int) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay

get the block number for an aligned position

getBlockNum() - Method in class org.biojava.nbio.structure.align.model.AFPChain

The number of blocks in the alignment

getBlockNumClu() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getBlockNumIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getBlockNumSpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getBlockResList() - Method in class org.biojava.nbio.structure.align.model.AFPChain

tracks the residues of the initial blocks (before optimization)

getBlockResSize() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getBlockRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getBlockRotationMatrix() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getBlocks() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Returns the List of alignment Blocks of the BlockSet.

getBlocks() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

getBlocks() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Convenience method to get a List of all Blocks from all BlockSets.

getBlocks() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

getBlockScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getBlockSequenceAlignment(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Calculate the sequence alignment Strings for the alignment Blocks in an alignment.

getBlockSequenceAlignment(MultipleAlignment, List<Integer>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Calculate the sequence alignment Strings for the alignment Blocks in an alignment.

getBlockSet() - Method in interface org.biojava.nbio.structure.align.multiple.Block

Returns the parent BlockSet of the Block.

getBlockSet() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

getBlockSet(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Returns the BlockSet with the specified index of the MultipleAlignment.

getBlockSet(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

getBlockSets() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Returns the BlockSet List of the multiple structure alignment.

getBlockSets() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

getBlockShiftVector() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getBlockSize() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getBondOrder() - Method in interface org.biojava.nbio.structure.Bond

Gets the bond order of this bond.

getBondOrder() - Method in class org.biojava.nbio.structure.BondImpl

Gets the bond order of this bond.

getBonds() - Method in interface org.biojava.nbio.structure.Atom

Get all Bonds this atom is part of.

getBonds() - Method in class org.biojava.nbio.structure.AtomImpl

Get all Bonds this atom is part of.

getBonds() - Method in class org.biojava.nbio.structure.chem.ChemComp

getBravLattice() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

getBridge1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

getBridge2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

getBsa() - Method in class org.biojava.nbio.structure.asa.GroupAsa

Returns the BSA value for this group, i.e.

getBsaToAsaRatio() - Method in class org.biojava.nbio.structure.asa.GroupAsa

Returns the bsa/asa(uncomplexed) ratio, i.e.

getBtype() - Method in class org.biojava.nbio.structure.secstruc.Ladder

getBuckle(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the buckle in degrees for the given base pair

getByCategory(CathCategory) - Method in interface org.biojava.nbio.structure.cath.CathDatabase

Return list of CATH descriptions for node representatives at a CATH category (e.g.

getByCategory(CathCategory) - Method in class org.biojava.nbio.structure.cath.CathInstallation

getByCategory(ScopCategory) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

Get all records of a particular classification.

getByCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

getByChainId(String, String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

getByLargestContacts() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

getByLargestContactsNotLowestAngle() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

getByLowestAngle() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

getByName(String) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique

Returns the ExpTechnique given an experimental technique name as used in the PDB, e.g.

getByName(String) - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice

getByUniProtId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

getC() - Method in interface org.biojava.nbio.structure.AminoAcid

Get C atom.

getC() - Method in class org.biojava.nbio.structure.AminoAcidImpl

Get C atom.

getC() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

getC() - Method in class org.biojava.nbio.structure.xtal.CrystalCell

getC2Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

getC3Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

getC4Axis(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

getCA() - Method in interface org.biojava.nbio.structure.AminoAcid

Get CA atom.

getCA() - Method in class org.biojava.nbio.structure.AminoAcidImpl

Get CA atom.

getCa1() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

getCa1Length() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getCa2Length() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getCache() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

getCacheFilePath() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

getCacheFilePath() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

getCacheLocation() - Method in class org.biojava.nbio.structure.cath.CathInstallation

getCacheLocation() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

Get the location of the cache directory (usually set to the PDB_CACHE_DIR property).

getCacheLocation() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

getCachePath() - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the path that contains the caching file for utility data, such as domain definitions.

getCalculationTime() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getCalculationTime() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Returns the running time of the structure alignment calculation, in milliseconds.

getCalculationTime() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

getCalculationTime() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

getCalphaCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getCategories() - Method in class demo.DemoSCOP

Get various categories

getCategory() - Method in class org.biojava.nbio.structure.cath.CathNode

getCategory() - Method in class org.biojava.nbio.structure.scop.ScopDescription

getCATH() - Method in class org.biojava.nbio.structure.cath.CathDomain

getCathDatabase() - Static method in class org.biojava.nbio.structure.cath.CathFactory

Returns the default (singleton) CathDatabase.

getCathDatabase(String) - Static method in class org.biojava.nbio.structure.cath.CathFactory

Returns a CATH database of the specified version.

getCathDownloadUrl() - Method in class org.biojava.nbio.structure.cath.CathInstallation

getCathNode(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase

Return the CathNode for a node ID.

getCathNode(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

getCathVersion() - Method in interface org.biojava.nbio.structure.cath.CathDatabase

Return the CATH release version.

getCathVersion() - Method in class org.biojava.nbio.structure.cath.CathInstallation

getCB() - Method in interface org.biojava.nbio.structure.AminoAcid

Get CB atom.

getCB() - Method in class org.biojava.nbio.structure.AminoAcidImpl

Get CB atom.

getCECalculator() - Method in class org.biojava.nbio.structure.align.ce.CeMain

getCell() - Method in class org.biojava.nbio.structure.EntityInfo

getCellIndices(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Get the index of a unit cell to which the query point belongs.

getCellLine() - Method in class org.biojava.nbio.structure.EntityInfo

getCellTranslation(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

getCellTranslations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

getCellularLocation() - Method in class org.biojava.nbio.structure.EntityInfo

getCenter(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils

Get the centroid for the set of atoms starting from position pos, length fragmentLenght

getCenter1() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

getCenter2() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

getCenterOfMass() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

getCenters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getCenterVector(Atom[]) - Static method in class org.biojava.nbio.structure.Calc

Returns the Vector that needs to be applied to shift a set of atoms to the Centroid.

getCenterVector(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc

Returns the Vector that needs to be applied to shift a set of atoms to the Centroid, if the centroid is already known

getCentroid() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getCentroid() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getCentroid() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getCentroid() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getCentroid(Atom[]) - Static method in class org.biojava.nbio.structure.Calc

Returns the centroid of the set of atoms.

getChain() - Method in interface org.biojava.nbio.structure.Group

Returns the parent Chain of the Group.

getChain() - Method in class org.biojava.nbio.structure.HetatomImpl

Returns the parent Chain of the Group.

getChain(String) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the first model

getChain(String) - Method in class org.biojava.nbio.structure.StructureImpl

Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the first model

getChain(String, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the given model index

getChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl

Retrieve a Chain (polymeric, non-polymeric or water) based on the 'internal' chain id (asymId) for the given model index

getChain1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

getChain2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

getChainBoundingBox(int, int) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox

Get the chain BoundingBox for the given cell index (cellIdx=0 would be original AU) and chain index

getChainByIndex(int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a chain by its index within the Structure .

getChainByIndex(int) - Method in class org.biojava.nbio.structure.StructureImpl

Retrieve a chain by its index within the Structure .

getChainByIndex(int, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a chain by its indices within the Structure and model.

getChainByIndex(int, int) - Method in class org.biojava.nbio.structure.StructureImpl

Retrieve a chain by its indices within the Structure and model.

getChainId() - Method in class org.biojava.nbio.structure.align.client.StructureName

Gets the chain ID, for structures where it is unique and well-defined.

getChainId() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier

getChainId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getChainId() - Method in interface org.biojava.nbio.structure.Group

Utility method for returning the chainId of the Group or null if no Chain has been set.

getChainId() - Method in class org.biojava.nbio.structure.HetatomImpl

Utility method for returning the chainId of the Group or null if no Chain has been set.

getChainId() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom

getChainId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

getChainId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

getChainId() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Returns the chain identifier (asym id) that this transformation should be applied to.

getChainId1() - Method in class org.biojava.nbio.structure.align.client.PdbPair

getChainID1() - Method in class org.biojava.nbio.structure.io.SSBondImpl

getChainID1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

getChainId2() - Method in class org.biojava.nbio.structure.align.client.PdbPair

getChainID2() - Method in class org.biojava.nbio.structure.io.SSBondImpl

getChainID2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

getChainIds() - Method in class org.biojava.nbio.structure.EntityInfo

Return the list of member chain ids (asym ids) that are described by this EntityInfo, only unique chain IDs are contained in the list.

getChainIds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

This method is provisional and should only be used for coloring Subunits.

getChainIds() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature

getChainIdsInEntry(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader

getChainIdToIndexMap() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

getChainLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getChainName() - Method in class org.biojava.nbio.structure.DBRef

The name of the corresponding chain.

getChainName() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom

getChainName() - Method in class org.biojava.nbio.structure.ResidueNumber

getChainName() - Method in class org.biojava.nbio.structure.ResidueRange

getChainRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getChains() - Method in class org.biojava.nbio.structure.cath.CathDomain

Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.

getChains() - Method in class org.biojava.nbio.structure.EntityInfo

Get the list of chains that are part of this EntityInfo.

getChains() - Method in class org.biojava.nbio.structure.Model

Get all chains: polymeric, non-polymeric and water

getChains() - Method in class org.biojava.nbio.structure.scop.ScopDomain

Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.

getChains() - Method in interface org.biojava.nbio.structure.Structure

Retrieve all chains for the first model.

getChains() - Method in class org.biojava.nbio.structure.StructureImpl

Retrieve all chains for the first model.

getChains(int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve all chains of a model.

getChains(int) - Method in class org.biojava.nbio.structure.StructureImpl

Retrieve all chains of a model.

getCharge() - Method in interface org.biojava.nbio.structure.Atom

Get the charge of this atom

getCharge() - Method in class org.biojava.nbio.structure.AtomImpl

getCharge() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getChemComp() - Method in interface org.biojava.nbio.structure.Group

Get the chemical component that closer describes this group.

getChemComp() - Method in class org.biojava.nbio.structure.HetatomImpl

getChemComp(String) - Method in class org.biojava.nbio.structure.chem.AllChemCompProvider

Returns a new instance of a chemical component definition.

getChemComp(String) - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory

getChemComp(String) - Method in interface org.biojava.nbio.structure.chem.ChemCompProvider

Returns a new instance of a chemical component definition.

getChemComp(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

getChemComp(String) - Method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

Loads the definitions for this ChemComp from a local file and instantiates a new object.

getChemComp(String) - Method in class org.biojava.nbio.structure.chem.ReducedChemCompProvider

getChemComp(String) - Method in class org.biojava.nbio.structure.chem.ZipChemCompProvider

(non-Javadoc)

getChemCompProvider() - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory

getChildren() - Method in class org.biojava.nbio.structure.scop.ScopNode

getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

Returns the radius of a circumscribed sphere, that goes through all vertices

getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

Returns the radius of a circumscribed sphere, that goes through all vertices

getCirumscribedRadius() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron

getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

Returns the radius of a circumscribed sphere, that goes through all vertices

getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism

Returns the radius of a circumscribed sphere (length of diagonal of rectangular prism/2, that goes through at least four vertices

getCirumscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

Returns the radius of a circumscribed sphere, that goes through all vertices

getClaFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

getClassId() - Method in class org.biojava.nbio.structure.cath.CathDomain

getClassId() - Method in class org.biojava.nbio.structure.scop.ScopDomain

getClassification() - Method in class org.biojava.nbio.structure.PDBHeader

getClassificationId() - Method in class org.biojava.nbio.structure.scop.ScopDescription

getClassificationId() - Method in class org.biojava.nbio.structure.scop.ScopDomain

getClassificationId(CathCategory) - Method in class org.biojava.nbio.structure.cath.CathDomain

getClassificationId(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopDescription

Return a portion of the classificationID corresponding to the specified category (class, fold, superfamily, family).

getClaURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror

getCluster() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

get the number of the cluster this alignment belongs to

getCluster() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

getCluster() - Method in class org.biojava.nbio.structure.contact.StructureInterface

getClustererMethod() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

getClustererMethod() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Method to cluster subunits.

getClusterIds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getClusters() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

Calculate the interface clusters for this StructureInterfaceList using a contact overlap score to measure the similarity of interfaces.

getClusters() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

getClusters(double) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

Calculate the interface clusters for this StructureInterfaceList using Jaccard contact set scores to measure the similarity of interfaces.

getClustersNcs() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

Get the interface clusters for this StructureInterfaceList grouped by NCS-equivalence.

getCol() - Method in class org.biojava.nbio.structure.align.helper.IndexPair

getCols() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

getCols() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

getColumnDimension() - Method in class org.biojava.nbio.structure.jama.Matrix

Get column dimension.

getColumnPackedCopy() - Method in class org.biojava.nbio.structure.jama.Matrix

Make a one-dimensional column packed copy of the internal array.

getComFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

getComment() - Method in class org.biojava.nbio.structure.cath.CathDomain

getComments(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

Get comments about a SCOP domain by its sunid

getComments(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

getCommonValence() - Method in enum org.biojava.nbio.structure.Element

Returns the common valence for this Element.

getCompId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getCompId() - Method in class org.biojava.nbio.structure.chem.ChemCompBond

getCompId() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

getComplexSignature() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature

getComplexStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature

getComponent(int) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Make a Stoichiometry object that corresponds to a single component.

getCompositionId() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature

getCompositionId(String) - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature

getComURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror

getConn() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getConnectedFrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder

getConnectedTo() - Method in class org.biojava.nbio.structure.secstruc.Ladder

getContact(Atom, Atom) - Method in class org.biojava.nbio.structure.contact.AtomContactSet

Returns the corresponding AtomContact or null if no contact exists between the 2 given atoms

getContact(Group, Group) - Method in class org.biojava.nbio.structure.contact.GroupContactSet

Returns the corresponding GroupContact or null if no contact exists between the 2 given groups

getContactOverlapScore(StructureInterface, boolean) - Method in class org.biojava.nbio.structure.contact.StructureInterface

Calculates the Jaccard contact set score (intersection over union) between this StructureInterface and the given one.

getContacts() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

getContacts() - Method in class org.biojava.nbio.structure.contact.Grid

Deprecated.
use Grid.getAtomContacts() instead

getContacts() - Method in class org.biojava.nbio.structure.contact.StructureInterface

getContacts() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

getContactsToOtherCell(GridCell) - Method in class org.biojava.nbio.structure.contact.GridCell

Calculates all distances of atoms between this cell and the given cell returning those that are within the given cutoff as a list of Contacts containing the indices of the pair and the calculated distance.

getContactsWithinCell() - Method in class org.biojava.nbio.structure.contact.GridCell

Calculates all distances of atoms within this cell returning those that are within the given cutoff as a list of Contacts containing the indices of the pair and the calculated distance.

getContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.AtomContactSet

Returns the list of contacts from this set that are within the given distance.

getContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.GroupContact

Returns the list of atom contacts in this GroupContact that are within the given distance.

getContainer() - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl

getContainer() - Method in interface org.biojava.nbio.structure.io.cif.CifFileConsumer

Retrieve the created container representing a CIF file.

getContainer() - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl

getContainer() - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl

getContig() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl

getConvergenceSteps() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

getCoordpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup

getCoords() - Method in interface org.biojava.nbio.structure.Atom

Get the coordinates.

getCoords() - Method in class org.biojava.nbio.structure.AtomImpl

Get the coordinates.

getCoordsAsPoint3d() - Method in interface org.biojava.nbio.structure.Atom

Get the coordinates.

getCoordsAsPoint3d() - Method in class org.biojava.nbio.structure.AtomImpl

Get the coordinates.

getCoreElectronCount() - Method in enum org.biojava.nbio.structure.Element

Returns the number of core electrons for this Element.

getCoreLength() - Method in interface org.biojava.nbio.structure.align.multiple.Block

Returns the number of aligned positions (columns) without gaps in the Block.

getCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

getCoreLength() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all Block core lengths.

getCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

getCoreLength() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all BlockSet core lengths.

getCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

getCorePositions(Block) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Calculate a List of alignment indicies that correspond to the core of a Block, which means that all structures have a residue in that positon.

getCoreResidues(double, double) - Method in class org.biojava.nbio.structure.contact.StructureInterface

Returns the residues belonging to the interface core, defined as those residues at the interface (BSA>0) and for which the BSA/ASA ratio is above the given bsaToAsaCutoff

getCovalentRadius() - Method in enum org.biojava.nbio.structure.Element

Returns the covalent radius of this Element.

getCoverage1() - Method in class org.biojava.nbio.structure.align.model.AFPChain

Get the coverage of protein 1 with the alignment

getCoverage2() - Method in class org.biojava.nbio.structure.align.model.AFPChain

Get the coverage of protein 2 with the alignment

getCoverages() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Returns the coverage of the alignment for each structure in the alignment as a fraction between 0.0 and 1.0.

getCoverages() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

getCovered() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

getCPPoint() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

getCreate_co() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getCrystalCell() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Return the crystal cell

getCrystalIds() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Returns a pair of identifiers for each of the 2 member molecules that identify them uniquely in the crystal: <molecule id (asym unit id)>+<operator id>+<crystal translation>

getCrystallographicInfo() - Method in class org.biojava.nbio.structure.PDBHeader

getCrystallographicInfo() - Method in interface org.biojava.nbio.structure.Structure

Get crystallographic information for this structure

getCrystallographicInfo() - Method in class org.biojava.nbio.structure.StructureImpl

Gets crystallographic information for this structure

getCrystalTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

getCurrent(String) - Static method in class org.biojava.nbio.structure.PDBStatus

Gets the current version of a PDB ID.

getCurrentChain() - Method in class org.biojava.nbio.structure.AtomIterator

Get the chain that contains the current atom.

getCurrentChain() - Method in class org.biojava.nbio.structure.GroupIterator

Get the current Chain.

getCurrentModel() - Method in class org.biojava.nbio.structure.AtomIterator

Get the model number of the model containing the current atom.

getCurrentModel() - Method in class org.biojava.nbio.structure.GroupIterator

Get the model number of the current model.

getCurrentPDBIds() - Static method in class org.biojava.nbio.structure.PDBStatus

Returns all current PDB IDs

getCut_sites() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites

getCutoff() - Method in class org.biojava.nbio.structure.contact.Grid

getD() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition

Return the block diagonal eigenvalue matrix

getData() - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper

getDatabase() - Method in class org.biojava.nbio.structure.DBRef

The database of the db-ref.

getDate() - Method in class org.biojava.nbio.structure.cath.CathDomain

getDbAccession() - Method in class org.biojava.nbio.structure.DBRef

Sequence database accession code.

getDbIdCode() - Method in class org.biojava.nbio.structure.DBRef

Sequence database identification code.

getDBRefs() - Method in interface org.biojava.nbio.structure.Structure

Get the list of database references

getDBRefs() - Method in class org.biojava.nbio.structure.StructureImpl

Get the list of database references

getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor

getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor

getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor

getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor

getDbSearchLegend() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor

getDBSearchParameters() - Static method in class org.biojava.nbio.structure.align.StrucAligParameters

getDbSearchResult(AFPChain) - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor

getDbSeqBegin() - Method in class org.biojava.nbio.structure.DBRef

Initial sequence number of the database seqment.

getDbSeqEnd() - Method in class org.biojava.nbio.structure.DBRef

Ending sequence position of the database segment.

getdCutoff() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters

The maximum allowed distance between the centroids of two equivalent Subunits, in A.

getDefaultParameters() - Static method in class org.biojava.nbio.structure.align.StrucAligParameters

getDelta() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup

getDensityCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getDepDate() - Method in class org.biojava.nbio.structure.PDBHeader

Return the deposition date of the structure in the PDB.

getDescription() - Method in class org.biojava.nbio.structure.cath.CathNode

getDescription() - Method in class org.biojava.nbio.structure.EntityInfo

getDescription() - Method in class org.biojava.nbio.structure.PDBHeader

Deprecated.
will be removed later. Use PDBHeader.getKeywords() if you use description to keep the keywords.

getDescription() - Method in class org.biojava.nbio.structure.scop.ScopDescription

getDescription() - Method in class org.biojava.nbio.structure.Site

gets the REMARK 800 description of the site

getDescription2() - Method in class org.biojava.nbio.structure.align.model.AFPChain

Get a textual description for the protein 2 of the alignment.

getDescriptionByCathId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase

Return CATH description for CATH domain ID.

getDescriptionByCathId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

getDescriptionByNodeId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase

Return CATH description for node representative by node ID.

getDescriptionByNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

getDescriptor() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

getDescriptors() - Method in class org.biojava.nbio.structure.chem.ChemComp

getDesFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

getDesURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror

getDetails() - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord

getDetails() - Method in class org.biojava.nbio.structure.EntityInfo

getDetails() - Method in interface org.biojava.nbio.structure.SeqMisMatch

getDetails() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

getDiagonalAtK(Atom[], int) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils

Get distances along diagonal k from coordinate array coords.

getDiagonalDistance() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getDiagonalDistance2() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getDimension() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getDimension() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getDimension() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getDimensions() - Method in class org.biojava.nbio.structure.contact.BoundingBox

Returns the dimensions of this bounding box.

getDir(String, boolean) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Gets the directory in which the file for a given MMCIF file would live, creating it if necessary.

getDirection() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

getDisCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

Get the distance cutoff used during AFP chain connectivity checks

getDisCut() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

getDisFilter() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getDisSmooth() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getDist() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

getDist1() - Method in class org.biojava.nbio.structure.align.ce.CECalculator

getDist1() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

getDist2() - Method in class org.biojava.nbio.structure.align.ce.CECalculator

getDist2() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

getDisTable1() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getDisTable2() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getDistance() - Method in class org.biojava.nbio.structure.contact.AtomContact

getDistance() - Method in class org.biojava.nbio.structure.contact.Contact

getDistance(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

calculate distance between two atoms.

getDistanceCutoff() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

getDistanceCutoff() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getDistanceFast(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Will calculate the square of distances between two atoms.

getDistanceIncrement() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

getDistanceMatrix() - Method in class org.biojava.nbio.structure.align.model.AFPChain

A matrix with ca1length rows and ca2length columns.

getDistanceMatrix() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Returns the List containing the interatomic distance Matrix of each structure.

getDistanceMatrix() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

getDistanceMatrix() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

The distance matrix this alignment is based on

getDistanceMatrix(Atom[]) - Method in class org.biojava.nbio.structure.domain.pdp.GetDistanceMatrix

A set of Calpha atoms that are representing the protein

getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils

Matrix of all distances between two sets of Atoms.

getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

GetDistanceMatrix - Class in org.biojava.nbio.structure.domain.pdp

GetDistanceMatrix() - Constructor for class org.biojava.nbio.structure.domain.pdp.GetDistanceMatrix

getDistMat() - Method in class org.biojava.nbio.structure.align.StructurePairAligner

return the difference of distance matrix between the two structures

getDkMatrix(Atom[], Atom[], int, double[], double[], int, int) - Method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

getDkMatrix(Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

getDNAOneLetter(String) - Static method in class org.biojava.nbio.structure.chem.ChemCompTools

getDNATwoLetter(Character) - Static method in class org.biojava.nbio.structure.chem.ChemCompTools

getDoi() - Method in class org.biojava.nbio.structure.JournalArticle

Get the value of DOI field.

getDomainByCathId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase

Return CATH domain for CATH domain ID.

getDomainByCathId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

getDomainByScopID(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)

getDomainByScopID(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

getDomainCounter() - Method in class org.biojava.nbio.structure.cath.CathDomain

getDomainDescriptionFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation

getDomainId() - Method in class org.biojava.nbio.structure.cath.CathDomain

getDomainId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getDomainId() - Method in class org.biojava.nbio.structure.scop.ScopDomain

getDomainListFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation

getDomainName() - Method in class org.biojava.nbio.structure.cath.CathDomain

getDomainNames(String) - Method in interface org.biojava.nbio.structure.domain.DomainProvider

Get a list of constituent domain identifiers

getDomains() - Method in class org.biojava.nbio.structure.domain.pdp.CutDomain

getDomains() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser

getDomainsById(String) - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase

Get a particular ECOD domain by the domain ID (e.g.

getDomainsById(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

Get a particular ECOD domain by the domain ID (e.g.

getDomainsByNodeId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase

Return all CATH domains for a particular CATH node.

getDomainsByNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

getDomainsForPdb(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase

Return all CATH domains for a PDB ID.

getDomainsForPdb(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

getDomainsForPdb(String) - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase

Get a list of all ECOD domains for a particular PDB ID

getDomainsForPdb(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

public EcodInstallation(String cacheLocation) { this( cacheLocation, DEFAULT_VERSION ); } /** Get a list of all ECOD domains for a particular PDB ID

getDomainsForPDB(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

Get a list of ScopDomains that have been assigned to a PDB ID

getDomainsForPDB(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

getDomallFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation

getDonor1() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

getDonor2() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

getDoublePivot() - Method in class org.biojava.nbio.structure.jama.LUDecomposition

Return pivot permutation vector as a one-dimensional double array

getDuplicationHint() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

getDuplicationHint() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

getDVar() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getEcNums() - Method in class org.biojava.nbio.structure.EntityInfo

getEcodDatabase() - Static method in class org.biojava.nbio.structure.ecod.EcodFactory

Returns the (singleton) database for the current default version

getEcodDatabase(String) - Static method in class org.biojava.nbio.structure.ecod.EcodFactory

getEditorList() - Method in class org.biojava.nbio.structure.JournalArticle

Get the list of editors of the JournalArticle

getElement() - Method in interface org.biojava.nbio.structure.Atom

Get element of the atom, e.g.

getElement() - Method in class org.biojava.nbio.structure.AtomImpl

Get element of the atom, e.g.

getElement1() - Method in class org.biojava.nbio.structure.quaternary.OrderedPair

getElement2() - Method in class org.biojava.nbio.structure.quaternary.OrderedPair

getElementaryAxes() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Return the operator for all elementary axes of symmetry of the structure, that is, the axes stored in the List as unique and from which all the symmetry axes are constructed.

getElementaryAxesObjects() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Return all elementary axes of symmetry of the structure, that is, the axes stored in the List as unique and from which all the symmetry axes are constructed.

getElementaryAxis(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

getElementFromHillIndex(int) - Static method in enum org.biojava.nbio.structure.Element

Returns the Element that corresponds to the specified Hill Order.

getElementType() - Method in enum org.biojava.nbio.structure.Element

Returns the Element Type for this Element.

getElipsisRadii() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

The effective value of this distance for a certain body is known as its radius of / gyration with respect to the given axis.

getEmptyChemComp() - Static method in class org.biojava.nbio.structure.chem.ChemComp

Creates a new instance of the dummy empty ChemComp.

getEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

getEnd() - Method in class org.biojava.nbio.structure.ResidueRange

getEnergy() - Method in class org.biojava.nbio.structure.secstruc.HBond

getEngineered() - Method in class org.biojava.nbio.structure.EntityInfo

getEnsemble() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Returns the parent Ensemble of the MultipleAlignment.

getEnsemble() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

getEntities() - Method in class org.biojava.nbio.structure.io.sifts.SiftsXMLParser

getEntityById(int) - Method in interface org.biojava.nbio.structure.Structure

Request a particular entity by its entity id (mol id in legacy PDB format)

getEntityById(int) - Method in class org.biojava.nbio.structure.StructureImpl

Request a particular entity by its entity id (mol id in legacy PDB format)

getEntityId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

getEntityInfo() - Method in interface org.biojava.nbio.structure.Chain

Returns the EntityInfo for this chain.

getEntityInfo() - Method in class org.biojava.nbio.structure.ChainImpl

getEntityInfos() - Method in interface org.biojava.nbio.structure.Structure

Get all the EntityInfo for this Structure.

getEntityInfos() - Method in class org.biojava.nbio.structure.StructureImpl

Get all the EntityInfo for this Structure.

getEntityType() - Method in interface org.biojava.nbio.structure.Chain

Returns the EntityType of this chain.

getEntityType() - Method in class org.biojava.nbio.structure.ChainImpl

getEntityType() - Method in enum org.biojava.nbio.structure.EntityType

Returns the type of the Entity as a String

getEnumValuesAsString(Class<T>) - Static method in class org.biojava.nbio.structure.align.util.CliTools

Constructs a comma-separated list of values for an enum.

getEqr() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

returns the number of euqivalent residues in this alignment

getEvalCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getEvCode() - Method in class org.biojava.nbio.structure.Site

gets the REMARK 800 EVIDENCE CODE for the site.

getExampleUnitCell() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice

getExperimentalTechniques() - Method in class org.biojava.nbio.structure.PDBHeader

Return the Set of ExperimentalTechniques, usually the set is of size 1 except for hybrid experimental techniques when the Set will contain 2 or more values

getExpressionSystem() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemAtccNumber() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemCell() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemCellLine() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemCellularLocation() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemGene() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemOrgan() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemOrganelle() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemOtherDetails() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemPlasmid() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemStrain() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemTaxId() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemTissue() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemVariant() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemVector() - Method in class org.biojava.nbio.structure.EntityInfo

getExpressionSystemVectorType() - Method in class org.biojava.nbio.structure.EntityInfo

getExtensions() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

getExtensions() - Method in enum org.biojava.nbio.structure.io.StructureFiletype

getExtensions() - Method in interface org.biojava.nbio.structure.io.StructureIOFile

Returns a list of extensions supported by this class

getFailedLines() - Method in class org.biojava.nbio.structure.scop.Astral

Gets a map describing lines read in the file that weren't understood.

getFamilyId() - Method in class org.biojava.nbio.structure.scop.ScopDomain

getFatCatAligner() - Method in class org.biojava.nbio.structure.align.fatcat.FatCat

getFetchBehavior() - Method in class org.biojava.nbio.structure.align.util.AtomCache

Get the behavior for fetching files from the server

getFetchBehavior() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

getFetchBehavior() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Get the behavior for fetching files from the server

getFGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getFGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getFile1() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

getFile2() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

getFileFormat() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

getFilename(String) - Method in class org.biojava.nbio.structure.io.BcifFileReader

getFilename(String) - Method in class org.biojava.nbio.structure.io.CifFileReader

getFilename(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Converts a PDB ID into a filename with the proper extension

getFilename(String) - Method in class org.biojava.nbio.structure.io.MMTFFileReader

getFilename(String) - Method in class org.biojava.nbio.structure.io.PDBFileReader

getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

getFileParsingParameters() - Method in class org.biojava.nbio.structure.io.PDBFileParser

getFileParsingParameters() - Method in interface org.biojava.nbio.structure.io.StructureProvider

Get the parameters that should be used for file parsing

getFileParsingParams() - Method in class org.biojava.nbio.structure.align.util.AtomCache

getFiletype() - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the currently active file type that will be parsed.

getFinalIndex(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block

Calculates and returns the last position of the specified structure in the alignment that is not null.

getFinalIndex(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

getFinalResidue(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block

Calculates and returns the last residue of the specified structure in the alignment that is not null.

getFinalResidue(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

getFirst() - Method in class org.biojava.nbio.structure.AtomPositionMap

getFirst() - Method in class org.biojava.nbio.structure.contact.Pair

getFirst(String) - Method in class org.biojava.nbio.structure.AtomPositionMap

getFirstAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface

getFirstGroupAsa(ResidueNumber) - Method in class org.biojava.nbio.structure.contact.StructureInterface

Gets the GroupAsa for the corresponding residue number of first chain

getFirstGroupAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Gets a map of ResidueNumbers to GroupAsas for all groups of first chain.

getFirstRepeat() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

Get the index of the first repeat used by this axis

getFirstRepeats(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Get the first repeat index of each axis of a specified level.

getFocusAfpList() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getFocusAfpn() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getFocusRes1() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getFocusRes2() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getFocusResn() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getFold() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

getFold() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

getFoldId() - Method in class org.biojava.nbio.structure.scop.ScopDomain

getFolds() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getFoldType() - Method in enum org.biojava.nbio.structure.xtal.TransformType

getFormat() - Method in class org.biojava.nbio.structure.cath.CathDomain

getFormula() - Method in class org.biojava.nbio.structure.chem.ChemComp

getFormulaWeight() - Method in class org.biojava.nbio.structure.chem.ChemComp

getFragCompat() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getFragLen() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getFragLen() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

getFragLen() - Method in class org.biojava.nbio.structure.align.model.AFP

getFragLenSq() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getFragment() - Method in class org.biojava.nbio.structure.EntityInfo

getFragment(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils

Get a continue subset of Atoms based by the starting position and the length

getFragmentFromIdxList(Atom[], int[]) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils

Get a subset of Atoms based by their positions

getFragmentId() - Method in class org.biojava.nbio.structure.cath.CathFragment

getFragmentLength() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getFragmentMiniDistance() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getFragmentNoClone(Atom[], int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils

Get a continue subset of Atoms based by the starting position and the length does not clone the original atoms.

getFragmentPairs() - Method in class org.biojava.nbio.structure.align.StructurePairAligner

get the results of step 1 - the FragmentPairs used for seeding the alignment

getFragmentsByPdbId(String) - Method in interface org.biojava.nbio.structure.cath.CathDatabase

getFragmentsByPdbId(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

getFragScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getFrom() - Method in class org.biojava.nbio.structure.domain.pdp.Segment

getFrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder

getFullAtomSequence(List<Group>, Map<Integer, Integer>, boolean) - Static method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner

Returns the full sequence of the Atom records of a parent with X instead of HETATMSs.

getFullMatrix() - Method in class org.biojava.nbio.structure.align.util.RotationAxis

Returns a matrix that describes both rotation and translation.

getGamma() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

getGamma() - Method in class org.biojava.nbio.structure.xtal.CrystalCell

getGapCreate() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getGapExtCol() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

getGapExtCol() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

getGapExtend() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getGapExtend() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

getGapExtend() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

getGapExtension() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

getGapExtension() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

getGapExtension() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

getGapExtension() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getGapExtRow() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

getGapExtRow() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

getGapLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getGapOpen() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

getGapOpen() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

getGapOpen() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

getGapOpen() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

getGapOpen() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

getGapOpen() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getGapOpenCol() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

getGapOpenCol() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

getGapOpenRow() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

getGapOpenRow() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

getGaps() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

return the number of gaps in this alignment

getGene() - Method in class org.biojava.nbio.structure.EntityInfo

getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

Returns a transformation matrix transform polyhedra for Cn structures.

getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getGeometicCenterTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

Returns a transformation matrix transform polyhedra for Cn structures.

getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

Returns the geometric center of polyhedron.

getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getGeometricCenter() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

Returns the geometric center of polyhedron.

getGroup() - Method in class org.biojava.nbio.structure.asa.GroupAsa

getGroup() - Method in interface org.biojava.nbio.structure.Atom

Return the parent Group of the Atom.

getGroup() - Method in class org.biojava.nbio.structure.AtomImpl

Return the parent Group of the Atom.

getGroup() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo

getGroupAsas() - Method in class org.biojava.nbio.structure.asa.AsaCalculator

Calculates ASA for all atoms and return them as a GroupAsa array (one element per residue in structure) containing ASAs per residue and per atom.

getGroupByPDB(ResidueNumber) - Method in interface org.biojava.nbio.structure.Chain

Get a group by its PDB residue numbering.

getGroupByPDB(ResidueNumber) - Method in class org.biojava.nbio.structure.ChainImpl

getGroupByPDBResidueNumber(Structure, ResidueNumber) - Static method in class org.biojava.nbio.structure.StructureTools

Get a group represented by a ResidueNumber.

getGroupContacts() - Method in class org.biojava.nbio.structure.contact.StructureInterface

getGroupDistancesWithinShell(Structure, Atom, Set<ResidueNumber>, double, boolean, boolean) - Static method in class org.biojava.nbio.structure.StructureTools

Finds Groups in structure that contain at least one Atom that is within radius Angstroms of centroid.

getGroupFromChemCompDictionary(String) - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory

getGroups() - Method in class org.biojava.nbio.structure.Site

getGroups(Atom[]) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Returns the List of Groups of the corresponding representative Atom array.

getGroupsByPDB(ResidueNumber, ResidueNumber) - Method in interface org.biojava.nbio.structure.Chain

Get all groups that are located between two PDB residue numbers.

getGroupsByPDB(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.ChainImpl

getGroupsByPDB(ResidueNumber, ResidueNumber, boolean) - Method in interface org.biojava.nbio.structure.Chain

Get all groups that are located between two PDB residue numbers.

getGroupsByPDB(ResidueNumber, ResidueNumber, boolean) - Method in class org.biojava.nbio.structure.ChainImpl

getGroupsWithinShell(Structure, Atom, Set<ResidueNumber>, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools

getGroupsWithinShell(Structure, Group, double, boolean) - Static method in class org.biojava.nbio.structure.StructureTools

Returns a Set of Groups in a structure within the distance specified of a given group.

getGroupTable() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup

getH() - Method in class org.biojava.nbio.structure.jama.QRDecomposition

Return the Householder vectors

getHeaderVars() - Method in class org.biojava.nbio.structure.EntityInfo

getHeight() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

getHeight() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism

Returns the radius of a sphere, that is tangent to each of the octahedron's edges

getHelix(int) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

getHelixLayers() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getHelixLayers() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

getHelixRmsdThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

getHelixRmsdToRiseRatio() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

getHGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getHGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getHieFilename() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

getHieURL(String) - Method in class org.biojava.nbio.structure.scop.ScopMirror

getHigherOrderRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

getHillOrder() - Method in enum org.biojava.nbio.structure.Element

Returns the Hill Order of this Element.

getHomologyId() - Method in class org.biojava.nbio.structure.cath.CathDomain

getHSDMTree(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Calculate a phylogenetic tree of the MultipleAlignment using dissimilarity scores (DS), based in SDM Substitution Matrix (ideal for distantly related proteins, structure-derived) and the Neighbor Joining algorithm from forester.

getI() - Method in class org.biojava.nbio.structure.contact.Contact

getIAtoms() - Method in class org.biojava.nbio.structure.contact.Grid

getIclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

getiCode1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

getiCode2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

getId() - Method in class org.biojava.nbio.structure.align.model.AFP

getId() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getId() - Method in interface org.biojava.nbio.structure.Chain

Get the 'private' asymId (internal chain IDs in mmCif) for this chain.

getId() - Method in class org.biojava.nbio.structure.ChainImpl

getId() - Method in class org.biojava.nbio.structure.chem.ChemComp

getId() - Method in class org.biojava.nbio.structure.contact.StructureInterface

getId() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

getId() - Method in class org.biojava.nbio.structure.DBRef

Get the ID used by Hibernate.

getId() - Method in class org.biojava.nbio.structure.domain.pdp.Domain

getId() - Method in class org.biojava.nbio.structure.EntityInfo

get the ID used by Hibernate

getId() - Method in class org.biojava.nbio.structure.HetatomImpl

the Hibernate database ID

getId() - Method in class org.biojava.nbio.structure.PDBHeader

Get the ID used by Hibernate.

getId() - Method in class org.biojava.nbio.structure.PdbId

Get a String representation of this PdbId instance.
By default this function will try to get the PdbId in the short (4 letters) format.

getId() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

The identifier for this Biological Assembly, from 1 to n

getId() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Returns the identifier for this biological assembly transformation.

getId() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet

getId() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement

Returns the ID of this element.

getId() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice

getId() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

Gets the standard numeric identifier for the space group.

getId() - Method in enum org.biojava.nbio.structure.xtal.TransformType

getId(boolean) - Method in class org.biojava.nbio.structure.PdbId

Get a String representation of this PdbId instance, using the passed in behavior.

getIdbnsBegin() - Method in class org.biojava.nbio.structure.DBRef

Insertion code of initial residue of the segment, if PDB is the reference.

getIdbnsEnd() - Method in class org.biojava.nbio.structure.DBRef

Insertion code of the ending residue of the segment, if PDB is the reference.

getIdCode() - Method in class org.biojava.nbio.structure.DBRef

get the idCode for this entry

getIdCode() - Method in class org.biojava.nbio.structure.PDBHeader

Deprecated.
use PDBHeader.getPdbId()

getIdenticalSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain

getIdentifier() - Method in class org.biojava.nbio.structure.align.client.StructureName

Get the original form of the identifier

getIdentifier() - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier

getIdentifier() - Method in class org.biojava.nbio.structure.cath.CathDomain

getIdentifier() - Method in class org.biojava.nbio.structure.cluster.Subunit

The standard identifier of the Subunit.

getIdentifier() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getIdentifier() - Method in class org.biojava.nbio.structure.PassthroughIdentifier

getIdentifier() - Method in class org.biojava.nbio.structure.scop.ScopDomain

getIdentifier() - Method in interface org.biojava.nbio.structure.Structure

Get a string representing this structure's contents.

getIdentifier() - Method in interface org.biojava.nbio.structure.StructureIdentifier

Get the String form of this identifier.

getIdentifier() - Method in class org.biojava.nbio.structure.StructureImpl

Get a string representing this structure's contents.

getIdentifier() - Method in class org.biojava.nbio.structure.SubstructureIdentifier

Get the String form of this identifier.

getIdentifier() - Method in class org.biojava.nbio.structure.URLIdentifier

getIdentity() - Method in class org.biojava.nbio.structure.align.model.AFPChain

The percent of residues that are sequence-identical in the alignment.

getIdx1() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

the positions of the structure equivalent positions in atom set 1

getIdx2() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

the positions of the structure equivalent atoms in atom set 2

getIdxlist() - Method in class org.biojava.nbio.structure.align.helper.JointFragments

getImagEigenvalues() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition

Return the imaginary parts of the eigenvalues

getIndex() - Method in class org.biojava.nbio.structure.align.helper.GapArray

getIndex() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement

Returns the index of the SSE for its type.

getIndexPair() - Method in class org.biojava.nbio.structure.contact.Contact

getIndicesContacts() - Method in class org.biojava.nbio.structure.contact.Grid

Returns all contacts, i.e.

getInertiaTensor() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

getInitialK() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getInitials() - Method in class org.biojava.nbio.structure.Author

getInputStream(URL) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools

Connect to a URL and return result as an InputStream.

getInputStream(URL, boolean, int) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools

Open a URL and return an InputStream to it if acceptGzipEncoding == true, use GZIPEncoding to compress communication.

getInputStream(URL, int) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools

Connect to server and return result as an InputStream.

getInputStream(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Load or download the specified structure and return it as an InputStream for direct parsing.

getInsCode() - Method in class org.biojava.nbio.structure.ResidueNumber

getInsCode() - Method in interface org.biojava.nbio.structure.SeqMisMatch

getInsCode() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

getInsCode1() - Method in class org.biojava.nbio.structure.io.SSBondImpl

getInsCode2() - Method in class org.biojava.nbio.structure.io.SSBondImpl

getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

Returns the radius of an inscribed sphere, that is tangent to each of the icosahedron's faces

getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

Returns the radius of an inscribed sphere, that is tangent to each of the octahedron's faces

getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

Returns the radius of an inscribed sphere, that is tangent to each of the icosahedron's faces

getInscribedRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

Returns the radius of an inscribed sphere, that is tangent to each of the tetrahedrons's faces

getInsertBegin() - Method in class org.biojava.nbio.structure.DBRef

Initial insertion code of the PDB sequence segment.

getInsertEnd() - Method in class org.biojava.nbio.structure.DBRef

Ending insertion code of the PDB sequence segment.

getInstalledDomainDescription() - Method in class org.biojava.nbio.structure.cath.CathInstallation

getInstalledDomainList() - Method in class org.biojava.nbio.structure.cath.CathInstallation

getInstalledDomall() - Method in class org.biojava.nbio.structure.cath.CathInstallation

getInstalledNodeList() - Method in class org.biojava.nbio.structure.cath.CathInstallation

getInstance(QuatSymmetryResults) - Static method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

Returns an instance of AxisAligner for differnt type of QuatSymmetryResults (factory method)

getInteractingRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit

getInterfacingResidues(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface

Returns the residues belonging to the interface, i.e.

getInternal(Structure, List<AbstractCifFileSupplier.WrappedAtom>) - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier

getIntersection(DistanceBox<T>) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox

getIoTime() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getIoTime() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Returns the io time for this object, in milliseconds.

getIoTime() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

getIoTime() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

getJ() - Method in class org.biojava.nbio.structure.contact.Contact

getJAtoms() - Method in class org.biojava.nbio.structure.contact.Grid

getJclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

getJmolScript(Atom[]) - Method in class org.biojava.nbio.structure.align.util.RotationAxis

Returns a Jmol script which will display the axis of rotation.

getJmolScript(Atom[], int) - Method in class org.biojava.nbio.structure.align.util.RotationAxis

Returns a Jmol script which will display the axis of rotation.

getJoinRMSCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getJournalArticle() - Method in class org.biojava.nbio.structure.PDBHeader

Get the associated publication as defined by the JRNL records in a PDB file.

getJournalArticle() - Method in interface org.biojava.nbio.structure.Structure

Get the associated publication as defined by the JRNL records in a PDB file.

getJournalArticle() - Method in class org.biojava.nbio.structure.StructureImpl

get the associated publication as defined by the JRNL records in a PDB file.

getJournalName() - Method in class org.biojava.nbio.structure.JournalArticle

getKappa() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

getKeywords() - Method in class org.biojava.nbio.structure.PDBHeader

Gets the keywords (KEYWODS) record of the structure

getKimuraTree(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Calculate a phylogenetic tree of the MultipleAlignment using Kimura distances and the Neighbor Joining algorithm from forester.

getL() - Method in class org.biojava.nbio.structure.jama.CholeskyDecomposition

Return triangular factor.

getL() - Method in class org.biojava.nbio.structure.jama.LUDecomposition

Return lower triangular factor

getLargestSubunit() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getLast() - Method in class org.biojava.nbio.structure.AtomPositionMap

getLast(String) - Method in class org.biojava.nbio.structure.AtomPositionMap

getLayerLines() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

getLcmp() - Method in class org.biojava.nbio.structure.align.ce.CECalculator

getLcmp() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

getLength() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

getLength() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the total number of base pairs that were found, used after the call to analyze().

getLength() - Method in interface org.biojava.nbio.structure.Bond

Gets the distance between the two atoms of this bond.

getLength() - Method in class org.biojava.nbio.structure.BondImpl

Gets the distance between the two atoms of this bond.

getLength() - Method in class org.biojava.nbio.structure.cath.CathDomain

getLength() - Method in class org.biojava.nbio.structure.cath.CathFragment

getLength() - Method in class org.biojava.nbio.structure.cath.CathSegment

getLength() - Method in class org.biojava.nbio.structure.ResidueRangeAndLength

getLength() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement

Return the length (number of residues) in the SSE.

getLength() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism

Returns the radius of a circumscribed sphere, that goes through all vertices

getLength(int, int, String) - Method in class org.biojava.nbio.structure.AtomPositionMap

Calculates the number of residues of the specified chain in a given range, inclusive.

getLength(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap

Calculates the number of atoms between two ResidueNumbers, inclusive.

getLength1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

getLength2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

getLengthDirectional(int, int, String) - Method in class org.biojava.nbio.structure.AtomPositionMap

Calculates the number of residues of the specified chain in a given range.

getLengthDirectional(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap

Calculates the number of atoms between two ResidueNumbers, inclusive.

getLevel() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

getLfrom() - Method in class org.biojava.nbio.structure.secstruc.Ladder

getLigands() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getLigandsByProximity(Collection<Group>, Atom[], double) - Static method in class org.biojava.nbio.structure.StructureTools

Finds all ligand groups from the target which fall within the cutoff distance of some atom from the query set.

getLikeSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain

getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

getLineLoops() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron

getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism

getLineLoops() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

getList() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

getLocalFile(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Searches for previously downloaded files

getLocalFile(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Searches for previously downloaded files

getLocalFileName(String) - Static method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

Returns the file name that contains the definition for this ChemComp

getLocalTimeLimit() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

getLocalTimeStart() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

getLogger() - Static method in class org.biojava.nbio.structure.chem.ChemCompBond

getLowerBound() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getLowerLimit() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

getLto() - Method in class org.biojava.nbio.structure.secstruc.Ladder

getM() - Method in class org.biojava.nbio.structure.align.model.AFP

getMacromolecularSize() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

Returns the macromolecular size of this biological assembly, i.e.

getManual() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getMapProperty() - Method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot

getMatchingAtomRes(Chain, List<Chain>, boolean) - Static method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner

getMatMatrix() - Method in class org.biojava.nbio.structure.align.ce.CECalculator

Caution: this matrix is overwriten with very different data at several points in the alignment algorithm.

getMatMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

Caution: this matrix is overwriten with very different data at several points in the alignment algorithm.

getMatrix(int[], int[]) - Method in class org.biojava.nbio.structure.jama.Matrix

Get a submatrix.

getMatrix(int[], int, int) - Method in class org.biojava.nbio.structure.jama.Matrix

Get a submatrix.

getMatrix(int, int, int[]) - Method in class org.biojava.nbio.structure.jama.Matrix

Get a submatrix.

getMatrix(int, int, int, int) - Method in class org.biojava.nbio.structure.jama.Matrix

Get a submatrix.

getMatrixFromAlgebraic(String) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup

getMatTransform() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

getMaxAtoms() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

The maximum numbers of atoms to load in a protein structure (prevents memory overflows)

getMaxDimension() - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Gets the maximum dimension of the unit cell.

getMaxGap() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getMaxGapFrag() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getMaxGapSize() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

the Max gap size parameter G .

getMaxGapSize() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

CE specific parameter: set the Max gap size parameter G (during AFP extension).

getMaximumCovalentValence() - Method in enum org.biojava.nbio.structure.Element

Returns the maximum valence for this Element.

getMaximumExtend(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools

Returns the maximum extend of the structure in the x, y, or z direction.

getMaximumLocalCombinations() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

getMaximumValence() - Method in enum org.biojava.nbio.structure.Element

Returns the maximum valence for this Element.

getMaxIter() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getMaxNrIterationsForOptimization() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Get the maximum nr of times the (slow) optimiziation of alignment should iterate.

getMaxOptRMSD() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Returns the maximum RMSD cutoff to be applied during alignment optimization (default: 99 = unlimited)

getMaxOptRMSD() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

(jCE specific): maximum RMSD that shall be calculated for the alignment.

getMaxOrientationAngle() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters

The maximum orientation angle between two equivalent Subunits, in radians.

getMaxPenalty() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getMaxPropeller() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method returns the maximum propeller twist between bases used as criteria for the characterization of two bases as being paired.

getMaxPropeller() - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

This method returns the maximum propeller twist between bases used as criteria for the characterization of two bases as being paired.

getMaxrefine() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getMaxRmsd() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters

The maximum allowed RMSD of the alignment, in A.

getMaxRmsd() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

getMaxRmsd() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

getMaxRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

getMaxShear() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method returns the maximum shear between bases used as criteria for the characterization of two bases as being paired.

getMaxStagger() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method returns the maximum stagger between bases used as criteria for the characterization of two bases as being paired.

getMaxStagger() - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

This method returns the maximum stagger between bases used as criteria for the characterization of two bases as being paired.

getMaxStretch() - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method returns the maximum stretch between bases used as criteria for the characterization of two bases as being paired.

getMaxSymmOrder() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getMaxTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

getMaxTra() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

get the maximum number of Twists that are allowed...

getMaxTra() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

getMaxTra() - Method in class org.biojava.nbio.structure.align.model.AFPChain

get the maximum nr of Twists that are allowed...

getMCScore(MultipleAlignment, double, double, double) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

Calculates the MC score, specific for the MultipleAlignment algorithm.

getMembers() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

getMetalBondDefinitions() - Static method in class org.biojava.nbio.structure.io.cif.MetalBondConverter

getMethod() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage

getMethod() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

getMidRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

Returns the radius of a sphere, that is tangent to each of the icosahedron's edges

getMidRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

Returns the radius of a sphere, that is tangent to each of the octahedron's edges

getMidRadius() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

Returns the radius of a sphere, that is tangent to each of the tetrahedron's edges

getMinAlignedStructures() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

getMinBlockLen() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

getMinCoreLength() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getMinCPLength() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

getMinCPLength() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

getMinDistance() - Method in class org.biojava.nbio.structure.contact.GroupContact

getMinimumHelixAngle() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

getMinimumHelixRise() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

getMinimumSequenceLength() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Get the minimum number of residues of a subunits to be considered in the clusters.

getMinimumSequenceLengthFraction() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.

getMinimumValence() - Method in enum org.biojava.nbio.structure.Element

Returns the minimum valence for this Element.

getMinLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getMinLen() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

getMinLen() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

getMinMax(double[]) - Method in class org.biojava.nbio.structure.contact.BoundingBox

Returns an array of size 2 with min and max values of given double array

getMinRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

getMinTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

getMirrors() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

getMisCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getMisLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getMisScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getModDate() - Method in class org.biojava.nbio.structure.PDBHeader

Return the latest modification date of the structure.

getModel() - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom

getModel(int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve all Chains belonging to a model .

getModel(int) - Method in class org.biojava.nbio.structure.StructureImpl

Retrieve all Chains belonging to a model .

getModelCartnX() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getModelCartnY() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getModelCartnZ() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getModelNumbers() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

This method is provisional and should only be used for coloring Subunits.

getMoleculeIds() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Return the pair of identifiers identifying each of the 2 molecules of this interface in the asymmetry unit (usually the chain identifier if this interface is between 2 chains)

getMolecules() - Method in class org.biojava.nbio.structure.contact.StructureInterface

getMolId() - Method in class org.biojava.nbio.structure.EntityInfo

Return the molecule identifier, called entity_id in mmCIF dictionary.

getMomentsOfInertia() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getMonNstdFlag() - Method in class org.biojava.nbio.structure.chem.ChemComp

getMonNstdParentCompId() - Method in class org.biojava.nbio.structure.chem.ChemComp

getMTranspose() - Method in class org.biojava.nbio.structure.xtal.CrystalCell

getMultipleAlignment() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Returns the parent MultipleAlignment of the BlockSet.

getMultipleAlignment() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

getMultipleAlignment() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

The multiple alignment is calculated from the equivalent residues in the SubunitCluster.

getMultipleAlignment() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

getMultipleAlignment(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Returns the MultipleAlignments at the specified index in the ensemble.

getMultipleAlignment(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

getMultipleAlignments() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Returns the List of MultipleAlignments in the ensemble.

getMultipleAlignments() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

getMultiplicity() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

getMutation() - Method in class org.biojava.nbio.structure.EntityInfo

getN() - Method in interface org.biojava.nbio.structure.AminoAcid

Get N atom.

getN() - Method in class org.biojava.nbio.structure.AminoAcidImpl

Get N atom.

getName() - Method in interface org.biojava.nbio.structure.Atom

Get atom name, e.g.

getName() - Method in class org.biojava.nbio.structure.AtomImpl

Get atom name, e.g.

getName() - Method in class org.biojava.nbio.structure.cath.CathDomain

getName() - Method in interface org.biojava.nbio.structure.Chain

Get the 'public' authId (chain ID in PDB file)

getName() - Method in class org.biojava.nbio.structure.ChainImpl

getName() - Method in class org.biojava.nbio.structure.chem.ChemComp

getName() - Method in class org.biojava.nbio.structure.cluster.Subunit

The Name of a Subunit is a free-text field, user defined.

getName() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique

getName() - Method in class org.biojava.nbio.structure.scop.ScopDescription

getName() - Method in interface org.biojava.nbio.structure.Structure

Get biological name of Structure.

getName() - Method in class org.biojava.nbio.structure.StructureImpl

Get biological name of Structure.

getName() - Method in enum org.biojava.nbio.structure.xtal.BravaisLattice

getName1() - Method in class org.biojava.nbio.structure.align.client.PdbPair

getName1() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getName1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

getName2() - Method in class org.biojava.nbio.structure.align.client.PdbPair

getName2() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getName2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

getNames() - Method in class org.biojava.nbio.structure.scop.Astral

getnAtom() - Method in class org.biojava.nbio.structure.align.ce.CECalculator

getnAtom() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

getNaturalPos() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

getNavMap() - Method in class org.biojava.nbio.structure.AtomPositionMap

getNclose() - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

getNcsAsArray(Matrix4d[]) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get a list of length N*16 of a list of Matrix4d*N.

getNcsAsMatrix4d(double[][]) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get a list of N 4*4 matrices from a single list of doubles of length 16*N.

getNcsOperators() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Get the NCS operators.

getNcuts() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites

getNeighbors(Point3d) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox

getNeighborsWithCache(Point3d) - Method in class org.biojava.nbio.structure.symmetry.geometry.DistanceBox

getNext() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator

getNodeId() - Method in class org.biojava.nbio.structure.cath.CathNode

getNodeListFileName() - Method in class org.biojava.nbio.structure.cath.CathInstallation

getNonenantpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup

getNonPolyChain(String) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the first model

getNonPolyChain(String) - Method in class org.biojava.nbio.structure.StructureImpl

getNonPolyChain(String, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a non-polymeric Chain based on the 'internal' chain id (asymId) for the given model index

getNonPolyChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl

getNonPolyChains() - Method in class org.biojava.nbio.structure.Model

getNonPolyChains() - Method in interface org.biojava.nbio.structure.Structure

Return all non-polymeric chains for the first model

getNonPolyChains() - Method in class org.biojava.nbio.structure.StructureImpl

getNonPolyChains(int) - Method in interface org.biojava.nbio.structure.Structure

Return all non-polymeric chains for the given model index.

getNonPolyChains(int) - Method in class org.biojava.nbio.structure.StructureImpl

getNonPolyChainsByPDB(String) - Method in interface org.biojava.nbio.structure.Structure

Retrieve all non-polymeric Chains corresponding to the given 'public' chain name (authId) for the first model.

getNonPolyChainsByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl

getNonPolyChainsByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve all non-polymeric Chains corresponding to the 'public' chain name (authId) and the given model index.

getNonPolyChainsByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl

getNormAlignScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getNotObserved() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

getNrAtoms(Structure) - Static method in class org.biojava.nbio.structure.StructureTools

Count how many Atoms are contained within a Structure object.

getNrBioAssemblies() - Method in class org.biojava.nbio.structure.PDBHeader

Get the number of biological assemblies available in the PDB header

getNrCPU() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

getNrEQR() - Method in class org.biojava.nbio.structure.align.model.AFPChain

Get the number of structurally equivalent residues

getNrGroups(Structure) - Static method in class org.biojava.nbio.structure.StructureTools

Count how many groups are contained within a structure object.

getNrThreads() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

getNseg() - Method in class org.biojava.nbio.structure.domain.pdp.Domain

getnStart() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

getNStart() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

Returns the number of starts if this rotation represents a helical rotation

getNucleicChains(boolean) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method reports all the nucleic acid chains and has an option to remove duplicates if you are considering an analysis of only unique DNA or RNA helices in the Structure.

getNumAtomContacts() - Method in class org.biojava.nbio.structure.contact.GroupContact

getNumBonds() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

getNumBondsInGroup(List<Atom>) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Find the number of bonds in a group

getNumericalBondOrder() - Method in class org.biojava.nbio.structure.chem.ChemCompBond

Converts this ChemCompBond's value_order attribute into an int using the conversion:

getNumGroups(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Count the total number of groups in the structure

getNumIindices() - Method in class org.biojava.nbio.structure.contact.GridCell

getNumJindices() - Method in class org.biojava.nbio.structure.contact.GridCell

getNumLeft() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator

getNumLevels() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

getNumOperators() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

Gets the number of symmetry operators corresponding to this SpaceGroup (counting the identity operator)

getNumRepeats() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

Return the symmetry order determined by the order detector if the symmetry is significant.

getNumRepeats() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Get the number of repeats.

getNumRes() - Method in class org.biojava.nbio.structure.EntityInfo

getO() - Method in interface org.biojava.nbio.structure.AminoAcid

Get O atom.

getO() - Method in class org.biojava.nbio.structure.AminoAcidImpl

Get O atom.

getO3Prime() - Method in class org.biojava.nbio.structure.NucleotideImpl

Returns the O3' atom if present, otherwise null

getO5Prime() - Method in class org.biojava.nbio.structure.NucleotideImpl

Returns the O5' atom if present, otherwise null

getObsoleteBehavior() - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns how this instance deals with obsolete entries.

getObsoleteBehavior() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

getObsoleteBehavior() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Returns how this instance deals with obsolete entries.

getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.BcifFileReader

getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.CifFileReader

getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Location of obsolete files within the directory, as an array of paths.

getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.MMTFFileReader

getObsoleteDirPath() - Method in class org.biojava.nbio.structure.io.PDBFileReader

getOccupancy() - Method in interface org.biojava.nbio.structure.Atom

Get occupancy.

getOccupancy() - Method in class org.biojava.nbio.structure.AtomImpl

getOmega() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

getOneLetterCode() - Method in class org.biojava.nbio.structure.chem.ChemComp

getOneLetterCode(ChemComp) - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory

getOneLetterCode(ChemComp, ChemicalComponentDictionary) - Static method in class org.biojava.nbio.structure.chem.ChemCompTools

getOpening(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the opening in degrees for the given base pair

getOperator() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

Get the transformation operator for this axis as an homogeneous matrix

getOptAln() - Method in class org.biojava.nbio.structure.align.model.AFPChain

Tracks the Atom positions in the optimal alignment.

getOptAlnAsList(AFPChain) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Retrieves the optimum alignment from an AFPChain and returns it as a java collection.

getOptimization() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getOptimizationSteps() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getOptLen() - Method in class org.biojava.nbio.structure.align.model.AFPChain

The length of each block

getOptLength() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getOptRmsd() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getOrbits() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getOrbits() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getOrbits() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getOrder() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup

getOrder() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

getOrder() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

Get the order of this axis (closed symm) or the number of repeats (open symm)

getOrder(List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup

getOrderDetectorMethod() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getOrderedPairs() - Method in class org.biojava.nbio.structure.quaternary.CartesianProduct

Generates the list of ordered pair between two sets.

getOrgan() - Method in class org.biojava.nbio.structure.EntityInfo

getOrganelle() - Method in class org.biojava.nbio.structure.EntityInfo

getOrganismCommon() - Method in class org.biojava.nbio.structure.EntityInfo

getOrganismScientific() - Method in class org.biojava.nbio.structure.EntityInfo

getOrganismTaxId() - Method in class org.biojava.nbio.structure.EntityInfo

getOrientationMatrix() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

The orientation Matrix is a 3x3 Matrix with a column for each principal axis.

getOrigGroup() - Method in interface org.biojava.nbio.structure.SeqMisMatch

getOrigGroup() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

getOriginalCenters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getORmsdThr() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Get the Original RMSD threshold from which the alignment optimization is started

getOrthologousSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain

getOther(Atom) - Method in interface org.biojava.nbio.structure.Bond

A utility method to get the other atom in a bond, given one of its atoms.

getOther(Atom) - Method in class org.biojava.nbio.structure.BondImpl

A utility method to get the other atom in a bond, given one of its atoms.

getOutFile() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

getOutFile() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

getOxidationState() - Method in enum org.biojava.nbio.structure.Element

Returns a typical oxidation state for this Element.

getP() - Method in class org.biojava.nbio.structure.NucleotideImpl

Returns the P atom if present, otherwise null

getP1() - Method in class org.biojava.nbio.structure.align.model.AFP

getP2() - Method in class org.biojava.nbio.structure.align.model.AFP

getPair() - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

getPair() - Method in class org.biojava.nbio.structure.contact.AtomContact

getPair() - Method in class org.biojava.nbio.structure.contact.GroupContact

getPairingNames() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the names of the pairs in terms of A, G, T/U, and C for each base pair group in the list.

getPairingParameters() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method reports all the pair parameters, in the order of: buckle, propeller, opening (in degrees), shear, stagger, stretch (in Å).

getPairs() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage

getPairSequence() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the primary strand's sequence where parameters were found.

getPara(int, int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.SigEva

getParameters() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment

getParameters() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment

getParameters() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor

getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor

getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeMain

getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain

getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor

getParameters() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor

getParameters() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain

getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible

getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid

getParameters() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor

getParameters() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain

getParameters() - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner

Return the parameters of this algorithm instance.

getParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner

getParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor

getParameters() - Method in interface org.biojava.nbio.structure.align.StructureAlignment

Return the paramers for this algorithm.

getParams() - Method in class org.biojava.nbio.structure.align.StructurePairAligner

get the parameters.

getParams() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

getParent() - Method in class org.biojava.nbio.structure.DBRef

Get the structure object that this DBRef relates to.

getParent(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

Get the parent of a component.

getParentChains() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Finds the parent chains by looking up the references of first atom of each side of this interface

getParentCompounds() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Finds the parent entities by looking up the references of first atom of each side of this interface

getParentId() - Method in class org.biojava.nbio.structure.cath.CathNode

getParentSunid() - Method in class org.biojava.nbio.structure.scop.ScopNode

getPartner() - Method in class org.biojava.nbio.structure.secstruc.HBond

getPartner1() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge

getPartner2() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge

getPath() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

getPath() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

getPath() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

getPath() - Method in class org.biojava.nbio.structure.align.util.AtomCache

Get the path that is used to cache PDB files.

getPath() - Static method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

Get this provider's cache path

getPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Returns the path value.

getPathSize() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

getPathSize() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

getPaulingElectronegativity() - Method in enum org.biojava.nbio.structure.Element

Returns the Pauling electronegativity for this Element.

getPdb1() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

getPdb1() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

getPdb2() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

getPdb2() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

getPdbAln() - Method in class org.biojava.nbio.structure.align.model.AFPChain

used temporarily during XML serialization to track the PDB positions of the alignmnet

getPdbChainIdClusters() - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader

getPdbChainIdClusters(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader

getPDBCode() - Method in interface org.biojava.nbio.structure.Structure

Deprecated.
use Structure.getPdbId() to get a PdbId object or getPdbId().getId() to get a String

getPDBCode() - Method in class org.biojava.nbio.structure.StructureImpl

Deprecated.
use StructureImpl.getPdbId() to get a PdbId object or getPdbId().getId() to get a String

getPDBCode1() - Method in class org.biojava.nbio.structure.align.client.PdbPair

Deprecated.
use PdbPair.getPDBCode1() instead

getPDBCode2() - Method in class org.biojava.nbio.structure.align.client.PdbPair

Deprecated.
use PdbPair.getPDBCode2() instead

getPdbEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

getPdbFilePath() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

getPdbFilePath() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

getPdbGroup() - Method in interface org.biojava.nbio.structure.SeqMisMatch

getPdbGroup() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

getPDBHeader() - Method in interface org.biojava.nbio.structure.Structure

Return the header information for this PDB file.

getPDBHeader() - Method in class org.biojava.nbio.structure.StructureImpl

Return the header information for this PDB file.

getPdbId() - Method in class org.biojava.nbio.structure.align.client.StructureName

Get the PDB ID for this name, if any.

getPdbId() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

Gets the PdbId object.
Before 6.0.0, this method used to return a String.

getPdbId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

getPdbId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

getPdbId() - Method in class org.biojava.nbio.structure.PDBHeader

Gets the PDB identifier for this protein structure.

getPdbId() - Method in class org.biojava.nbio.structure.scop.ScopDomain

Gets the PDB identifier for this protein structure.

getPdbId() - Method in interface org.biojava.nbio.structure.Structure

Returns the PDB identifier associated with this StructureIdentifier.

getPdbId() - Method in class org.biojava.nbio.structure.StructureImpl

Returns the PDB identifier associated with this StructureIdentifier.

getPdbId() - Method in class org.biojava.nbio.structure.SubstructureIdentifier

Get the PDB identifier part of the SubstructureIdentifier

getPdbId1() - Method in class org.biojava.nbio.structure.align.client.PdbPair

getPdbId2() - Method in class org.biojava.nbio.structure.align.client.PdbPair

getPdbIdAndChain() - Method in class org.biojava.nbio.structure.cath.CathDomain

Returns a string of the form PDBID.CHAIN.

getPDBName() - Method in interface org.biojava.nbio.structure.Group

Get the PDB 3-letter name for this group.

getPDBName() - Method in class org.biojava.nbio.structure.HetatomImpl

getPdbResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

getPdbResNum() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

getPdbResNum() - Method in interface org.biojava.nbio.structure.SeqMisMatch

getPdbResNum() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

getPDBresnum1() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

getPDBresnum2() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

getPdbSerial() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier

getPDBserial() - Method in interface org.biojava.nbio.structure.Atom

Get PDB atom number.

getPDBserial() - Method in class org.biojava.nbio.structure.AtomImpl

Get PDB atom number.

getPdbStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

getPdbxAlign() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxAmbiguousFlag() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxAromaticFlag() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxAromaticFlag() - Method in class org.biojava.nbio.structure.chem.ChemCompBond

getPdbxComponentAtomId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxComponentCompId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxComponentId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxFormalCharge() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxIdealCoordinatesDetails() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxIdealCoordinatesMissingFlag() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxInitialDate() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxLeavingAtomFlag() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxModelCartnXIdeal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxModelCartnYIdeal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxModelCartnZIdeal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxModelCoordinatesDbCode() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxModelCoordinatesDetails() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxModelCoordinatesMissingFlag() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxModifiedDate() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxOrdinal() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxOrdinal() - Method in class org.biojava.nbio.structure.chem.ChemCompBond

getPdbxPolymerType() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxProcessingSite() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxRefId() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxReleaseStatus() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxReplacedBy() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxReplaces() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxResidueNumbering() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxStereoConfig() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getPdbxStereoConfig() - Method in class org.biojava.nbio.structure.chem.ChemCompBond

getPdbxSubcomponentList() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxSynonyms() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPdbxType() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPercId() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

getPeriod() - Method in enum org.biojava.nbio.structure.Element

Returns the period in the periodic table of this Element.

getPermutation() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

getPermutation() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

getPermutation(int) - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup

getPermutationSize() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getPhi() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

getPhi(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc

Calculate the phi angle.

getPivot() - Method in class org.biojava.nbio.structure.jama.LUDecomposition

Return pivot permutation vector

getPmid() - Method in class org.biojava.nbio.structure.JournalArticle

Get the value of PMID field.

getPointGroup() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

getPolyChain(String) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the first model

getPolyChain(String) - Method in class org.biojava.nbio.structure.StructureImpl

getPolyChain(String, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a polymeric Chain based on the 'internal' chain id (asymId) for the given model index

getPolyChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl

getPolyChainByPDB(String) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a polymeric Chain based on the 'public' chain name (authId) for the first model

getPolyChainByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl

getPolyChainByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a polymeric Chain based on the 'public' chain name (authId) for the given model index.

getPolyChainByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl

getPolyChains() - Method in class org.biojava.nbio.structure.Model

getPolyChains() - Method in interface org.biojava.nbio.structure.Structure

Return all polymeric chains for the first model

getPolyChains() - Method in class org.biojava.nbio.structure.StructureImpl

getPolyChains(int) - Method in interface org.biojava.nbio.structure.Structure

Return all polymeric chains for the given model index.

getPolyChains(int) - Method in class org.biojava.nbio.structure.StructureImpl

getPolygonVertices(int, double, Point3d) - Static method in class org.biojava.nbio.structure.symmetry.geometry.Prism

Returns the vertices of an n-fold polygon of given radius and center

getPolymerType() - Method in class org.biojava.nbio.structure.chem.ChemComp

getPolymerType() - Method in enum org.biojava.nbio.structure.chem.ResidueType

Gets the associated PolymerType, which are less specific

getPolymerType(ResidueType) - Static method in class org.biojava.nbio.structure.chem.ChemCompTools

getPos1() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

getPos2() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

getPosition(ResidueNumber) - Method in class org.biojava.nbio.structure.AtomPositionMap

Gets the 0-based index of residueNumber to the matched atoms

getPredominantGroupType() - Method in interface org.biojava.nbio.structure.Chain

Get the predominant GroupType for a given Chain, following these rules: if the ratio of number of residues of a certain GroupType to total non-water residues is above the threshold 0.95, then that GroupType is returned if there is no GroupType that is above the threshold then the GroupType with most members is chosen, logging it

getPredominantGroupType() - Method in class org.biojava.nbio.structure.ChainImpl

getPrimitiveMultiplicity() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

getPrincipalAxes() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

The principal axes of intertia

getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getPrincipalAxesOfInertia() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getPrincipalAxisIndex() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

getPrincipalMomentsOfInertia() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getPrincipalRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getProbability() - Method in class org.biojava.nbio.structure.align.model.AFPChain

The probability (FATCAT) or Z-score (CE) of the alignment.

getProgram() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

getProgramVersion() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

getProjectedDistance(Atom) - Method in class org.biojava.nbio.structure.align.util.RotationAxis

Get the distance from a point to the axis of rotation

getProjectedPoint(Atom) - Method in class org.biojava.nbio.structure.align.util.RotationAxis

Projects a given point onto the axis of rotation

getPropeller(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the propeller ("propeller-twist") in degrees for the given base pair

getProperties() - Method in interface org.biojava.nbio.structure.Group

Return properties.

getProperties() - Method in class org.biojava.nbio.structure.HetatomImpl

getProperty(String) - Method in interface org.biojava.nbio.structure.Group

Get a single property .

getProperty(String) - Method in class org.biojava.nbio.structure.HetatomImpl

getProteinSequence() - Method in class org.biojava.nbio.structure.cluster.Subunit

Get the protein sequence of the Subunit.

getProteinSequenceForStructure(Structure, Map<Integer, Group>) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher

Generates a ProteinSequence corresponding to the sequence of struct, and maintains a mapping from the sequence back to the original groups.

getProteinSequenceString() - Method in class org.biojava.nbio.structure.cluster.Subunit

Get the protein sequence of the Subunit as String.

getPsi() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

getPsi(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc

Calculate the psi angle.

getPublicationDate() - Method in class org.biojava.nbio.structure.JournalArticle

getPublisher() - Method in class org.biojava.nbio.structure.JournalArticle

getPx() - Method in class org.biojava.nbio.structure.scop.ScopDomain

getQ() - Method in class org.biojava.nbio.structure.jama.QRDecomposition

Generate and return the (economy-sized) orthogonal factor

getQuat4d(int) - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler

getQuat4d(int) - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler

getQuaternarySymmetry(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Given a symmetry result, it calculates the overall global symmetry, factoring out the alignment and detection steps of QuatSymmetryDetector algorithm.

getR() - Method in class org.biojava.nbio.structure.jama.QRDecomposition

Return the upper triangular factor

getRadius() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

Returns the radius for drawing polyhedra

getRadius() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getRadius() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

Returns the radius for drawing the minor rotation axis in the xy-plane

getRadius(Atom) - Static method in class org.biojava.nbio.structure.asa.AsaCalculator

Gets the van der Waals radius of the given atom following the values defined by Chothia (1976) J.Mol.Biol.105,1-14 NOTE: the vdw values defined by the paper assume no Hydrogens and thus "inflates" slightly the heavy atoms to account for Hydrogens.

getRadiusOfGyration() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

getRandomSeed() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

getRange() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

Get the range of this domain, in PDB residue numbers (mmCif's _pdbx_poly_seq_scheme.pdb_seq_num and pdb_ins_code).

getRange() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement

Returns the residue range of this SSE.

getRanges() - Method in class org.biojava.nbio.structure.AtomPositionMap

Returns a list of ResidueRanges corresponding to this entire AtomPositionMap.

getRanges() - Method in class org.biojava.nbio.structure.scop.ScopDomain

getRealEigenvalues() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition

Return the real parts of the eigenvalues

getReason() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

Return a String describing the reasons for the CE-Symm final decision in this particular result.

getRecordType() - Method in interface org.biojava.nbio.structure.AminoAcid

Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.

getRecordType() - Method in class org.biojava.nbio.structure.AminoAcidImpl

Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.

getReducedStructure(Structure) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools

Reduce a structure to a single-atom representation (e.g.

getRef() - Method in class org.biojava.nbio.structure.JournalArticle

Get the value of REF field.

getRefChainId() - Method in class org.biojava.nbio.structure.EntityInfo

Return the ref chain id value.

getReferenceFrames() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

getRefinedScoreThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getRefineMethod() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getRefn() - Method in class org.biojava.nbio.structure.JournalArticle

Get the value of REFN field.

getRefRMSD(List<Atom[]>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

Calculates the average RMSD from all structures to a reference s tructure, given a set of superimposed atoms.

getRefRMSD(MultipleAlignment, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

/** Calculates the average RMSD from all structures to a reference s tructure, given a set of superimposed atoms.

getRefTMScore(List<Atom[]>, List<Integer>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

Calculates the average TMScore from all structures to a reference structure, given a set of superimposed atoms.

getRefTMScore(MultipleAlignment, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

Calculates the average TMScore from all structures to a reference structure, given a set of superimposed atoms.

getRelation() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

The quaternary structure relation QsRelation between the two groups of Subunits.

getRelativeAsaC() - Method in class org.biojava.nbio.structure.asa.GroupAsa

Returns the relative (complexed) ASA, i.e.

getRelativeAsaU() - Method in class org.biojava.nbio.structure.asa.GroupAsa

Returns the relative (uncomplexed) ASA, i.e.

getRelDate() - Method in class org.biojava.nbio.structure.PDBHeader

Return the release date of the structure in the PDB.

getRepeatRelation(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Get the indices of participating repeats in Cauchy two-line form.

getRepeatRelation(int, int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

getRepeatRelation(SymmetryAxes.Axis) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

getRepeatsCyclicForm(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

getRepeatsCyclicForm(int, int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Get the indices of participating repeats in cyclic form.

getRepeatsCyclicForm(List<List<Integer>>, List<?>) - Static method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

getRepeatsCyclicForm(SymmetryAxes.Axis) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

getRepeatsCyclicForm(SymmetryAxes.Axis, List<?>) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

getRepeatsID() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

Return the symmetric repeats as structure identifiers, if the result is symmetric and it was refined, return null otherwise.

getRepeatTransform(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Return the transformation that needs to be applied to a repeat in order to superimpose onto repeat 0.

getRepeatTransform(int, int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Return the transformation that needs to be applied to repeat x in order to superimpose onto repeat y.

getRepeatUnitCenters() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit

getRepeatUnitIndices() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit

getRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit

getRepeatUnits() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

getReplaced(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

getReplaced(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

If ChemComp is replacing another one, get the old version otherwise return the same ChemComp again.

getReplacer(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

getReplacer(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

If ChemComp is replaced by another one, get the newer version otherwise return the same ChemComp again.

getRepresentative() - Method in class org.biojava.nbio.structure.cath.CathNode

getRepresentative() - Method in class org.biojava.nbio.structure.EntityInfo

Get the representative Chain for this EntityInfo.

getRepresentative() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature

getRepresentativeAtomArray(Chain) - Static method in class org.biojava.nbio.structure.StructureTools

Gets a representative atom for each group that is part of the chain backbone.

getRepresentativeAtomArray(Structure) - Static method in class org.biojava.nbio.structure.StructureTools

Gets a representative atom for each group that is part of the chain backbone.

getRepresentativeAtoms() - Method in class org.biojava.nbio.structure.cluster.Subunit

Get all the representative Atoms of the Subunit.

getRepresentativeAtoms(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the representative atoms for the provided name.

getRepresentativeAtoms(Structure) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Returns the representative Atom Array of the first model, if the structure is NMR, or the Array for each model, if it is a biological assembly with multiple models.

getRepresentativeAtoms(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache

getRepresentativeAtomsInContact(Chain, double) - Static method in class org.biojava.nbio.structure.StructureTools

Returns the set of intra-chain contacts for the given chain for C-alpha or C3' atoms (including non-standard aminoacids appearing as HETATM groups), i.e.

getRepresentativeAtomsOnly(List<Chain>) - Static method in class org.biojava.nbio.structure.io.CAConverter

Convert a List of chain objects to another List of chains, containing Representative atoms only.

getRepresentativeAtomsOnly(Chain) - Static method in class org.biojava.nbio.structure.io.CAConverter

Convert a Chain to a new Chain containing C-alpha atoms only.

getRepresentativeChain(String, String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader

getRepresentativeDomains() - Method in interface org.biojava.nbio.structure.domain.DomainProvider

Get the full list of representative domains for the PDB.

getRepresentatives(String) - Static method in class org.biojava.nbio.structure.scop.Astral

Get a list of representatives' names for the specified ASTRAL cutoff.

getRepresentatives(String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader

getRepresentatives(Astral.AstralSet) - Static method in class org.biojava.nbio.structure.scop.Astral

Get a list of representatives' names for the specified ASTRAL cutoff.

getResidue(int) - Method in class org.biojava.nbio.structure.AugmentedResidueRange

Returns the ResidueNumber that is at position positionInRange in this ResidueRange.

getResidue(int, AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange

Returns the ResidueNumber that is at position positionInRange in this ResidueRange.

getResidueNumber() - Method in interface org.biojava.nbio.structure.Group

Returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group.

getResidueNumber() - Method in class org.biojava.nbio.structure.HetatomImpl

Returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group.

getResidueRanges() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getResidueRanges() - Method in class org.biojava.nbio.structure.scop.ScopDomain

getResidueRanges() - Method in class org.biojava.nbio.structure.SubstructureIdentifier

getResidues() - Method in class org.biojava.nbio.structure.io.FastaStructureParser

For each residue in the fasta file, return the ResidueNumber in the corresponding structure.

getResidues() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

getResidueType() - Method in class org.biojava.nbio.structure.chem.ChemComp

getResidueTypeFromString(String) - Static method in enum org.biojava.nbio.structure.chem.ResidueType

Get ResidueType by chem_comp_type

getResidueTypes() - Method in enum org.biojava.nbio.structure.GroupType

Get a set of ResidueTypes loosely equivalent to this GroupType.

getResName1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

getResName2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

getResNames() - Method in class org.biojava.nbio.structure.EntityInfo

getResnum1() - Method in class org.biojava.nbio.structure.io.SSBondImpl

getResnum2() - Method in class org.biojava.nbio.structure.io.SSBondImpl

getResolution() - Method in class org.biojava.nbio.structure.cath.CathDomain

getResolution() - Method in class org.biojava.nbio.structure.PDBHeader

getResourceManager(String) - Static method in class org.biojava.nbio.structure.align.util.ResourceManager

getResScore() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getResSeq1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

getResSeq2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

getReverse() - Method in class org.biojava.nbio.structure.align.client.PdbPair

getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getReverseTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getRevisionRecords() - Method in class org.biojava.nbio.structure.PDBHeader

getRevNum() - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord

getRfree() - Method in class org.biojava.nbio.structure.PDBHeader

getRimResidues(double, double) - Method in class org.biojava.nbio.structure.contact.StructureInterface

Returns the residues belonging to the interface rim, defined as those residues at the interface (BSA>0) and for which the BSA/ASA ratio is below the given bsaToAsaCutoff

getRise() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

getRise(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the rise for the given base pair, relative to the one before it.

getRms() - Method in class org.biojava.nbio.structure.align.helper.JointFragments

getRms() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

getRMS(Atom[], Atom[], JointFragments) - Static method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner

Get the RMS of the JointFragments pair frag

getRmsd() - Method in class org.biojava.nbio.structure.align.model.AFP

getRmsd() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

getRmsd() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

The RMSD between the equivalent residues of the equivalent Subunits after superposition of the Subunit groups.

getRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

getRmsd(Point3d[], Point3d[]) - Method in interface org.biojava.nbio.structure.geometry.SuperPosition

Calculate the RMSD between two arrays of equivalent points that are not superposed.

getRmsd(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP

getRmsd(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQuat

getRmsd(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions

Use the SuperPosition.getRmsd(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.

getRmsd(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionSVD

getRMSD(List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

Calculates the RMSD of all-to-all structure comparisons (distances), given a set of superimposed atoms.

getRMSD(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

Calculates the RMSD of all-to-all structure comparisons (distances) of the given MultipleAlignment.

getRmsdAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions

Use the SuperPosition.getRmsd(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.

getRmsdCenters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

getRmsdCut() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

The cutoff to be used during AFP detection

getRmsdCut() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

getRmsdIntra() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

getRMSDMatrix(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Calculate the RMSD matrix of a MultipleAlignment, that is, entry (i,j) of the matrix contains the RMSD between structures i and j.

getRmsdThr() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

RMSD Threshold

getRmsdThreshold() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

getRMSDThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Structure similarity threshold (measured with RMSD) to consider for the structural subunit clustering.

getRmsdThrJoin() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

RMSD threshold for joining of AFPs

getRndSeed() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getRoll(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the roll for the given base pair, relative to the one before it.

getRootURL() - Method in class org.biojava.nbio.structure.scop.ScopMirror

Get the URL for the root download directory, or null if none is set.

getRot() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

getRotatedAtoms(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay

New structures are downloaded if they were not cached in the alignment and they are entirely transformed here with the superposition information in the Multiple Alignment.

getRotation(int) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

getRotationAxis() - Method in class org.biojava.nbio.structure.align.util.RotationAxis

Get a unit vector along the rotation axis

getRotationAxis() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

Get the transformation operator as a rotation axis.

getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getRotationGroup() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

getRotationJAMA(Matrix4d) - Static method in class org.biojava.nbio.structure.geometry.Matrices

Convert a transformation matrix into a JAMA rotation matrix.

getRotationMatrix() - Method in class org.biojava.nbio.structure.align.ce.CECalculator

Gets the rotation matrix from the last call to calc_rmsd.

getRotationMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

Gets the rotation matrix from the last call to calc_rmsd.

getRotationMatrix() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1

getRotationMatrix() - Method in class org.biojava.nbio.structure.align.util.RotationAxis

Get the rotation matrix corresponding to this axis

getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getRotationMatrix() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getRotationMatrix(double) - Method in class org.biojava.nbio.structure.align.util.RotationAxis

Get the rotation matrix corresponding to a rotation about this axis

getRotationMatrix(Matrix4d) - Static method in class org.biojava.nbio.structure.geometry.Matrices

Convert a transformation matrix into a rotation matrix.

getRotationPos() - Method in class org.biojava.nbio.structure.align.util.RotationAxis

Get a position on the rotation axis.

getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getRotationReferenceAxis() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getRotAxisAndAngle(Matrix3d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup

Given a rotation matrix calculates the rotation axis and angle for it.

getRotAxisAngle(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

getRotAxisType(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup

Given a transformation matrix containing a rotation returns the type of rotation: 1 for identity, 2 for 2-fold rotation, 3 for 3-fold rotation, 4 for 4-fold rotation, 6 for 6-fold rotation, -1 for inversions, -2 for mirror planes, -3 for 3-fold improper rotation, -4 for 4-fold improper rotation and -6 for 6-fold improper rotation

getRotMax(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay

getRow() - Method in class org.biojava.nbio.structure.align.helper.IndexPair

getRowDimension() - Method in class org.biojava.nbio.structure.jama.Matrix

Get row dimension.

getRowPackedCopy() - Method in class org.biojava.nbio.structure.jama.Matrix

Make a one-dimensional row packed copy of the internal array.

getRows() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

getRows() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

getRwork() - Method in class org.biojava.nbio.structure.PDBHeader

getS() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition

Return the diagonal matrix of singular values

getSaveOutputDir() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

getScaleableMatrixPanel(Matrix) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

getSCOP() - Static method in class org.biojava.nbio.structure.scop.ScopFactory

Get the current default instance for the default version

getSCOP(String) - Static method in class org.biojava.nbio.structure.scop.ScopFactory

Gets an instance of the specified scop version.

getScopDescriptionBySunid(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

Return the SCOP description for a node in the hierarchy by its "sunid" id.

getScopDescriptionBySunid(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

getScopDomainsBySunid(Integer) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

Get a SCOP domain by its sunid

getScopDomainsBySunid(Integer) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

getScopId() - Method in class org.biojava.nbio.structure.scop.ScopDomain

getScopNode(int) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

Access a particular ScopNode.

getScopNode(int) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

getScopVersion() - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

Returns the SCOP version

getScopVersion() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

getScore() - Method in class org.biojava.nbio.structure.align.model.AFP

getScore() - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

getScore() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

the alignment score

getScore() - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

getScore() - Method in class org.biojava.nbio.structure.domain.pdp.Domain

getScore() - Method in class org.biojava.nbio.structure.domain.pdp.Segment

getScore(String) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache

getScore(String) - Method in interface org.biojava.nbio.structure.align.multiple.ScoresCache

Get the value for a particular score.

getScore2(int, int, double[][], int, int[], int, int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

getScore2(int, int, double[][], int, int[], int, int, double, double) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

getScoreFromDistanceMatrices(int, int, int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

getScoreFromDistanceMatrices(int, int, int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

getScores() - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache

getScores() - Method in interface org.biojava.nbio.structure.align.multiple.ScoresCache

Get a collection of all scores that have been set.

getScores() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

getScores() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

Returns QuatSymmetryScores averaged over all rotations (except the first rotation, which is the unit operation E)

getScores() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

getScores() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

getScores() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

Returns QuatSymmetryScores averaged over all rotations (except the first rotation, which is the unit operation E)

getScoringStrategy() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

getScoringStrategy() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

getScrewTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis

Get the component of translation parallel to the axis of rotation

getSearchFile() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

An input file to be used for the DB search

getSecond() - Method in class org.biojava.nbio.structure.contact.Pair

getSecondAtomsForAsa(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface

getSecondGroupAsa(ResidueNumber) - Method in class org.biojava.nbio.structure.contact.StructureInterface

Gets the GroupAsa for the corresponding residue number of second chain

getSecondGroupAsas() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Gets a map of ResidueNumbers to GroupAsas for all groups of second chain.

getSecretion() - Method in class org.biojava.nbio.structure.EntityInfo

getSecStrucElements(List<Group>) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools

Obtain the List of secondary structure elements (SecStrucElement) of a List of Groups (assumed to be sequential, this is, connected in the original Structure).

getSecStrucElements(Structure) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools

Obtain the List of secondary structure elements (SecStrucElement) of a Structure.

getSecStrucInfo(Structure) - Static method in class org.biojava.nbio.structure.secstruc.SecStrucTools

Obtain the List of secondary structure information (SecStrucInfo) of a Structure.

getSecStructType(Group) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get the secondary structure as defined by DSSP.

getSecStructTypeFromDsspIndex(int) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Set the DSSP type based on a numerical index.

getSeedFragmentLength() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getSeedRmsdCutoff() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getSegId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

getSegmentAtPos(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

getSegmentId() - Method in class org.biojava.nbio.structure.cath.CathSegment

getSegments() - Method in class org.biojava.nbio.structure.cath.CathDomain

getSegments() - Method in class org.biojava.nbio.structure.domain.pdp.Domain

getSegments() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

getSelfAlignment() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

getSeqBegin() - Method in class org.biojava.nbio.structure.DBRef

Initial sequence number of the PDB sequence segment.

getSeqEnd() - Method in class org.biojava.nbio.structure.DBRef

Ending sequence number of the PDB sequence segment.

getSeqIdRange() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

Get the range of this domain, in 1-based residue indices (mmCif's _pdbx_poly_seq_scheme.seq_id) Note that EcodDomain.getRange() is used when constructing the domain.

getSeqMisMatches() - Method in interface org.biojava.nbio.structure.Chain

Gets annotated sequence mismatches for this chain.

getSeqMisMatches() - Method in class org.biojava.nbio.structure.ChainImpl

getSeqNum() - Method in class org.biojava.nbio.structure.ResidueNumber

getSeqNum() - Method in interface org.biojava.nbio.structure.SeqMisMatch

getSeqNum() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

getSeqresEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

getSeqResGroup(int) - Method in interface org.biojava.nbio.structure.Chain

Return the Group at given position, from within groups in the SEQRES records of the chain, i.e.

getSeqResGroup(int) - Method in class org.biojava.nbio.structure.ChainImpl

getSeqResGroups() - Method in interface org.biojava.nbio.structure.Chain

Returns a list of all groups in SEQRES records of the chain, i.e.

getSeqResGroups() - Method in class org.biojava.nbio.structure.ChainImpl

getSeqResGroups(GroupType) - Method in interface org.biojava.nbio.structure.Chain

Returns a List of all SEQRES groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.

getSeqResGroups(GroupType) - Method in class org.biojava.nbio.structure.ChainImpl

getSeqResLength() - Method in interface org.biojava.nbio.structure.Chain

Returns the number of groups in the SEQRES records of the chain, i.e.

getSeqResLength() - Method in class org.biojava.nbio.structure.ChainImpl

getSeqResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

getSeqResOneLetterSeq() - Method in class org.biojava.nbio.structure.ChainImpl

Get the one letter sequence so that Sequence is guaranteed to be the same length as seqResGroups.

getSeqResSequence() - Method in interface org.biojava.nbio.structure.Chain

Returns the PDB SEQRES sequence as a one-letter sequence string.

getSeqResSequence() - Method in class org.biojava.nbio.structure.ChainImpl

getSeqresStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

getSequence() - Method in class org.biojava.nbio.structure.cath.CathDomain

getSequence() - Method in class org.biojava.nbio.structure.cath.CathSegment

getSequenceAlignment(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Calculate the sequence alignment Strings for the whole alignment.

getSequenceAlignment(MultipleAlignment, List<Integer>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Calculate the sequence alignment Strings for the whole alignment.

getSequenceCoverageThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

The minimum coverage of the sequence alignment between two subunits to be clustered together.

getSequenceFamilyId() - Method in class org.biojava.nbio.structure.cath.CathDomain

getSequenceHeader() - Method in class org.biojava.nbio.structure.cath.CathDomain

getSequenceHeader() - Method in class org.biojava.nbio.structure.cath.CathSegment

getSequenceIdentityThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Sequence identity threshold to consider for the subunits clustering.

getSequences() - Method in class org.biojava.nbio.structure.io.FastaStructureParser

Gets the protein sequences read from the Fasta file.

getSeqWeight() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.

getSerialversionuid() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup

getSerNum() - Method in class org.biojava.nbio.structure.io.SSBondImpl

getServerName() - Static method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Return the String with the PDB server name, including the leading protocol String (http:// or ftp://).

getShear(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the shear in Å for the given base pair

getShift() - Method in class org.biojava.nbio.structure.align.ce.CECalculator

Gets the shift from the last call to calc_rmsd.

getShift() - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

Gets the shift from the last call to calc_rmsd.

getShift() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

returns the shift vector that has to be applied on structure to to shift on structure one

getShift(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

Return the shift for the given base pair, relative to the one before it.

getShortId() - Method in class org.biojava.nbio.structure.PdbId

Get the PDB Id in the short format.

getShortName() - Method in enum org.biojava.nbio.structure.xtal.TransformType

getShortSymbol() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

Gets the international short name (as used in PDB), e.g.

getShowDBresult() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

getSiftsMapping(String) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider

Return the SIFTS mappings by getting the info from individual SIFTS xml files at URL "https://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/%s.xml.gz"

getSimilarity() - Method in class org.biojava.nbio.structure.align.model.AFPChain

Returns the similarity score for the alignment.

getSingularValues() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition

Return the one-dimensional array of singular values

getSiteID() - Method in class org.biojava.nbio.structure.Site

getSites() - Method in interface org.biojava.nbio.structure.Structure

getSites() - Method in class org.biojava.nbio.structure.StructureImpl

getSize() - Method in class org.biojava.nbio.structure.domain.pdp.Domain

getSlide(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the slide for the given base pair, relative to the one before it.

getSOILD() - Method in class org.biojava.nbio.structure.cath.CathDomain

getSource() - Method in class org.biojava.nbio.structure.align.client.StructureName

getSource() - Method in class org.biojava.nbio.structure.cath.CathDomain

getSpaceGroup() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Get the SpaceGroup

getSpaceGroup(int) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser

Gets the space group for the given standard identifier.

getSpaceGroup(String) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser

Get the space group for the given international short name, using the PDB format, e.g.

getSpaceGroupAsString(SpaceGroup) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get the string representation of a space group.

getSparse() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getSpeciesId() - Method in class org.biojava.nbio.structure.scop.ScopDomain

getSphereCount() - Static method in class org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler

getSphereCount() - Static method in class org.biojava.nbio.structure.symmetry.geometry.SphereSampler

getSplitDirPath() - Method in class org.biojava.nbio.structure.io.BcifFileReader

getSplitDirPath() - Method in class org.biojava.nbio.structure.io.CifFileReader

getSplitDirPath() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Location of split files within the directory, as an array of paths.

getSplitDirPath() - Method in class org.biojava.nbio.structure.io.MMTFFileReader

getSplitDirPath() - Method in class org.biojava.nbio.structure.io.PDBFileReader

getSplitpat1() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup

getSplitpat2() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup

getSsBondListFromBondList(List<Bond>) - Static method in class org.biojava.nbio.structure.io.SSBondImpl

getSSBonds() - Method in interface org.biojava.nbio.structure.Structure

Get the list of disulfide Bonds as they have been defined in the PDB files

getSSBonds() - Method in class org.biojava.nbio.structure.StructureImpl

Get the list of disulfide Bonds as they have been defined in the PDB files

getSSEThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getStagger(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the stagger in Å for the given base pair

getStart() - Method in class org.biojava.nbio.structure.cath.CathFragment

getStart() - Method in class org.biojava.nbio.structure.cath.CathSegment

getStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

getStart() - Method in class org.biojava.nbio.structure.ResidueRange

getStartIndex(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block

Calculates and returns the first position of the specified structure in the alignment that is not null.

getStartIndex(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

getStartPage() - Method in class org.biojava.nbio.structure.JournalArticle

getStartResidue(int) - Method in interface org.biojava.nbio.structure.align.multiple.Block

Calculates and returns the first residue of the specified structure in the alignment that is not null.

getStartResidue(int) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor

StartupParameters is a bean to store all the possible command line parameters.

getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor

getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor

getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor

getStartupParametersInstance() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor

getStatus(String) - Static method in class org.biojava.nbio.structure.PDBStatus

Get the status of a PDB id.

getStatus(String[]) - Static method in class org.biojava.nbio.structure.PDBStatus

Get the status of a collection of PDB ids (in a single API query).

getStepParameters() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method reports all the base-pair step parameters, in the order of: tilt, roll, twist (in degrees), shift, slide, rise (in Å).

getStoichiometry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

getStop() - Method in class org.biojava.nbio.structure.cath.CathFragment

getStop() - Method in class org.biojava.nbio.structure.cath.CathSegment

getStrain() - Method in class org.biojava.nbio.structure.EntityInfo

getStrategy() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

getStretch(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the stretch in Å for the given base pair

getString(String) - Method in class org.biojava.nbio.structure.align.util.ResourceManager

getStructuralTree(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Calculate a phylogenetic tree of the MultipleAlignment using RMSD distances and the Neighbor Joining algorithm from forester.

getStructure() - Method in interface org.biojava.nbio.structure.Chain

Returns the parent Structure of this chain.

getStructure() - Method in class org.biojava.nbio.structure.ChainImpl

getStructure() - Method in class org.biojava.nbio.structure.cluster.Subunit

The parent Structure from which the Subunit atoms were obtained.

getStructure() - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

Gets the structure.

getStructure() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

getStructure(File) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

getStructure(File) - Method in interface org.biojava.nbio.structure.io.StructureIOFile

Read file from File and returns a Structure object.

getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.BcifFileReader

getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.CifFileReader

getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Handles the actual parsing of the file into a Structure object.

getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.MMTFFileReader

getStructure(InputStream) - Method in class org.biojava.nbio.structure.io.PDBFileReader

getStructure(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Request a Structure based on a name.

getStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

getStructure(String) - Method in interface org.biojava.nbio.structure.io.StructureIOFile

Open filename and return a Structure object.

getStructure(String) - Static method in class org.biojava.nbio.structure.StructureIO

Loads a structure based on a name.

getStructure(String) - Static method in class org.biojava.nbio.structure.StructureTools

Short version of StructureTools.getStructure(String, PDBFileParser, AtomCache) which creates new parsers when needed

getStructure(String, PDBFileParser, AtomCache) - Static method in class org.biojava.nbio.structure.StructureTools

Flexibly get a structure from an input String.

getStructure(URL) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

getStructure(StructureIdentifier) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Get the structure corresponding to the given StructureIdentifier.

getStructureById(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Get the structure for a PDB ID

getStructureById(String) - Method in interface org.biojava.nbio.structure.io.StructureProvider

Get the structure for a PDB ID

getStructureById(PdbId) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Get the structure for a PDB ID

getStructureById(PdbId) - Method in interface org.biojava.nbio.structure.io.StructureProvider

Get the structure for a PDB ID

getStructureCoverageThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

The minimum coverage of the structure alignment between two subunits to be clustered together.

getStructureFiletype() - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

getStructureForCathDomain(StructureName) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns a Structure corresponding to the CATH identifier supplied in structureName, using the the CathDatabase at CathFactory.getCathDatabase().

getStructureForCathDomain(StructureName, CathDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns a Structure corresponding to the CATH identifier supplied in structureName, using the specified CathDatabase.

getStructureForDomain(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the representation of a ScopDomain as a BioJava Structure object.

getStructureForDomain(String, ScopDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the representation of a ScopDomain as a BioJava Structure object.

getStructureForDomain(ScopDomain) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the representation of a ScopDomain as a BioJava Structure object.

getStructureForDomain(ScopDomain, ScopDatabase) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the representation of a ScopDomain as a BioJava Structure object.

getStructureForDomain(ScopDomain, ScopDatabase, boolean) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Returns the representation of a ScopDomain as a BioJava Structure object.

getStructureForPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Loads a structure directly by PDB ID

getStructureForPdbId(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Loads a structure directly by PDB ID

getStructureId() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

getStructureIdentifier() - Method in interface org.biojava.nbio.structure.Structure

Get an identifier corresponding to this structure

getStructureIdentifier() - Method in class org.biojava.nbio.structure.StructureImpl

getStructureIdentifier(int) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Returns the StructureIdentifier associated with the structure index from its parent Ensemble.

getStructureIdentifier(int) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

getStructureIdentifiers() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Returns a List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).

getStructureIdentifiers() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

getStructureInfo(Structure) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get summary information for the structure.

getStructures() - Method in class org.biojava.nbio.structure.io.FastaStructureParser

Gets the protein structures mapped from the Fasta file.

getSubstitutionMatrix() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.

getSubstructureMatchingProteinSequence(ProteinSequence, Structure) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher

Get a substructure of wholeStructure containing only the Groups that are included in sequence.

getSubunitClusters() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

Returns the List of SubunitCluster used to calculate symmetry.

getSubunitCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

Return the number of Subunits involved in the symmetry.

getSubunitCount() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getSubunitMap() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

Map of Subunit equivalencies from the first to the second group.

getSubunitRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

getSubunits() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Subunits contained in the SubunitCluster.

getSubunits() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getSubunits() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getSubunits() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getSubunits() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

Returns the List of Subunits used to calculate symmetry.

getSubunits1() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

Original Subunits of the first group.

getSubunits2() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

Original Subunits of the second group.

getSubunitTypeCount() - Method in class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature

getSunid() - Method in class org.biojava.nbio.structure.scop.ScopDomain

getSunid() - Method in class org.biojava.nbio.structure.scop.ScopNode

getSunID() - Method in class org.biojava.nbio.structure.scop.ScopDescription

getSuperfamilyId() - Method in class org.biojava.nbio.structure.scop.ScopDomain

getSuperpositionAlgorithm() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Method to superpose subunits (i.e., structural aligner).

getSurfaceResidues(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface

Returns the residues belonging to the surface

getSurname() - Method in class org.biojava.nbio.structure.Author

getSym1() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

getSym2() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

getSymDeviation() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getSymmetry() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

getSymmetryAxes() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Return all symmetry axes of of the structure: the set of axes that describe all parts of the structure.

getSymmetryClass(double) - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.C2RotationSolver

getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.HelixSolver

getSymmetryOperations() - Method in interface org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver

getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.RotationSolver

getSymmetryOperations() - Method in class org.biojava.nbio.structure.symmetry.core.SystematicSolver

getSymmetryOrder(Map<Integer, Integer>, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Helper for AlignmentTools.getSymmetryOrder(Map, Map, int, float) with a true identity function (X->X).

getSymmetryOrder(Map<Integer, Integer>, Map<Integer, Integer>, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Tries to detect symmetry in an alignment.

getSymmetryOrder(AFPChain, int, float) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Guesses the order of symmetry in an alignment

getSymmGroup() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

getSymmLevels() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getSymmLevels() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

getSymmType() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getSymmType() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

getSynonyms() - Method in class org.biojava.nbio.structure.EntityInfo

getSynthetic() - Method in class org.biojava.nbio.structure.EntityInfo

getT() - Method in class org.biojava.nbio.structure.align.model.AFP

getTempFactor() - Method in interface org.biojava.nbio.structure.Atom

Get temp factor.

getTempFactor() - Method in class org.biojava.nbio.structure.AtomImpl

getText(Group) - Method in class org.biojava.nbio.structure.io.GroupToSDF

getTGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getTGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getThePdbId() - Method in class org.biojava.nbio.structure.cath.CathDomain

Returns the PDB ID.

getThreeLetterCode() - Method in class org.biojava.nbio.structure.chem.ChemComp

getTilt(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the tilt for the given base pair, relative to the one before it.

getTissue() - Method in class org.biojava.nbio.structure.EntityInfo

getTitle() - Method in class org.biojava.nbio.structure.EntityInfo

getTitle() - Method in class org.biojava.nbio.structure.JournalArticle

Get the value of title

getTitle() - Method in class org.biojava.nbio.structure.PDBHeader

getTm() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

getTmIntra() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

getTMScore() - Method in class org.biojava.nbio.structure.align.model.AFPChain

Returns the tmScore of the alignment.

getTMScore(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPChainScorer

getTMScore(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.util.AFPChainScorer

getTMScore(Atom[], Atom[], int, int) - Static method in class org.biojava.nbio.structure.Calc

Calculate the TM-Score for the superposition.

getTMScore(Atom[], Atom[], int, int, boolean) - Static method in class org.biojava.nbio.structure.Calc

Calculate the TM-Score for the superposition.

getTMThreshold() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Structure similarity threshold (measured with TMScore) to consider for the structural subunit clustering.

getTo() - Method in class org.biojava.nbio.structure.domain.pdp.Segment

getTo() - Method in class org.biojava.nbio.structure.secstruc.Ladder

getTopologyId() - Method in class org.biojava.nbio.structure.cath.CathDomain

getTorsionPenalty() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getTotal() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator

getTotalArea() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Returns the total area buried upon formation of this interface, defined as: 1/2[ (ASA1u-ASA1c) + (ASA2u-ASA2u) ] , with:

getTotalArea() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

Return the average buried surface area for this interface cluster

getTotalLenIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getTotalLenOpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getTotalRmsdIni() - Method in class org.biojava.nbio.structure.align.model.AFPChain

this is the init-RMSD, not the final RMSD after refinement.

getTotalRmsdOpt() - Method in class org.biojava.nbio.structure.align.model.AFPChain

The RMSD of the final alignment.

getTraceRmsd() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

getTraces() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getTraceTmScoreMin() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

getTrans() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

getTranscoefpat() - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup

getTransfAlgebraic() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

getTransfAlgebraic(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

Gets a transformation algebraic string given its index.

getTransform() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

The transformation 4D matrix that needs to be applied to the second group of Subunits to superimpose them onto the first group of Subunits, given the equivalent residues in the SubunitCluster and the Subunit equivalencies.

getTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.AxisAligner

getTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

getTransformation() - Method in class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

getTransformation() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

getTransformation(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

Gets a transformation by index expressed in crystal axes basis.

getTransformation(Matrix, Atom) - Static method in class org.biojava.nbio.structure.Calc

Convert JAMA rotation and translation to a Vecmath transformation matrix.

getTransformation(Matrix, Matrix) - Static method in class org.biojava.nbio.structure.geometry.Matrices

Convert JAMA rotation and translation to a Vecmath transformation matrix.

getTransformationMap() - Method in class org.biojava.nbio.structure.io.PDBBioAssemblyParser

Returns a map of bioassembly transformations

getTransformationMatrix() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Return the transformation (both rotational and translational component) as a 4x4 transformation matrix.

getTransformations() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Returns a transformation matrix for each structure giving the 3D superimposition information of the multiple structure alignment.

getTransformations() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

getTransformations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

Gets all transformations except for the identity in crystal axes basis.

getTransformationsOrthonormal() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Gets all symmetry transformation operators corresponding to this structure's space group (including the identity, at index 0) expressed in the orthonormal basis.

getTransformId() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

getTransformMap(BioAssemblyInfo, Map<String, Integer>) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Convert a bioassembly information into a map of transform, chainindices it relates to.

getTransforms() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Return the 2 crystal transform operations performed on each of the molecules of this interface.

getTransforms() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

Return the list of BiologicalAssemblyTransformations needed to generate the biological assembly.

getTransformType() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

Returns the TransformType of this transformation: AU, crystal translation, fractional translation , 2 3 4 6-fold rotations, 2 3 4 6-fold screw rotations, -1 -3 -2 -4 -6 inversions/rotoinversions.

getTranslatedBbs(Vector3d) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox

Returns a new BoundingBoxes object containing the same bounds as this BoundingBoxes object translated by the given translation

getTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis

getTranslation(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AFPAlignmentDisplay

getTranslationVector(Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Extract the translational vector as an Atom of a transformation matrix.

getTranslationVector(Matrix4d) - Static method in class org.biojava.nbio.structure.geometry.Matrices

Extract the translational vector of a transformation matrix.

getTranslScrewComponent() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

getTranslScrewComponent(Matrix4d) - Static method in class org.biojava.nbio.structure.xtal.CrystalTransform

Given a transformation matrix containing a rotation and translation returns the screw component of the rotation.

getTree(CathDomain) - Method in interface org.biojava.nbio.structure.cath.CathDatabase

Return the CATH sub-tree for a particular domain.

getTree(CathDomain) - Method in class org.biojava.nbio.structure.cath.CathInstallation

getTree(ScopDomain) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

get the SCOP sub-tree for a particular domain.

getTree(ScopDomain) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

getTurn() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

getTwi() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getTwist(int) - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This method returns the twist for the given base pair, relative to the one before it.

getTwistedGroups() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner

getTwoFoldsPerpendicular() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

getType() - Method in class org.biojava.nbio.structure.AminoAcidImpl

getType() - Method in class org.biojava.nbio.structure.chem.ChemComp

getType() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

getType() - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord

getType() - Method in class org.biojava.nbio.structure.EntityInfo

Get the type of entity this EntityInfo describes.

getType() - Method in interface org.biojava.nbio.structure.Group

Get Type of group, one of GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE

getType() - Method in class org.biojava.nbio.structure.HetatomImpl

Get Type of group, one of GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE

getType() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

getType() - Method in class org.biojava.nbio.structure.NucleotideImpl

getType() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge

getType() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement

Returns the SecStrucType of this element.

getType() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo

getTypeSymbol() - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

getU() - Method in class org.biojava.nbio.structure.jama.LUDecomposition

Return upper triangular factor

getU() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition

Return the left singular vectors

getUid() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getUnalignedGroups(Atom[]) - Static method in class org.biojava.nbio.structure.StructureTools

List of groups from the structure not included in ca (e.g.

getUnaryOperators() - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver

Returns a list of operators for this assembly.

getUniProtAccessionId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

getUniprotEnd() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

getUniProtId() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

getUniProtId() - Method in interface org.biojava.nbio.structure.SeqMisMatch

getUniProtId() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

getUniProtPos() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

getUniProtResName() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

getUniprotStart() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

getUniqueInterfaces() - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder

Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates.

getUniqueInterfaces(double) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder

Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates.

getUnitCellAsArray(PDBCrystallographicInfo) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get the length six array of the unit cell information.

getUnitv() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

getUnitVectors() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getUnrefinedScoreThreshold() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getUpdateFrequency() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

The expected ECOD update frequency determines whether the version "latest" should be re-downloaded

getUpperBound() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

getUpperLimit() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

getUrl() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

Get the top-level ECOD server URL.

getUrl() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet

getURL() - Method in class org.biojava.nbio.structure.URLIdentifier

getUsed() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

getUsedAtomNames() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

getUserConfigHelp() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams

The help text for each of these parameters.

getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

getUserConfigHelp() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

getUserConfigHelp() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

getUserConfigParameterNames() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams

The labels to be displayed to the user for each parameter

getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

getUserConfigParameterNames() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

getUserConfigParameters() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams

get the list of parameters that the user can change through the user interface.

getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

getUserConfigParameters() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

getUserConfigParameters() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

getUserConfigTypes() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams

Get the data types of the parameters

getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

getUserConfigTypes() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

getUserConfigTypes() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getUserOrder() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

getV() - Method in class org.biojava.nbio.structure.jama.EigenvalueDecomposition

Return the eigenvector matrix

getV() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition

Return the right singular vectors

getValenceElectronCount() - Method in enum org.biojava.nbio.structure.Element

Returns the number of valence electrons for this Element.

getValidFolds(List<Integer>) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Find valid symmetry orders for a given stoichiometry.

getValue() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl

getValue() - Method in class org.biojava.nbio.structure.align.helper.GapArray

getValueOrder() - Method in class org.biojava.nbio.structure.chem.ChemCompBond

getVariant() - Method in class org.biojava.nbio.structure.EntityInfo

getVDWRadius() - Method in enum org.biojava.nbio.structure.Element

Returns the van der Waals radius of this Element.

getVector3dScrewTranslation() - Method in class org.biojava.nbio.structure.align.util.RotationAxis

getVersion() - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment

getVersion() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment

getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeCPMain

getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeMain

getVersion() - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain

getVersion() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain

getVersion() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible

getVersion() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid

getVersion() - Method in class org.biojava.nbio.structure.align.model.AFPChain

getVersion() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain

getVersion() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Returns the version of the algorithm used to generate the MultipleAlignment objects.

getVersion() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

getVersion() - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner

Get the Version information for this Algorithm.

getVersion() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner

getVersion() - Method in interface org.biojava.nbio.structure.align.StructureAlignment

Get the Version information for this Algorithm.

getVersion() - Method in class org.biojava.nbio.structure.cath.CathDomain

getVersion() - Method in interface org.biojava.nbio.structure.ecod.EcodDatabase

Return the release version.

getVersion() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser

getVersion() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

Return the ECOD version, as parsed from the file.

getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

Returns the vertices of an n-fold polygon of given radius and center

getVertices() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron

getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

Returns the vertices of an n-fold polygon of given radius and center

getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism

Returns the vertices of an n-fold polygon of given radius and center

getVertices() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

Returns the vertices of an n-fold polygon of given radius and center

getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

getViewCount() - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron

getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism

getViewCount() - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

getViewMatrix(int) - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron

getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism

getViewMatrix(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

getViewName(int) - Method in interface org.biojava.nbio.structure.symmetry.geometry.Polyhedron

getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism

getViewName(int) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

getVolume() - Method in class org.biojava.nbio.structure.JournalArticle

getVolume() - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Returns the volume of this unit cell.

getWaterChain(String) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a water Chain based on the 'internal' chain id (asymId) for the first model

getWaterChain(String) - Method in class org.biojava.nbio.structure.StructureImpl

getWaterChain(String, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a water chain based on the 'internal' chain id (asymId) for the given model index

getWaterChain(String, int) - Method in class org.biojava.nbio.structure.StructureImpl

getWaterChainByPDB(String) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a water Chain based on the 'public' chain name (authId) for the first model

getWaterChainByPDB(String) - Method in class org.biojava.nbio.structure.StructureImpl

getWaterChainByPDB(String, int) - Method in interface org.biojava.nbio.structure.Structure

Retrieve a water Chain based on the 'public' chain name (authId) for the given model index

getWaterChainByPDB(String, int) - Method in class org.biojava.nbio.structure.StructureImpl

getWaterChains() - Method in class org.biojava.nbio.structure.Model

getWaterChains() - Method in interface org.biojava.nbio.structure.Structure

Return all water chains for the first model

getWaterChains() - Method in class org.biojava.nbio.structure.StructureImpl

getWaterChains(int) - Method in interface org.biojava.nbio.structure.Structure

Return all water chains for the given model index

getWaterChains(int) - Method in class org.biojava.nbio.structure.StructureImpl

getWeightedRmsd(Point3d[], Point3d[], double[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP

getWidth() - Method in class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism

Returns the radius of an inscribed sphere, that is tangent to each of the octahedron's faces

getWinSize() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

The window size to look at

getWinSize() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

getX() - Method in interface org.biojava.nbio.structure.Atom

Get coordinate X.

getX() - Method in class org.biojava.nbio.structure.AtomImpl

Get coordinate X.

getXGroup() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getXGroupName() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

getXYZEuler(Matrix) - Static method in class org.biojava.nbio.structure.Calc

Convert a rotation Matrix to Euler angles.

getY() - Method in interface org.biojava.nbio.structure.Atom

Get coordinate Y.

getY() - Method in class org.biojava.nbio.structure.AtomImpl

Get coordinate Y.

getZ() - Method in interface org.biojava.nbio.structure.Atom

Get coordinate Z.

getZ() - Method in class org.biojava.nbio.structure.AtomImpl

Get coordinate Z.

getZYZEuler(Matrix) - Static method in class org.biojava.nbio.structure.Calc

Gets euler angles for a matrix given in ZYZ convention.

GLIDE - org.biojava.nbio.structure.xtal.TransformType

GLOBAL_ALIGN1 - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

GLOBAL_ALIGN2 - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

glycine - org.biojava.nbio.structure.chem.ResidueType

Gotoh - Class in org.biojava.nbio.structure.align.pairwise

a class to perform Gotoh algorithm

Gotoh(Alignable) - Constructor for class org.biojava.nbio.structure.align.pairwise.Gotoh

GRAPH_COMPONENT - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod

GRAPH_COMPONENT - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod

GraphComponentOrderDetector - Class in org.biojava.nbio.structure.symmetry.internal

The GraphOrderDetector transforms the self-alignment into a Graph and extracts its maximally connected Components.

GraphComponentOrderDetector() - Constructor for class org.biojava.nbio.structure.symmetry.internal.GraphComponentOrderDetector

GraphComponentRefiner - Class in org.biojava.nbio.structure.symmetry.internal

The GraphRefiner transforms the self-alignment into a Graph and extracts its maximally connected Components.

GraphComponentRefiner() - Constructor for class org.biojava.nbio.structure.symmetry.internal.GraphComponentRefiner

grayOutCEOrig(Atom[], int, int, CECalculator, Matrix, int, double[], double) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Grays out the main diagonal of a duplicated distance matrix.

grayOutPreviousAlignment(AFPChain, Atom[], int, int, CECalculator, Matrix, int, double[], double) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Grid - Class in org.biojava.nbio.structure.contact

A grid to be used for calculating atom contacts through a spatial hashing algorithm.

Grid(double) - Constructor for class org.biojava.nbio.structure.contact.Grid

Creates a Grid, the cutoff is in the same units as the coordinates (Angstroms if they are atom coordinates) and can be specified to a precision of 0.01.

GridCell - Class in org.biojava.nbio.structure.contact

A grid cell to be used in contact calculation via spatial hashing algorithm.

GridCell(Grid) - Constructor for class org.biojava.nbio.structure.contact.GridCell

Group - Interface in org.biojava.nbio.structure

This is the data structure for a single Group of atoms.

GroupAsa - Class in org.biojava.nbio.structure.asa

A class to store the results of ASA calculations, it can hold ASA values per atom present in Group

GroupAsa(Group) - Constructor for class org.biojava.nbio.structure.asa.GroupAsa

GroupContact - Class in org.biojava.nbio.structure.contact

A pair of residues that are in contact

GroupContact() - Constructor for class org.biojava.nbio.structure.contact.GroupContact

GroupContactSet - Class in org.biojava.nbio.structure.contact

A set of residue-residue contacts.

GroupContactSet() - Constructor for class org.biojava.nbio.structure.contact.GroupContactSet

GroupContactSet(AtomContactSet) - Constructor for class org.biojava.nbio.structure.contact.GroupContactSet

Constructs a GroupContactSet by collapsing the given AtomContactSet into residue-residue (group-group) contacts.

GroupIterator - Class in org.biojava.nbio.structure

An iterator over all groups of a structure.

GroupIterator(Structure) - Constructor for class org.biojava.nbio.structure.GroupIterator

Constructs a GroupIterator object over all models

GroupIterator(Structure, int) - Constructor for class org.biojava.nbio.structure.GroupIterator

Constructs a GroupIterator object over a specific model

GroupToSDF - Class in org.biojava.nbio.structure.io

GroupToSDF() - Constructor for class org.biojava.nbio.structure.io.GroupToSDF

GroupType - Enum in org.biojava.nbio.structure

This contains basic categories for Group types.

GTSlikeScore(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint

guessFiletype(String) - Static method in class org.biojava.nbio.structure.StructureIO

Attempts to guess the type of a structure file based on the extension

guessOrderFromAngle(double, int) - Method in class org.biojava.nbio.structure.align.util.RotationAxis

Returns the rotation order o that gives the lowest value of |2PI / o - theta, given that the value is strictly lower than threshold, for orders o=1,...,maxOrder.

guessPDBID(String) - Static method in class org.biojava.nbio.structure.URLIdentifier

Recognizes PDB IDs that occur at the beginning of name followed by some delimiter.

guessScopDomain(String, ScopDatabase) - Static method in class org.biojava.nbio.structure.align.client.StructureName

Guess a scop domain.

guessSequentialAlignment(Map<Integer, Integer>, boolean) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Takes a potentially non-sequential alignment and guesses a sequential version of it.

GuiWrapper - Class in org.biojava.nbio.structure.align.ce

A class to wrap some of the strucutre.gui classes using Reflection

GuiWrapper() - Constructor for class org.biojava.nbio.structure.align.ce.GuiWrapper

H

H - org.biojava.nbio.structure.Element

HALOGEN - org.biojava.nbio.structure.ElementType

handleChain(Chain, int, List<AbstractCifFileSupplier.WrappedAtom>) - Method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier

has3D() - Method in interface org.biojava.nbio.structure.Group

Return true or false, depending if this group has 3D coordinates or not.

has3D() - Method in class org.biojava.nbio.structure.HetatomImpl

hasAltLoc() - Method in interface org.biojava.nbio.structure.Group

Check if this group has alternate location groups.

hasAltLoc() - Method in class org.biojava.nbio.structure.HetatomImpl

hasAminoAtoms() - Method in interface org.biojava.nbio.structure.Group

Calculate if this group has all atoms required for an amino acid backbone.

hasAminoAtoms() - Method in class org.biojava.nbio.structure.HetatomImpl

Calculate if this group has all atoms required for an amino acid backbone.

hasAnyContact(Collection<Point3d>) - Method in class org.biojava.nbio.structure.contact.Grid

hasAnyContact(Point3d[]) - Method in class org.biojava.nbio.structure.contact.Grid

Fast determination of whether any atoms from a given set fall within the cutoff of iAtoms.

hasAtom(String) - Method in interface org.biojava.nbio.structure.Group

Tell whether a particular atom exists within this group.

hasAtom(String) - Method in class org.biojava.nbio.structure.HetatomImpl

Tell whether a particular atom exists within this group.

hasBond(Atom) - Method in interface org.biojava.nbio.structure.Atom

Test if another atom has a bond to this atom

hasBond(Atom) - Method in class org.biojava.nbio.structure.AtomImpl

Test if another atom has a bond to this atom

hasChain(String) - Method in interface org.biojava.nbio.structure.Structure

Check if a chain with the chainId aymId is contained in this structure.

hasChain(String) - Method in class org.biojava.nbio.structure.StructureImpl

Check if a chain with the chainId aymId is contained in this structure.

hasContact(Atom, Atom) - Method in class org.biojava.nbio.structure.contact.AtomContactSet

hasContact(AtomIdentifier, AtomIdentifier) - Method in class org.biojava.nbio.structure.contact.AtomContactSet

hasContact(ResidueIdentifier, ResidueIdentifier) - Method in class org.biojava.nbio.structure.contact.GroupContactSet

Tell whether the given pair is a contact in this GroupContactSet, in a chain-identifier independent way: contacts happening between different copies of the same Compound(Entity) will be considered equal as long as they have the same residue numbers.

hasContact(Group, Group) - Method in class org.biojava.nbio.structure.contact.GroupContactSet

Tell whether the given group pair is a contact in this GroupContactSet, the comparison is done by matching residue numbers and chain identifiers

hasContact(ResidueNumber, ResidueNumber) - Method in class org.biojava.nbio.structure.contact.GroupContactSet

Tell whether the given pair is a contact in this GroupContactSet, the comparison is done by matching residue numbers and chain identifiers

hasContactsWithinDistance(double) - Method in class org.biojava.nbio.structure.contact.AtomContactSet

Returns true if at least 1 contact from this set is within the given distance.

hasContactToAtom(Point3d[], Point3d[], Point3d, double) - Method in class org.biojava.nbio.structure.contact.GridCell

Tests whether any atom in this cell has a contact with the specified query atom

hasDeuteratedEquiv(Atom, Group) - Static method in class org.biojava.nbio.structure.StructureTools

Check to see if a Hydrogen has a Deuterated brother in the group.

hashCode() - Method in class org.biojava.nbio.structure.align.client.PdbPair

hashCode() - Method in class org.biojava.nbio.structure.align.client.StructureName

hashCode() - Method in class org.biojava.nbio.structure.align.model.AFPChain

hashCode() - Method in class org.biojava.nbio.structure.Author

hashCode() - Method in class org.biojava.nbio.structure.chem.ChemComp

hashCode() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

hashCode() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier

hashCode() - Method in class org.biojava.nbio.structure.contact.Pair

hashCode() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

hashCode() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

hashCode() - Method in class org.biojava.nbio.structure.io.SSBondImpl

hashCode() - Method in class org.biojava.nbio.structure.PdbId

hashCode() - Method in class org.biojava.nbio.structure.ResidueNumber

hashCode() - Method in class org.biojava.nbio.structure.ResidueRange

hashCode() - Method in class org.biojava.nbio.structure.ResidueRangeAndLength

hashCode() - Method in class org.biojava.nbio.structure.scop.ScopDescription

hashCode() - Method in class org.biojava.nbio.structure.secstruc.BetaBridge

hashCode() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc

hashCode() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo

hashCode() - Method in class org.biojava.nbio.structure.Site

hashCode() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup

hashCode() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature

hashCode() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

hasJournalArticle() - Method in class org.biojava.nbio.structure.PDBHeader

Return whether or not the entry has an associated journal article or publication.

hasJournalArticle() - Method in interface org.biojava.nbio.structure.Structure

Return whether or not the entry has an associated journal article or ation.

hasJournalArticle() - Method in class org.biojava.nbio.structure.StructureImpl

Return whether or not the entry has an associated journal article or publication.

hasMore() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator

hasNcsOps() - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder

hasNext() - Method in class org.biojava.nbio.structure.AtomIterator

Is there a next atom ?

hasNext() - Method in class org.biojava.nbio.structure.GroupIterator

is there a group after the current one in the structure?

hasNonDeuteratedEquiv(Atom, Group) - Static method in class org.biojava.nbio.structure.StructureTools

Check to see if an Deuterated atom has a non deuterated brother in the group.

hasNonPolyChain(String) - Method in interface org.biojava.nbio.structure.Structure

Check if a non polymeric chain with chainId asymId is contained in the structure.

hasNonPolyChain(String) - Method in class org.biojava.nbio.structure.StructureImpl

Check if a non polymeric chain with chainId asymId is contained in the structure.

hasParent() - Method in class org.biojava.nbio.structure.chem.ChemComp

hasPdbChain(String) - Method in interface org.biojava.nbio.structure.Structure

Check if a chain with chain name authId is contained in the structure

hasPdbChain(String) - Method in class org.biojava.nbio.structure.StructureImpl

Check if a chain with chain name authId is contained in the structure

HBond - Class in org.biojava.nbio.structure.secstruc

Container that represents a hidrogen bond.

HBond() - Constructor for class org.biojava.nbio.structure.secstruc.HBond

HBond(HBond) - Constructor for class org.biojava.nbio.structure.secstruc.HBond

HBOND - org.biojava.nbio.structure.BondType

HBONDHIGHENERGY - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc

higher limit for H-bond energy

HBONDLOWENERGY - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc

Minimal H-bond energy in cal/mol

He - org.biojava.nbio.structure.Element

HelicalRepeatUnit - Class in org.biojava.nbio.structure.symmetry.core

HelicalRepeatUnit(QuatSymmetrySubunits) - Constructor for class org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit

Helix - Class in org.biojava.nbio.structure.symmetry.core

Helix() - Constructor for class org.biojava.nbio.structure.symmetry.core.Helix

helix3 - org.biojava.nbio.structure.secstruc.SecStrucType

helix4 - org.biojava.nbio.structure.secstruc.SecStrucType

helix5 - org.biojava.nbio.structure.secstruc.SecStrucType

HelixAxisAligner - Class in org.biojava.nbio.structure.symmetry.axis

HelixAxisAligner(QuatSymmetryResults) - Constructor for class org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner

HelixExtender - Class in org.biojava.nbio.structure.symmetry.core

HelixExtender(QuatSymmetrySubunits, Helix) - Constructor for class org.biojava.nbio.structure.symmetry.core.HelixExtender

HelixLayers - Class in org.biojava.nbio.structure.symmetry.core

HelixLayers() - Constructor for class org.biojava.nbio.structure.symmetry.core.HelixLayers

HelixSolver - Class in org.biojava.nbio.structure.symmetry.core

HelixSolver(QuatSymmetrySubunits, int, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.HelixSolver

HETATM - org.biojava.nbio.structure.GroupType

The type for hetero groups (everything else)

HetatomImpl - Class in org.biojava.nbio.structure

Generic Implementation of a Group interface.

HetatomImpl() - Constructor for class org.biojava.nbio.structure.HetatomImpl

Construct a Hetatom instance.

HetatomImpl.PerformanceBehavior - Enum in org.biojava.nbio.structure

Behaviors for how to balance memory vs.

HEXAGONAL - org.biojava.nbio.structure.xtal.BravaisLattice

Hf - org.biojava.nbio.structure.Element

Hg - org.biojava.nbio.structure.Element

hieFileName - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation

Ho - org.biojava.nbio.structure.Element

Homology - org.biojava.nbio.structure.cath.CathCategory

HYDROPHOBIC - org.biojava.nbio.structure.BondType

hypot(double, double) - Static method in class org.biojava.nbio.structure.jama.Maths

sqrt(a^2 + b^2) without under/overflow.

I

I - org.biojava.nbio.structure.Element

IcosahedralSampler - Class in org.biojava.nbio.structure.symmetry.geometry

Represents an even coverage of quaternion space by 60 points.

Icosahedron - Class in org.biojava.nbio.structure.symmetry.geometry

Icosahedron() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

IdenticalSequenceFamily - org.biojava.nbio.structure.cath.CathCategory

identity(int, int) - Static method in class org.biojava.nbio.structure.jama.Matrix

Generate identity matrix

IDENTITY - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder

IDENTITY - Static variable in class org.biojava.nbio.structure.xtal.CrystalTransform

IDENTITY_THRESHOLD - Static variable in class org.biojava.nbio.structure.io.EntityFinder

Identity value for 2 chains to be considered part of same entity

IdentityMap() - Constructor for class org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap

IdxComparator - Class in org.biojava.nbio.structure.align.helper

IdxComparator() - Constructor for class org.biojava.nbio.structure.align.helper.IdxComparator

In - org.biojava.nbio.structure.Element

index - Variable in class org.biojava.nbio.structure.align.helper.GapArray

indexOf(String, String) - Method in class org.biojava.nbio.structure.symmetry.utils.BlastClustReader

IndexPair - Class in org.biojava.nbio.structure.align.helper

IndexPair() - Constructor for class org.biojava.nbio.structure.align.helper.IndexPair

IndexPair(short, short) - Constructor for class org.biojava.nbio.structure.align.helper.IndexPair

INFRARED_SPECTROSCOPY - org.biojava.nbio.structure.ExperimentalTechnique

initializeBreakFlag(boolean[][]) - Method in interface org.biojava.nbio.structure.align.ce.MatrixListener

initializeCellTranslations() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

initPaths() - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Should be called whenever any of the path variables change.

initStructure(int, int, int, int, int, String) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

initSumOfDistances(int, int, int, int, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

initSumOfDistances(int, int, int, int, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

insertSeqResGroup(Chain, Group, int) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Insert the group in the given position in the sequence.

InterfaceFinder - Class in org.biojava.nbio.structure.contact

A class containing methods to find interfaces in a given structure.

InterfaceFinder(Structure) - Constructor for class org.biojava.nbio.structure.contact.InterfaceFinder

inverse() - Method in class org.biojava.nbio.structure.jama.Matrix

Matrix inverse or pseudoinverse

invert(Atom) - Static method in class org.biojava.nbio.structure.Calc

invertAlignment(AFPChain) - Method in class org.biojava.nbio.structure.align.ce.CeCPMain

Swaps the order of structures in an AFPChain

IONIC - org.biojava.nbio.structure.BondType

Ir - org.biojava.nbio.structure.Element

IS_DOMAIN_ASSEMBLY - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser

Deprecated way of indicating there is an assembly.

IS_REPRESENTATIVE - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser

Indicates a manual representative

isAlignSeqRes() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.

isAminoAcid() - Method in interface org.biojava.nbio.structure.Group

Check if this group is an aminoacid group, from the definition in Chemical Component Dictionary

isAminoAcid() - Method in class org.biojava.nbio.structure.HetatomImpl

isAutoFetch() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

isBend() - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

isBetaStrand() - Method in enum org.biojava.nbio.structure.secstruc.SecStrucType

A Beta-Strand is an extended set of sequential Bridges that, together with other Beta-Strands, is part of a Beta-Sheet.

isBioAssembly() - Method in class org.biojava.nbio.structure.align.client.StructureName

isBiologicalAssembly() - Method in interface org.biojava.nbio.structure.Structure

Get flag that indicates if this structure is a biological assembly

isBiologicalAssembly() - Method in class org.biojava.nbio.structure.StructureImpl

Gets flag that indicates if this structure is a biological assembly

isCacheEnabled() - Method in class org.biojava.nbio.structure.domain.SerializableCache

isCathID() - Method in class org.biojava.nbio.structure.align.client.StructureName

isCellReasonable() - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Checks whether the dimensions of this crystal cell are reasonable for protein crystallography: if all 3 dimensions are below 10.0 the cell is considered unrealistic and false returned

isChalcogen() - Method in enum org.biojava.nbio.structure.Element

Returns true if Element is a chalcogen (O, S, Se, Te, Po).

isCompatible(ResidueGroup) - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup

Determine if two Residuegroups (maximally connected components of the alignment Graph) are compatible, based in the following criterion:

isComplete() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

isConnected(AminoAcid, AminoAcid) - Static method in class org.biojava.nbio.structure.Calc

Test if two amino acids are connected, i.e.

isCrystallographic() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique

isCrystallographic() - Method in interface org.biojava.nbio.structure.Structure

Test if this structure is a crystallographic structure, i.e.

isCrystallographic() - Method in class org.biojava.nbio.structure.StructureImpl

Whether this Structure is a crystallographic structure or not.

isCrystallographic(Set<ExperimentalTechnique>) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique

Given a Set of ExperimentalTechniques returns true if at least one is crystallographic

isDefined() - Method in class org.biojava.nbio.structure.align.util.RotationAxis

isDoAngleCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

isDoDensityCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

isDoDistanceCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

isDomainSplit() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

isDoRMSCheck() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

isDownloadAll() - Method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

By default this provider will download only some of the ChemComp files.

isEcodDomain() - Method in class org.biojava.nbio.structure.align.client.StructureName

isEmpty() - Method in class org.biojava.nbio.structure.chem.ChemComp

Indicates whether this compound was created with

isEnantiomorphic() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

isEquivalent(CrystalTransform) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

Returns true if the given CrystalTransform is equivalent to this one.

isErrorXML(String) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser

returns true if the alignment XML contains an error message

isFile() - Method in class org.biojava.nbio.structure.align.client.StructureName

Indicates that the identifier was determined to correspond to a file.

isFlexible() - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

isFractionalTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

Tells whether this transformation contains a fractional translational component (whatever its rotational component).

isFullRank() - Method in class org.biojava.nbio.structure.jama.QRDecomposition

Is the matrix full rank?

isGaps() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

isGuiModuleInstalled() - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

isHalogen() - Method in enum org.biojava.nbio.structure.Element

Returns true if Element is a halogen (F, Cl, Br, I, At).

isHeaderOnly() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Parse only the PDB file header out of the files

isHeavyAtom() - Method in enum org.biojava.nbio.structure.Element

Returns true is the Element is an not Hydrogen (or an isotope of Hydrogen).

isHelixType() - Method in enum org.biojava.nbio.structure.secstruc.SecStrucType

Helix type can be 3-10 helix, pi-helix or alpha-helix.

isHetAtomInFile() - Method in interface org.biojava.nbio.structure.Group

Tells whether the group is annotated as HETATM in the file.

isHetAtomInFile() - Method in class org.biojava.nbio.structure.HetatomImpl

isHeteroAtom() - Method in enum org.biojava.nbio.structure.Element

Returns true if Element is not Hydrogen and not Carbon.

isHighConfidenceScores(double, double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Whether the subunits can be considered "identical" by sequence alignment.

isHomomeric() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Returns true if the 2 molecules of this interface are the same entity (i.e.

isHydrogen() - Method in enum org.biojava.nbio.structure.Element

Returns true if this Element is Hydrogen.

isIdenticalByEntityIdTo(SubunitCluster) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Tells whether the other SubunitCluster contains exactly the same Subunit.

isIdenticalTo(SubunitCluster) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Tells whether the other SubunitCluster contains exactly the same Subunit.

isIdentity() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Tells whether this transformation is in identity.

isIdentity() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

Tells whether this transformation is the identity: no rotation and no translation

isInfinite() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Returns true if the transformation applied to the second molecule of this interface has an infinite character (pure translation or screw rotation) and both molecules of the interface have the same asymmetric unit identifier (chain id): in such cases the interface would lead to infinite fiber-like (linear or helical) assemblies

isInfinite() - Method in enum org.biojava.nbio.structure.xtal.TransformType

Tells whether the transform type produces infinite assemblies if interface happens between identical chains

isInternalSymmetry() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

The internal symmetry option divides each Subunit of each SubunitCluster into its internally symmetric repeats.

isIsologous() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Tell whether the interface is isologous, i.e.

isJoinFast() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

isJoinPlo() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

isLocal() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

A local result means that only a subset of the original Subunits was used for symmetry determination.

isLocalLimitsExceeded() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

isLocalLimitsExceeded(Set<?>) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

isMetal() - Method in enum org.biojava.nbio.structure.Element

Returns true if ElementType is a metal.

isMetal() - Method in enum org.biojava.nbio.structure.ElementType

Returns true if ElementType is a metal.

isMetalloid() - Method in enum org.biojava.nbio.structure.Element

Returns true if ElementType is a metalloid.

isMetalloid() - Method in enum org.biojava.nbio.structure.ElementType

Returns true if ElementType is a metalloid.

isNmr() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique

isNmr() - Method in interface org.biojava.nbio.structure.Structure

Test if this structure is an NMR structure.

isNmr() - Method in class org.biojava.nbio.structure.StructureImpl

Whether this Structure is a NMR structure or not.

isNmr(Set<ExperimentalTechnique>) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique

Given a Set of ExperimentalTechniques returns true if at least one is NMR

isNonMetal() - Method in enum org.biojava.nbio.structure.Element

Returns true if ElementType is a non-metal.

isNonMetal() - Method in enum org.biojava.nbio.structure.ElementType

Returns true if ElementType is a non-metal.

isNonsingular() - Method in class org.biojava.nbio.structure.jama.LUDecomposition

Is the matrix nonsingular?

isNonStandardCoordFrameConvention() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Whether this structure is non-standard coordinate frame convention, for which our scale matrix calculation and thus the crystal reconstruction will be incorrect.

isNonStandardSg() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Whether this structure has a non-standard space group not supported by Biojava.

isNoOverlap() - Method in class org.biojava.nbio.structure.contact.Grid

Tells whether (after having added atoms to grid) the i and j grids are not overlapping.

isNucleicAcid() - Method in interface org.biojava.nbio.structure.Chain

Tell whether given chain is DNA or RNA

isNucleicAcid() - Method in class org.biojava.nbio.structure.ChainImpl

isNucleotide() - Method in interface org.biojava.nbio.structure.Group

Check if this group is a nucleotide group, from the definition in Chemical Component Dictionary

isNucleotide() - Method in class org.biojava.nbio.structure.HetatomImpl

isNucleotide(String) - Static method in class org.biojava.nbio.structure.StructureTools

Test if the three-letter code of an ATOM entry corresponds to a nucleotide or to an aminoacid.

isOnTheFly() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

On-the-fly Jmol bioassembly generation.

isOptimizeAlignment() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Whether the CE algorithm should extend the best found trace with dynamic programming, while keeping RMSD at about the same level.

isOptimizeAlignment() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.

isOptimizeAlignment() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.

isOutputPDB() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

When writing the results to a file, don;t write as XML but write aligned PDB file

isParseBioAssembly() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should the biological assembly info (REMARK 350) be parsed from the PDB file?

isParseCAOnly() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

The flag if only the C-alpha atoms of the structure should be parsed.

isParseSecStruc() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Is secondary structure assignment being parsed from the file? default is null

isPdbId() - Method in class org.biojava.nbio.structure.align.client.StructureName

isPolymeric() - Method in interface org.biojava.nbio.structure.Group

Check if this group is a polymeric group, from the definition in Chemical Component Dictionary

isPolymeric() - Method in class org.biojava.nbio.structure.HetatomImpl

isPrint - Static variable in class org.biojava.nbio.structure.align.ce.CECalculator

isPrint - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

isPrintCE() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

Display the output string in CE style

isPrintFatCat() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

isPrintXML() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

isProtein() - Method in interface org.biojava.nbio.structure.Chain

Tell whether given chain is a protein chain

isProtein() - Method in class org.biojava.nbio.structure.ChainImpl

isPseudoStoichiometric() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

isPseudoStoichiometric() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

isPseudoStoichiometric() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

A pseudostoichiometric SubunitCluster was obtained using the SubunitClustererMethod.STRUCTURE similarity, or SubunitClustererMethod.SEQUENCE similarity with low scores.

isPublished() - Method in class org.biojava.nbio.structure.JournalArticle

isPureCrystalTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

Tells whether this transformation is a pure crystal lattice translation, i.e.

isPureNonPolymer() - Method in interface org.biojava.nbio.structure.Chain

Returns true if the given chain is composed of non-polymeric (including water) groups only.

isPureNonPolymer() - Method in class org.biojava.nbio.structure.ChainImpl

isPureTranslation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

Tells whether this transformation is a pure translation: either a pure crystal (lattice) translation or a fractional (within unit cell) translation: space groups Ixxx, Cxxx, Fxxx have operators with fractional translations within the unit cell.

isReachable() - Method in class org.biojava.nbio.structure.scop.ScopMirror

isRefined() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

isReplaced(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

isReplaced(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

isReplacer(String) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

isReplacer(ChemComp) - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

isRotation() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

Tells whether this transformation is a rotation disregarding the translational component, i.e.

isScopName() - Method in class org.biojava.nbio.structure.align.client.StructureName

isScrew() - Method in enum org.biojava.nbio.structure.xtal.TransformType

Tells whether the transform type is a screw or glide plane

isSequentialAlignment() - Method in class org.biojava.nbio.structure.align.model.AFPChain

Get whether this alignment has the normal topology, ie the residues aligned in each block increase sequentially over the original protein.

isSequentialAlignment(AFPChain, boolean) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Checks that the alignment given by afpChain is sequential.

isShortAlign() - Method in class org.biojava.nbio.structure.align.model.AFPChain

isShortCompatible(String) - Static method in class org.biojava.nbio.structure.PdbId

Checks whether an Extended PDB ID is shortable, assuming it is a valid extended PDB ID.

isShow3d() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

isShowAFPRanges() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

isShowAFPRanges() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

isShowMenu() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

isSignificant() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

Conditions checked are: score above the threshold, number of repeats higher than 1 and refinement succeeded.

isSignificantResult() - Method in class org.biojava.nbio.structure.align.model.AFPChain

isSPD() - Method in class org.biojava.nbio.structure.jama.CholeskyDecomposition

Is the matrix symmetric and positive definite?

isStandard() - Method in class org.biojava.nbio.structure.chem.ChemComp

isStandardChemComp(ChemComp) - Static method in class org.biojava.nbio.structure.chem.ChemCompTools

isSupersededBy(QuatSymmetryResults) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

Determine if this symmetry result is a subset of the other Symmetry result.

isSymRelated() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Tells whether the interface corresponds to one mediated by crystallographic symmetry, i.e.

isTryAllCPs() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

isUnaryExpression(String) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools

Checks if the passed in expression is a unary operator expression Example: (1,2,3) or (1-60) are unary operator expressions (1-60)(61-88) is a binary operator expression, representing a cartesian product of the two parenthesised lists

isURL() - Method in class org.biojava.nbio.structure.align.client.StructureName

isUseEntityIdForSeqIdentityDetermination() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Whether to use the entity id of subunits to infer that sequences are identical.

isUseGlobalMetrics() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use metrics calculated relative to the whole sequence or structure, rather than the aligned part only

isUseRMSD() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use RMSD for evaluating structure similarity

isUseSequenceCoverage() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use sequence coverage for evaluating sequence similarity

isUseStructureCoverage() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use structure coverage for evaluating sequence similarity

isUseTMScore() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use TMScore for evaluating structure similarity

isValidExtendedPdbId(String) - Static method in class org.biojava.nbio.structure.PdbId

Check whether id represents a valid PDB ID in the extended format.

isValidShortPdbId(String) - Static method in class org.biojava.nbio.structure.PdbId

Check whether id represents a valid PDB ID in the short format.

isWater() - Method in interface org.biojava.nbio.structure.Group

Determines if this group is water.

isWater() - Method in class org.biojava.nbio.structure.HetatomImpl

isWaterOnly() - Method in interface org.biojava.nbio.structure.Chain

Tests if a chain is consisting of water molecules only

isWaterOnly() - Method in class org.biojava.nbio.structure.ChainImpl

iterator() - Method in class org.biojava.nbio.structure.AugmentedResidueRange

Returns a new Iterator over every ResidueNumber in this ResidueRange.

iterator() - Method in class org.biojava.nbio.structure.contact.AtomContactSet

iterator() - Method in class org.biojava.nbio.structure.contact.GroupContactSet

iterator() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

iterator() - Method in interface org.biojava.nbio.structure.Group

Get an Atom Iterator.

iterator() - Method in class org.biojava.nbio.structure.HetatomImpl

iterator() - Method in class org.biojava.nbio.structure.math.SymbolTable

Return an Iterator for the keys in the table.

iterator() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup

iterator() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

iterator(AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRange

Returns a new Iterator over every ResidueNumber in this ResidueRange.

iterator(AtomPositionMap) - Method in class org.biojava.nbio.structure.ResidueRangeAndLength

Returns a new Iterator over every ResidueNumber in this ResidueRange.

J

jointFragments(JointFragments[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener

JointFragments - Class in org.biojava.nbio.structure.align.helper

A utility class that defines which set of atoms are considered to be on equivalent positions.

JointFragments() - Constructor for class org.biojava.nbio.structure.align.helper.JointFragments

JournalArticle - Class in org.biojava.nbio.structure

PDB-specific

JournalArticle() - Constructor for class org.biojava.nbio.structure.JournalArticle

K

K - org.biojava.nbio.structure.Element

key - Variable in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements

keys() - Method in class org.biojava.nbio.structure.math.SymbolTable

Return an Iterable for the keys in the table.

keySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

Kr - org.biojava.nbio.structure.Element

L

La - org.biojava.nbio.structure.Element

Ladder - Class in org.biojava.nbio.structure.secstruc

A Ladder is a set of one or more consecutive bridges of identical type.

Ladder() - Constructor for class org.biojava.nbio.structure.secstruc.Ladder

LANTHANOID - org.biojava.nbio.structure.ElementType

LAST_REMEDIATION_DATE - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory

Date of the latest PDB file remediation

LATEST_VERSION - Static variable in class org.biojava.nbio.structure.cath.CathFactory

LATEST_VERSION - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

lBetaPeptideCGammaLinking - org.biojava.nbio.structure.chem.ResidueType

lDNALinking - org.biojava.nbio.structure.chem.ResidueType

LEFT - org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint

length() - Method in interface org.biojava.nbio.structure.align.multiple.Block

Returns the total number of aligned positions (columns) in the Block.

length() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

length() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Returns the total number of aligned residues (columns) in the alignment: the sum of all Block lengths.

length() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

length() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Returns the total number of aligned residues (columns) in the multiple alignment: the sum of all BlockSet lengths.

length() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

length() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

The length of the alignment is the number of Subunit equivalencies it contains.

length() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

LESS_MEMORY_SLOWER_PERFORMANCE - org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior

Try to minimize memory consumption, at the price of slower speed when accessing atoms by name

lGammaPeptideCDeltaLinking - org.biojava.nbio.structure.chem.ResidueType

Li - org.biojava.nbio.structure.Element

LikeSequenceFamily - org.biojava.nbio.structure.cath.CathCategory

LINEAR - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass

lineSplit - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration

lineSplit - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory

LinkRecord(String, String, String, String, String, String, String, String, String, String, String, String, String, String) - Constructor for class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

load() - Static method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

Loads the SIFTS mapping.

load(boolean) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

Loads the SIFTS mapping.

loadFromDirectAccess() - Method in class demo.DemoMMCIFReader

An example demonstrating how to directly use the mmCif file parsing classes.

loadSimple() - Method in class demo.DemoMMCIFReader

A basic example how to load an mmCif file and get a Structure object

loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.align.client.StructureName

loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier

loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.cath.CathDomain

loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.PassthroughIdentifier

Passthrough identifiers don't know how to load a structure

loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.scop.ScopDomain

loadStructure(AtomCache) - Method in interface org.biojava.nbio.structure.StructureIdentifier

Loads a structure encompassing the structure identified.

loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.SubstructureIdentifier

Loads the complete structure based on SubstructureIdentifier.getPdbId().

loadStructure(AtomCache) - Method in class org.biojava.nbio.structure.URLIdentifier

Load the structure from the URL

loadStructureFromBcifByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

loadStructureFromBcifByPdbId(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache

loadStructureFromCache() - Method in class demo.DemoLoadStructure

loadStructureFromCifByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

loadStructureFromCifByPdbId(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache

loadStructureFromMmtfByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

loadStructureFromMmtfByPdbId(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Load a Structure from MMTF either from the local file system.

loadStructureFromPdbByPdbId(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

loadStructureFromPdbByPdbId(PdbId) - Method in class org.biojava.nbio.structure.align.util.AtomCache

loadStructureIO() - Method in class demo.DemoLoadStructure

LOCAL_ONLY - org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

Never fetch from the server; Throw errors for missing files

LocalPDBDirectory - Class in org.biojava.nbio.structure.io

Superclass for classes which download and interact with the PDB's FTP server, specifically PDBFileReader and CifFileReader.

LocalPDBDirectory() - Constructor for class org.biojava.nbio.structure.io.LocalPDBDirectory

LocalPDBDirectory(String) - Constructor for class org.biojava.nbio.structure.io.LocalPDBDirectory

Subclasses should provide default and single-string constructors.

LocalPDBDirectory.FetchBehavior - Enum in org.biojava.nbio.structure.io

Controls when the class should fetch files from the ftp server

LocalPDBDirectory.ObsoleteBehavior - Enum in org.biojava.nbio.structure.io

Behaviors for when an obsolete structure is requested.

LocalProteinDomainParser - Class in org.biojava.nbio.structure.domain

Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures.

LocalScopDatabase - Interface in org.biojava.nbio.structure.scop

Classes which implement ScopDatabase in a way which allows them to serve queries without accessing the internet should implement this interface instead.

logger - Static variable in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

logger - Static variable in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner

lPeptideAminoTerminus - org.biojava.nbio.structure.chem.ResidueType

lPeptideCarboxyTerminus - org.biojava.nbio.structure.chem.ResidueType

lPeptideLinking - org.biojava.nbio.structure.chem.ResidueType

lpolysaccharide - org.biojava.nbio.structure.chem.PolymerType

polysaccharide(L)

Lr - org.biojava.nbio.structure.Element

lRNALinking - org.biojava.nbio.structure.chem.ResidueType

lSaccharide - org.biojava.nbio.structure.chem.ResidueType

lSaccharide14and14linking - org.biojava.nbio.structure.chem.ResidueType

lSaccharide14and16linking - org.biojava.nbio.structure.chem.ResidueType

lu() - Method in class org.biojava.nbio.structure.jama.Matrix

LU Decomposition

Lu - org.biojava.nbio.structure.Element

LUDecomposition - Class in org.biojava.nbio.structure.jama

LU Decomposition.

LUDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.LUDecomposition

LU Decomposition provides a data structure to access L, U and piv.

M

MACROLIDE - org.biojava.nbio.structure.EntityType

Macrolide.

main(String[]) - Static method in class demo.ChemCompDistribution

main(String[]) - Static method in class demo.DemoAsa

main(String[]) - Static method in class demo.DemoAtomCache

main(String[]) - Static method in class demo.DemoBerkeleyScop

main(String[]) - Static method in class demo.DemoBioAssemblies

main(String[]) - Static method in class demo.DemoCATH

main(String[]) - Static method in class demo.DemoCE

main(String[]) - Static method in class demo.DemoCeSymm

main(String[]) - Static method in class demo.DemoChangeChemCompProvider

main(String[]) - Static method in class demo.DemoCommandLineStartup

main(String[]) - Static method in class demo.DemoContacts

main(String[]) - Static method in class demo.DemoCrystalInterfaces

main(String[]) - Static method in class demo.DemoDomainsplit

main(String[]) - Static method in class demo.DemoFATCAT

main(String[]) - Static method in class demo.DemoLoadSecStruc

main(String[]) - Static method in class demo.DemoLoadStructure

main(String[]) - Static method in class demo.DemoMMCIFReader

main(String[]) - Static method in class demo.DemoMmcifToPdbConverter

main(String[]) - Static method in class demo.DemoMmtfReader

Main function to run the demo

main(String[]) - Static method in class demo.DemoMmtfWriter

main(String[]) - Static method in class demo.DemoMultipleMC

main(String[]) - Static method in class demo.DemoQsAlign

main(String[]) - Static method in class demo.DemoSCOP

main(String[]) - Static method in class demo.DemoSecStrucCalc

main(String[]) - Static method in class demo.DemoSymmetry

main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain

main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.CeMain

Example Parameters: -pdbFilePath /tmp -autoFetch -printCE -pdb1 1cnv -pdb2 3cna

main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.CeSideChainMain

main(String[]) - Static method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain

main(String[]) - Static method in class org.biojava.nbio.structure.align.fatcat.FatCat

See demo/FatCatDemo.java for an example how to run.

main(String[]) - Static method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner

main(String[]) - Static method in class org.biojava.nbio.structure.align.StructurePairAligner

example usage of this class

main(String[]) - Static method in class org.biojava.nbio.structure.Calc

main(String[]) - Static method in class org.biojava.nbio.structure.ecod.EcodInstallation

main(String[]) - Static method in class org.biojava.nbio.structure.io.FastaAFPChainConverter

Prints out the XML representation of an AFPChain from a file containing exactly two FASTA sequences.

main(String[]) - Static method in class org.biojava.nbio.structure.io.MMTFFileReader

main(String[]) - Static method in class org.biojava.nbio.structure.PDBStatus

makeBonds() - Method in class org.biojava.nbio.structure.io.BondMaker

Creates bond objects and corresponding references in Atom objects: peptide bonds: inferred from sequence and distances nucleotide bonds: inferred from sequence and distances intra-group (residue) bonds: read from the chemical component dictionary, via ChemCompProvider

mandatoryArgs - Static variable in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor

mapSeqresRecords(Chain, Chain) - Method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner

Map the seqRes groups to the atomRes chain.

marshal(List<String>) - Method in class org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter

mat - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

mat - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

match(char, char, boolean) - Static method in class org.biojava.nbio.structure.basepairs.BasePairParameters

This returns true if a is the complement of b, false otherwise.

matches(Group) - Method in interface org.biojava.nbio.structure.AtomPositionMap.GroupMatcher

matchSequenceToStructure(ProteinSequence, Structure) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher

Given a sequence and the corresponding Structure, get the ResidueNumber for each residue in the sequence.

Maths - Class in org.biojava.nbio.structure.jama

Maths() - Constructor for class org.biojava.nbio.structure.jama.Maths

Matrices - Class in org.biojava.nbio.structure.geometry

Matrices contains static methods to operate and transform matrices used in 3D geometry (transformation matrices and rotation matrices).

Matrix - Class in org.biojava.nbio.structure.jama

Jama = Java Matrix class.

Matrix(double[][]) - Constructor for class org.biojava.nbio.structure.jama.Matrix

Construct a matrix from a 2-D array.

Matrix(double[][], int, int) - Constructor for class org.biojava.nbio.structure.jama.Matrix

Construct a matrix quickly without checking arguments.

Matrix(double[], int) - Constructor for class org.biojava.nbio.structure.jama.Matrix

Construct a matrix from a one-dimensional packed array

Matrix(int, int) - Constructor for class org.biojava.nbio.structure.jama.Matrix

Construct an m-by-n matrix of zeros.

Matrix(int, int, double) - Constructor for class org.biojava.nbio.structure.jama.Matrix

Construct an m-by-n constant matrix.

matrixFromEuler(double, double, double) - Static method in class org.biojava.nbio.structure.Calc

This conversion uses NASA standard aeroplane conventions as described on page: http://www.euclideanspace.com/maths/geometry/rotations/euler/index.htm Coordinate System: right hand Positive angle: right hand Order of euler angles: heading first, then attitude, then bank.

matrixInOptimizer(double[][]) - Method in interface org.biojava.nbio.structure.align.ce.MatrixListener

MatrixListener - Interface in org.biojava.nbio.structure.align.ce

max() - Method in class org.biojava.nbio.structure.math.SymbolTable

Return the largest key in the table.

MAX_ATOMS - Static variable in class org.biojava.nbio.structure.io.FileParsingParameters

The maximum number of atoms we will add to a structure, this protects from memory overflows in the few really big protein structures.

MAX_CUTS - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

MAX_PEPTIDE_BOND_LENGTH - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc

max distance CA atoms in peptide bond (backbone discontinuity)

MAXCONT - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

MAXDOM - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

maxGapSize - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

maxGapSize - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

MAXLEN - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

maxNrIterationsForOptimization - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

maxOptRMSD - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

maxOptRMSD - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

MAXSIZE - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

MC_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

Md - org.biojava.nbio.structure.Element

mergeIdentical(SubunitCluster) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Merges the other SubunitCluster into this one if it contains exactly the same Subunit.

mergeIdenticalByEntityId(SubunitCluster) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Merges the other SubunitCluster into this one if it contains exactly the same Subunit.

mergeSequence(SubunitCluster, SubunitClustererParameters) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).

mergeSequence(SubunitCluster, SubunitClustererParameters, Alignments.PairwiseSequenceAlignerType, GapPenalty, SubstitutionMatrix<AminoAcidCompound>) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Merges the other SubunitCluster into this one if their representatives sequences are similar (according to the criteria in params).

mergeStructure(SubunitCluster, SubunitClustererParameters) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

Merges the other SubunitCluster into this one if their representative Atoms are structurally similar (according to the criteria in params).

METAL - org.biojava.nbio.structure.BondType

MetalBondConsumer - Interface in org.biojava.nbio.structure.io.cif

Consume metal bond data.

MetalBondConsumerImpl - Class in org.biojava.nbio.structure.io.cif

Created by andreas on 6/9/16.

MetalBondConsumerImpl() - Constructor for class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl

MetalBondConverter - Class in org.biojava.nbio.structure.io.cif

Created by andreas on 6/6/16.

MetalBondConverter() - Constructor for class org.biojava.nbio.structure.io.cif.MetalBondConverter

MetalBondDistance - Class in org.biojava.nbio.structure.chem

A bean that contains cutoffs for correctly detecting metal bonds.

MetalBondDistance() - Constructor for class org.biojava.nbio.structure.chem.MetalBondDistance

METALLOID - org.biojava.nbio.structure.ElementType

Mg - org.biojava.nbio.structure.Element

mid - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange

midpoint of the alignment

min() - Method in class org.biojava.nbio.structure.math.SymbolTable

Return the smallest key in the table.

MIN_DOMAIN_LENGTH - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

MIN_PDB_FILE_SIZE - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory

Minimum size for a valid structure file (CIF or PDB), in bytes

MIN_VALID_CELL_SIZE - Static variable in class org.biojava.nbio.structure.xtal.CrystalCell

minCPLength - Variable in class org.biojava.nbio.structure.align.ce.CECPParameters

minCPLength - Variable in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

MINDIST - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc

min distance between two residues

minus(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

C = A - B

minusEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

A = A - B

MismatchedBasePairParameters - Class in org.biojava.nbio.structure.basepairs

This class allows for finding inter-strand base pairs that are not necessarily canonical Watson-Crick pairs.

MismatchedBasePairParameters(Structure, boolean, boolean, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This constructor is used to create the TertiaryBasePairParameters object.

MMCIF_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration

MMTF - org.biojava.nbio.structure.io.StructureFiletype

MMTF_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration

MMTF_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.MMTFFileReader

MMTF_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.MMTFFileReader

MmtfActions - Class in org.biojava.nbio.structure.io.mmtf

A class of functions for reading and writing Biojava structures using MMTF

MmtfActions() - Constructor for class org.biojava.nbio.structure.io.mmtf.MmtfActions

MMTFFileReader - Class in org.biojava.nbio.structure.io

A class to read MMTF files and cache them locally.

MMTFFileReader() - Constructor for class org.biojava.nbio.structure.io.MMTFFileReader

Constructs a new MMTFFileReader, initializing the extensions member variable.

MMTFFileReader(String) - Constructor for class org.biojava.nbio.structure.io.MMTFFileReader

Constructs a new MMTFFileReader, initializing the extensions member variable.

MmtfStructureReader - Class in org.biojava.nbio.structure.io.mmtf

A biojava specific structure inflator for MMTF.

MmtfStructureReader() - Constructor for class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

Instantiates a new bio java structure decoder.

MmtfStructureWriter - Class in org.biojava.nbio.structure.io.mmtf

Class to take Biojava structure data and covert to the DataApi for encoding.

MmtfStructureWriter(Structure, StructureAdapterInterface) - Constructor for class org.biojava.nbio.structure.io.mmtf.MmtfStructureWriter

Pass data from Biojava structure to another generic output type.

MmtfSummaryDataBean - Class in org.biojava.nbio.structure.io.mmtf

Class to store the summary data for a given structure.

MmtfSummaryDataBean() - Constructor for class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

MmtfUtils - Class in org.biojava.nbio.structure.io.mmtf

A utils class of functions needed for Biojava to read and write to mmtf.

MmtfUtils() - Constructor for class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Mn - org.biojava.nbio.structure.Element

Mo - org.biojava.nbio.structure.Element

Model - Class in org.biojava.nbio.structure

An internal utility class for StructureImpl to make it easier to manage poly and nonpoly chains.

Model() - Constructor for class org.biojava.nbio.structure.Model

MomentsOfInertia - Class in org.biojava.nbio.structure.geometry

The moment of inertia, otherwise known as the angular mass or rotational inertia, of a rigid body determines the torque needed for a desired angular acceleration about a rotational axis.

MomentsOfInertia() - Constructor for class org.biojava.nbio.structure.geometry.MomentsOfInertia

Creates a new empty instance of MomentsOfInertia

MomentsOfInertia.SymmetryClass - Enum in org.biojava.nbio.structure.geometry

MONOCLINIC - org.biojava.nbio.structure.xtal.BravaisLattice

multiIterator(AtomPositionMap, List<? extends ResidueRange>) - Static method in class org.biojava.nbio.structure.ResidueRange

Returns a new Iterator over every ResidueNumber in the list of ResidueRanges.

multiIterator(AtomPositionMap, ResidueRange...) - Static method in class org.biojava.nbio.structure.ResidueRange

Returns a new Iterator over every ResidueNumber in the list of ResidueRanges.

MultipleAlignment - Interface in org.biojava.nbio.structure.align.multiple

A MultipleAlignment is a Data Structure to store the core information of a multiple structure alignment, as a return type.

MultipleAlignmentDisplay - Class in org.biojava.nbio.structure.align.multiple.util

Utility functions to generalize the visualization of MultipleAlignments in molecular viewers.

MultipleAlignmentDisplay() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay

MultipleAlignmentEnsemble - Interface in org.biojava.nbio.structure.align.multiple

A MultipleAlignmentEnsemble is a collection of MultipleAlignments that share the same structures (Atoms) and creation properties (algorithm, version, creation time, etc.).

MultipleAlignmentEnsembleImpl - Class in org.biojava.nbio.structure.align.multiple

A general implementation of a MultipleAlignmentEnsemble.

MultipleAlignmentEnsembleImpl() - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

Default Constructor.

MultipleAlignmentEnsembleImpl(List<StructureIdentifier>) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

Constructor using structure identifiers.

MultipleAlignmentEnsembleImpl(AFPChain, Atom[], Atom[], boolean) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

Constructor from an AFPChain instance.

MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

Copy constructor.

MultipleAlignmentImpl - Class in org.biojava.nbio.structure.align.multiple

A general implementation of a MultipleAlignment.

MultipleAlignmentImpl() - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

Default Constructor.

MultipleAlignmentImpl(MultipleAlignmentEnsemble) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

Constructor linking to an existing ensemble.

MultipleAlignmentImpl(MultipleAlignmentImpl) - Constructor for class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

Copy constructor.

MultipleAlignmentScorer - Class in org.biojava.nbio.structure.align.multiple.util

Utility class for calculating common scores of MultipleAlignments.

MultipleAlignmentScorer() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

MultipleAlignmentTools - Class in org.biojava.nbio.structure.align.multiple.util

Utility functions for working with MultipleAlignment.

MultipleAlignmentTools() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

MultipleAlignmentWriter - Class in org.biojava.nbio.structure.align.multiple.util

This class contains functions for the conversion of MultipleAlignment to various String outputs.

MultipleAlignmentWriter() - Constructor for class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

MultipleAlignmentXMLConverter - Class in org.biojava.nbio.structure.align.xml

Helper methods to convert all the hierarchy levels of a MultipleAlignment into an XML format.

MultipleAlignmentXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter

MultipleAlignmentXMLParser - Class in org.biojava.nbio.structure.align.xml

Parse an XML file representing a MultipleAlignmentEnsemble, so that the original alignment can be recovered.

MultipleAlignmentXMLParser() - Constructor for class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser

MultipleMcMain - Class in org.biojava.nbio.structure.align.multiple.mc

Main class of the Java implementation of the Combinatorial Extension - Monte Carlo (CEMC) Algorithm, as it was originally described by C.Guda, E.D.Scheeff, P.E.

MultipleMcMain(StructureAlignment) - Constructor for class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain

Default constructor.

MultipleMcOptimizer - Class in org.biojava.nbio.structure.align.multiple.mc

This class takes a MultipleAlignment seed previously generated and runs a Monte Carlo optimization in order to improve the overall score and highlight common structural motifs.

MultipleMcOptimizer(MultipleAlignment, MultipleMcParameters, int) - Constructor for class org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer

Constructor.

MultipleMcParameters - Class in org.biojava.nbio.structure.align.multiple.mc

Contains the parameters to be sent to the MC optimization.

MultipleMcParameters() - Constructor for class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

Constructor with DEFAULT values of the parameters.

MultipleStructureAligner - Interface in org.biojava.nbio.structure.align

Interface for the Multiple Structure Alignment Algorithms.

MultipleSuperimposer - Interface in org.biojava.nbio.structure.align.multiple.util

Interface for Multiple Alignment superposition algorithms.

mutate(Structure, String, String, String) - Method in class org.biojava.nbio.structure.Mutator

creates a new structure which is identical with the original one.

mutateResidue(AminoAcid, String) - Method in class org.biojava.nbio.structure.Mutator

create a new residue which is of the new type.

Mutator - Class in org.biojava.nbio.structure

A class that can change one amino acid to another.

Mutator() - Constructor for class org.biojava.nbio.structure.Mutator

N

n - Variable in class org.biojava.nbio.structure.align.ce.CeCPMain.CPRange

last allowed n-term

N - org.biojava.nbio.structure.Element

N_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools

The atom name for the backbone amide nitrogen

Na - org.biojava.nbio.structure.Element

name - Variable in class org.biojava.nbio.structure.align.client.StructureName

name - Variable in enum org.biojava.nbio.structure.secstruc.BridgeType

name - Variable in enum org.biojava.nbio.structure.secstruc.SecStrucType

Nb - org.biojava.nbio.structure.Element

nBestTrace - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

nBestTrace - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

nBestTraces - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

nBestTraces - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

NCS_CHAINID_SUFFIX_CHAR - Static variable in class org.biojava.nbio.structure.xtal.CrystalBuilder

Nd - org.biojava.nbio.structure.Element

Ne - org.biojava.nbio.structure.Element

NEUTRON_DIFFRACTION - org.biojava.nbio.structure.ExperimentalTechnique

newline - Static variable in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor

newline - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCat

newline - Static variable in class org.biojava.nbio.structure.align.model.AFPChain

newline - Static variable in class org.biojava.nbio.structure.align.model.AfpChainWriter

newline - Static variable in class org.biojava.nbio.structure.PDBHeader

NEWLINE - Static variable in class org.biojava.nbio.structure.cath.CathInstallation

next() - Method in class org.biojava.nbio.structure.AtomIterator

Return next atom.

next() - Method in class org.biojava.nbio.structure.GroupIterator

get next Group.

nextStep(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

nextStep(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

Ni - org.biojava.nbio.structure.Element

NINETY_FIVE_175 - org.biojava.nbio.structure.scop.Astral.AstralSet

NINETY_FIVE_175A - org.biojava.nbio.structure.scop.Astral.AstralSet

NINETY_FIVE_175B - org.biojava.nbio.structure.scop.Astral.AstralSet

NINETY_FIVE_201 - org.biojava.nbio.structure.scop.Astral.AstralSet

NINETY_FIVE_202 - org.biojava.nbio.structure.scop.Astral.AstralSet

NINETY_FIVE_203 - org.biojava.nbio.structure.scop.Astral.AstralSet

nIter - Static variable in class org.biojava.nbio.structure.align.ce.CECalculator

nIter - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

nnz() - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix

return the number of nonzero entries (not the most efficient implementation)

nnz() - Method in class org.biojava.nbio.structure.math.SparseVector

No - org.biojava.nbio.structure.Element

NO_ROTATION - org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod

NOBLE_GAS - org.biojava.nbio.structure.ElementType

nodeListFileName - Static variable in class org.biojava.nbio.structure.cath.CathInstallation

nonPolymer - org.biojava.nbio.structure.chem.ResidueType

NONPOLYMER - org.biojava.nbio.structure.EntityType

Non-polymeric entities: ligands, metal ions, buffer molecules, etc

nonredundant - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

norm() - Method in class org.biojava.nbio.structure.math.SparseVector

Calculates the 2-norm

norm1() - Method in class org.biojava.nbio.structure.jama.Matrix

One norm

norm2() - Method in class org.biojava.nbio.structure.jama.Matrix

Two norm

norm2() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition

Two norm

normF() - Method in class org.biojava.nbio.structure.jama.Matrix

Frobenius norm

normInf() - Method in class org.biojava.nbio.structure.jama.Matrix

Infinity norm

NOT_DOMAIN_ASSEMBLY - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser

String for single-domain assemblies

NOT_REFINED - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod

NOT_REPRESENTATIVE - Static variable in class org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser

Indicates not a manual representative

Np - org.biojava.nbio.structure.Element

nrModels() - Method in interface org.biojava.nbio.structure.Structure

Return the number of models .

nrModels() - Method in class org.biojava.nbio.structure.StructureImpl

return number of models.

nTrace - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

nTrace - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

nTraces - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

nTraces - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

NUC_CARBON_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

NUC_NITROGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

NUCLEOTIDE - org.biojava.nbio.structure.GroupType

The type for nucleotide groups (dna and rna)

NUCLEOTIDE_REPRESENTATIVE - Static variable in class org.biojava.nbio.structure.StructureTools

The atom used as representative for nucleotides, equivalent to StructureTools.CA_ATOM_NAME for proteins

NucleotideImpl - Class in org.biojava.nbio.structure

A nucleotide group is almost the same as a Hetatm group.

NucleotideImpl() - Constructor for class org.biojava.nbio.structure.NucleotideImpl

nullifyComments() - Method in class org.biojava.nbio.structure.scop.ScopInstallation

Removes all of the comments (dir.com file) in order to free memory.

numberOfComponents() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

O

O - org.biojava.nbio.structure.Element

O_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools

The atom name for the backbone carbonyl oxygen

O2_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools

The atom name of the backbone O2' in RNA

O3_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools

The atom name of the backbone O3' in RNA

O4_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools

The atom name of the backbone O4' in RNA

O5_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools

The atom name of the backbone O4' in RNA

OBLATE - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass

Octahedron - Class in org.biojava.nbio.structure.symmetry.geometry

Octahedron() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Octahedron

ONEBAR - org.biojava.nbio.structure.xtal.TransformType

OP1_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools

The atom name of the backbone O4' in RNA

OP2_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools

The atom name of the backbone O4' in RNA

OPEN - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType

openURLConnection(URL) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools

Open HttpURLConnection.

openURLConnection(URL, int) - Static method in class org.biojava.nbio.structure.align.util.URLConnectionTools

Open HttpURLConnection.

OperatorResolver - Class in org.biojava.nbio.structure.quaternary

A class to resolve the operators for transformations

OperatorResolver() - Constructor for class org.biojava.nbio.structure.quaternary.OperatorResolver

OptimalCECPMain - Class in org.biojava.nbio.structure.align.ce

A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.

OptimalCECPMain() - Constructor for class org.biojava.nbio.structure.align.ce.OptimalCECPMain

OptimalCECPParameters - Class in org.biojava.nbio.structure.align.ce

Contains the parameters that can be sent to CE

OptimalCECPParameters() - Constructor for class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

optimize() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer

Optimization method based in a Monte-Carlo approach.

optimize() - Method in class org.biojava.nbio.structure.symmetry.internal.SymmOptimizer

Optimization method based in a Monte-Carlo approach.

optimizeAln(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer

optimize the alignment by dynamic programming

optimizeResult(int[], int, int[][]) - Method in class org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer

order() - Method in class org.biojava.nbio.structure.symmetry.internal.ResidueGroup

The order of symmetry of the group is the number of connected residues.

OrderDetector - Interface in org.biojava.nbio.structure.symmetry.internal

A method to decide the order of symmetry (number of subunits) given a structure self-alignment, calculated by CE-Symm.

OrderedPair<T> - Class in org.biojava.nbio.structure.quaternary

An ordered pair represents a component of a cartesian product.

org.biojava.nbio.structure - package org.biojava.nbio.structure

org.biojava.nbio.structure.align - package org.biojava.nbio.structure.align

Classes for the alignment of structures.

org.biojava.nbio.structure.align.ce - package org.biojava.nbio.structure.align.ce

Classes related to the implementation of the CE alignment algorithm, here called jCE.

org.biojava.nbio.structure.align.client - package org.biojava.nbio.structure.align.client

This package deals with the server communication for auto-downloading pre-calculated alignments.

org.biojava.nbio.structure.align.fatcat - package org.biojava.nbio.structure.align.fatcat

Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.

org.biojava.nbio.structure.align.fatcat.calc - package org.biojava.nbio.structure.align.fatcat.calc

org.biojava.nbio.structure.align.helper - package org.biojava.nbio.structure.align.helper

Helper classes for structural alignment.

org.biojava.nbio.structure.align.model - package org.biojava.nbio.structure.align.model

org.biojava.nbio.structure.align.multiple - package org.biojava.nbio.structure.align.multiple

org.biojava.nbio.structure.align.multiple.mc - package org.biojava.nbio.structure.align.multiple.mc

org.biojava.nbio.structure.align.multiple.util - package org.biojava.nbio.structure.align.multiple.util

org.biojava.nbio.structure.align.pairwise - package org.biojava.nbio.structure.align.pairwise

Classes for the pairwise alignment of structures.

org.biojava.nbio.structure.align.quaternary - package org.biojava.nbio.structure.align.quaternary

org.biojava.nbio.structure.align.seq - package org.biojava.nbio.structure.align.seq

org.biojava.nbio.structure.align.util - package org.biojava.nbio.structure.align.util

org.biojava.nbio.structure.align.xml - package org.biojava.nbio.structure.align.xml

Serialization and deserialization for structure alignment results (as AFPChain object) to XML.

org.biojava.nbio.structure.asa - package org.biojava.nbio.structure.asa

org.biojava.nbio.structure.basepairs - package org.biojava.nbio.structure.basepairs

org.biojava.nbio.structure.cath - package org.biojava.nbio.structure.cath

org.biojava.nbio.structure.chem - package org.biojava.nbio.structure.chem

org.biojava.nbio.structure.cluster - package org.biojava.nbio.structure.cluster

org.biojava.nbio.structure.contact - package org.biojava.nbio.structure.contact

org.biojava.nbio.structure.domain - package org.biojava.nbio.structure.domain

org.biojava.nbio.structure.domain.pdp - package org.biojava.nbio.structure.domain.pdp

org.biojava.nbio.structure.ecod - package org.biojava.nbio.structure.ecod

org.biojava.nbio.structure.geometry - package org.biojava.nbio.structure.geometry

org.biojava.nbio.structure.io - package org.biojava.nbio.structure.io

Input and Output of Structures

org.biojava.nbio.structure.io.cif - package org.biojava.nbio.structure.io.cif

org.biojava.nbio.structure.io.mmtf - package org.biojava.nbio.structure.io.mmtf

org.biojava.nbio.structure.io.sifts - package org.biojava.nbio.structure.io.sifts

org.biojava.nbio.structure.io.util - package org.biojava.nbio.structure.io.util

org.biojava.nbio.structure.jama - package org.biojava.nbio.structure.jama

Matrix package for from JAMA

org.biojava.nbio.structure.math - package org.biojava.nbio.structure.math

org.biojava.nbio.structure.quaternary - package org.biojava.nbio.structure.quaternary

org.biojava.nbio.structure.scop - package org.biojava.nbio.structure.scop

Parsers and API for SCOP, Structural Classification of Proteins.

org.biojava.nbio.structure.secstruc - package org.biojava.nbio.structure.secstruc

org.biojava.nbio.structure.symmetry.axis - package org.biojava.nbio.structure.symmetry.axis

org.biojava.nbio.structure.symmetry.core - package org.biojava.nbio.structure.symmetry.core

org.biojava.nbio.structure.symmetry.geometry - package org.biojava.nbio.structure.symmetry.geometry

org.biojava.nbio.structure.symmetry.internal - package org.biojava.nbio.structure.symmetry.internal

org.biojava.nbio.structure.symmetry.misc - package org.biojava.nbio.structure.symmetry.misc

org.biojava.nbio.structure.symmetry.utils - package org.biojava.nbio.structure.symmetry.utils

org.biojava.nbio.structure.xtal - package org.biojava.nbio.structure.xtal

org.biojava.nbio.structure.xtal.io - package org.biojava.nbio.structure.xtal.io

orientation(Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions

The orientation represents the rotation of the principal axes with respect to the axes of the coordinate system (unit vectors [1,0,0], [0,1,0] and [0,0,1]).

orientationAngle(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions

The angle of the relative orientation of the two sets of points in 3D.

orientationAngle(Point3d[], Point3d[], boolean) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions

The angle of the relative orientation of the two sets of points in 3D.

orientationMetric(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions

The orientation metric is obtained by comparing the quaternion orientations of the principal axes of each set of points in 3D.

orientationMetric(Quat4d, Quat4d) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions

The orientation metric is obtained by comparing two unit quaternion orientations.

oRmsdThr - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

OrthologousSequenceFamily - org.biojava.nbio.structure.cath.CathCategory

ORTHORHOMBIC - org.biojava.nbio.structure.xtal.BravaisLattice

Os - org.biojava.nbio.structure.Element

OTHER_NONMETAL - org.biojava.nbio.structure.ElementType

otherChemComp - org.biojava.nbio.structure.chem.ResidueType

otherPolymer - org.biojava.nbio.structure.chem.PolymerType

other

overlaps(BoundingBox, double) - Method in class org.biojava.nbio.structure.contact.BoundingBox

Returns true if this bounding box overlaps given one, i.e.

OXIGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

P

P - org.biojava.nbio.structure.Element

P_ATOM_NAME - Static variable in class org.biojava.nbio.structure.StructureTools

The atom name of the backbone phosphate in RNA

Pa - org.biojava.nbio.structure.Element

Pair<T> - Class in org.biojava.nbio.structure.contact

A Pair of objects.

Pair(T, T) - Constructor for class org.biojava.nbio.structure.contact.Pair

Creates a Pair from the specified elements.

pairingNames - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

pairingParameters - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

pairParameters - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

pairSequence - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

parallel - org.biojava.nbio.structure.secstruc.BridgeType

params - Variable in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor

params - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

params - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

params - Variable in class org.biojava.nbio.structure.align.ce.CeMain

params - Variable in class org.biojava.nbio.structure.align.ce.OptimalCECPMain

params - Variable in class org.biojava.nbio.structure.align.util.AtomCache

parent - Variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo

parse(String) - Static method in class org.biojava.nbio.structure.ResidueRange

Parse the residue range from a string.

parse(String) - Static method in enum org.biojava.nbio.structure.scop.Astral.AstralSet

parse(String, AtomPositionMap) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength

Parses a residue range.

parseBinaryOperatorExpression(String) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools

parseFile(String, Structure, boolean) - Static method in class org.biojava.nbio.structure.secstruc.DSSPParser

Parse a DSSP output file and return the secondary structure annotation as a List of SecStrucState objects.

parseInputStream(InputStream, Structure, boolean) - Static method in class org.biojava.nbio.structure.secstruc.DSSPParser

Parse a DSSP output file and return the secondary structure annotation as a List of SecStrucState objects.

parseMultiple(String) - Static method in class org.biojava.nbio.structure.ResidueRange

parseMultiple(String, AtomPositionMap) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength

parseMultiple(List<String>) - Static method in class org.biojava.nbio.structure.ResidueRange

parseMultiple(List<String>, AtomPositionMap) - Static method in class org.biojava.nbio.structure.ResidueRangeAndLength

parseMultiXML(String) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser

parseOperatorExpressionString(String) - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver

Parses the operator expression and save the operators as a list of unary or binary operators (i.e.

parsePDBFile(BufferedReader) - Method in class org.biojava.nbio.structure.io.PDBFileParser

Parse a PDB file and return a datastructure implementing PDBStructure interface.

parsePDBFile(InputStream) - Method in class org.biojava.nbio.structure.io.PDBFileParser

Parse a PDB file and return a datastructure implementing PDBStructure interface.

parseSpaceGroup(String) - Static method in class org.biojava.nbio.structure.xtal.SpaceGroup

Get the space group for the given international short name, using the PDB format, e.g.

parseSpaceGroupsXML(InputStream) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser

Load all SpaceGroup information from the file spacegroups.xml

parseString(String, Structure, boolean) - Static method in class org.biojava.nbio.structure.secstruc.DSSPParser

Parse a DSSP format String and return the secondary structure annotation as a List of SecStrucState objects.

parseSymopLib(InputStream) - Static method in class org.biojava.nbio.structure.xtal.SymoplibParser

A parser for the symop.lib file provided by CCP4.

parseUnaryOperatorExpression(String) - Static method in class org.biojava.nbio.structure.quaternary.BioAssemblyTools

parseXmlFile(InputStream) - Method in class org.biojava.nbio.structure.io.sifts.SiftsXMLParser

parseXMLfile(String) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser

Creates a list of MultipleAlignment ensembles from an XML file.

PARTIAL_COMPLETE - org.biojava.nbio.structure.align.quaternary.QsRelation

All the Subunits of one Structure have an equivalent in the other Structure, but the other Structure contains additional non-matched Subunits.

PARTIAL_INCOMPLETE - org.biojava.nbio.structure.align.quaternary.QsRelation

Only a subset of Subunits of one Structure have an equivalent in the other Structure, and the other Structure also contains additional non-matched Subunits.

PassthroughIdentifier - Class in org.biojava.nbio.structure

A stub StructureIdentifier, representing the full structure in all cases.

PassthroughIdentifier(String) - Constructor for class org.biojava.nbio.structure.PassthroughIdentifier

PATTERN_EXTENDED_PDBID - Static variable in class org.biojava.nbio.structure.PdbId

A regular expression that matches a PDB ID in the extended format.

PATTERN_SHORT_PDBID - Static variable in class org.biojava.nbio.structure.PdbId

A regular expression that matches a PDB ID in the short format.

PATTERN_SHORTABLE_EXTENDED_PDBID - Static variable in class org.biojava.nbio.structure.PdbId

/ * A regular expression that matches an extended PDB ID that is compatible with the short format.

Pb - org.biojava.nbio.structure.Element

Pd - org.biojava.nbio.structure.Element

PDB - org.biojava.nbio.structure.align.client.StructureName.Source

PDB - org.biojava.nbio.structure.io.StructureFiletype

PDB_AUTHOR_ASSIGNMENT - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo

Secondary strucuture assigned by the PDB author

PDB_CACHE_DIR - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration

PDB_DIR - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration

PDB_FILE_SERVER_PROPERTY - Static variable in class org.biojava.nbio.structure.io.LocalPDBDirectory

pdb_flag - Variable in class org.biojava.nbio.structure.HetatomImpl

stores if 3d coordinates are available.

PDB_FORMAT - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration

pdb_name - Variable in class org.biojava.nbio.structure.HetatomImpl

3 letter name of amino acid in pdb file.

PDB_OBSOLETE_DIR - Static variable in class org.biojava.nbio.structure.io.PDBFileReader

pdb_REMARK_350_Handler(String) - Method in class org.biojava.nbio.structure.io.PDBBioAssemblyParser

Parses REMARK 350 line.

PDB_SPLIT_DIR - Static variable in class org.biojava.nbio.structure.io.PDBFileReader

PDBBioAssemblyParser - Class in org.biojava.nbio.structure.io

Parses REMARK 350 records in a PDB file and creates transformations to construct the quaternary structure of a protein from an asymmetric unit

PDBBioAssemblyParser() - Constructor for class org.biojava.nbio.structure.io.PDBBioAssemblyParser

PDBCrystallographicInfo - Class in org.biojava.nbio.structure

A class to hold crystallographic information about a PDB structure.

PDBCrystallographicInfo() - Constructor for class org.biojava.nbio.structure.PDBCrystallographicInfo

PDBFileParser - Class in org.biojava.nbio.structure.io

This class implements the actual PDB file parsing.

PDBFileParser() - Constructor for class org.biojava.nbio.structure.io.PDBFileParser

PDBFileReader - Class in org.biojava.nbio.structure.io

The wrapper class for parsing a PDB file.

PDBFileReader() - Constructor for class org.biojava.nbio.structure.io.PDBFileReader

Constructs a new PDBFileReader, initializing the extensions member variable.

PDBFileReader(String) - Constructor for class org.biojava.nbio.structure.io.PDBFileReader

Constructs a new PDBFileReader, initializing the extensions member variable.

PDBHeader - Class in org.biojava.nbio.structure

A class that contains PDB Header information.

PDBHeader() - Constructor for class org.biojava.nbio.structure.PDBHeader

pdbId - Variable in class org.biojava.nbio.structure.align.client.StructureName

PdbId - Class in org.biojava.nbio.structure

A wrapper class for the PDB identifier.

PdbId(String) - Constructor for class org.biojava.nbio.structure.PdbId

PDBID_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier

URL parameter specifying the PDB ID

PdbPair - Class in org.biojava.nbio.structure.align.client

A pair for structure alignment.

PdbPair(String, String) - Constructor for class org.biojava.nbio.structure.align.client.PdbPair

PdbPair(StructureName, StructureName) - Constructor for class org.biojava.nbio.structure.align.client.PdbPair

PdbPairsMessage - Class in org.biojava.nbio.structure.align.xml

PdbPairsMessage() - Constructor for class org.biojava.nbio.structure.align.xml.PdbPairsMessage

PdbPairXMLConverter - Class in org.biojava.nbio.structure.align.xml

PdbPairXMLConverter() - Constructor for class org.biojava.nbio.structure.align.xml.PdbPairXMLConverter

PDBParseException - Exception in org.biojava.nbio.structure.io

An exception during the parsing of a PDB file.

PDBParseException(String) - Constructor for exception org.biojava.nbio.structure.io.PDBParseException

Constructs a PDBParseException object.

PDBParseException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.io.PDBParseException

Constructs a PDBParseException object.

PDBParseException(Throwable) - Constructor for exception org.biojava.nbio.structure.io.PDBParseException

Constructs a PDBParseException object.

PDBRecord - Interface in org.biojava.nbio.structure

An interface implemented by all classes that represent PDB records.

PDBStatus - Class in org.biojava.nbio.structure

Methods for getting the status of a PDB file (current, removed, unreleased) and for accessing different versions of the structure.

PDBStatus() - Constructor for class org.biojava.nbio.structure.PDBStatus

PDBStatus.Status - Enum in org.biojava.nbio.structure

Represents a simplified 3 state status of PDB IDs.

PDBTemporaryStorageUtils - Class in org.biojava.nbio.structure.io.util

Internal use only.

PDBTemporaryStorageUtils() - Constructor for class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils

PDBTemporaryStorageUtils.LinkRecord - Class in org.biojava.nbio.structure.io.util

Temporary data storage for LINK records.

PDPDistanceMatrix - Class in org.biojava.nbio.structure.domain.pdp

PDPDistanceMatrix() - Constructor for class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

PDPParameters - Class in org.biojava.nbio.structure.domain.pdp

PDPParameters() - Constructor for class org.biojava.nbio.structure.domain.pdp.PDPParameters

peptide - org.biojava.nbio.structure.chem.PolymerType

polypeptide(L)

peptideLike - org.biojava.nbio.structure.chem.ResidueType

peptideNucleicAcid - org.biojava.nbio.structure.chem.PolymerType

Peptide nucleic acids

PermutationGenerator - Class in org.biojava.nbio.structure.symmetry.utils

PermutationGenerator(int) - Constructor for class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator

PermutationGroup - Class in org.biojava.nbio.structure.symmetry.core

PermutationGroup() - Constructor for class org.biojava.nbio.structure.symmetry.core.PermutationGroup

PHOSPHOROUS_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

PLANAR - org.biojava.nbio.structure.BondType

plus(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

C = A + B

plus(SparseSquareMatrix) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix

return C = A + B

plus(SparseVector) - Method in class org.biojava.nbio.structure.math.SparseVector

Calcualtes return a + b

plus(Structure, Matrix) - Static method in class org.biojava.nbio.structure.Calc

calculate structure + Matrix coodinates ...

plusEquals(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

A = A + B

Pm - org.biojava.nbio.structure.Element

Po - org.biojava.nbio.structure.Element

Polyhedron - Interface in org.biojava.nbio.structure.symmetry.geometry

POLYMER - org.biojava.nbio.structure.EntityType

Polymeric entities: poly-peptides and nucleotide chains

polymerType - Variable in enum org.biojava.nbio.structure.chem.ResidueType

The associated PolymerType

PolymerType - Enum in org.biojava.nbio.structure.chem

Enumerates the classification of polymers.

polymerTypeFromString(String) - Static method in enum org.biojava.nbio.structure.chem.PolymerType

POLYNUCLEOTIDE_ONLY - Static variable in enum org.biojava.nbio.structure.chem.PolymerType

Convenience Set of polymer types classified as DNA.

polysaccharide - org.biojava.nbio.structure.chem.PolymerType

polysaccharide(D)

POST_TRANSITION_METAL - org.biojava.nbio.structure.ElementType

postProcess(FatCatParameters, AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor

postProcessAlignment(AFPChain, Atom[], Atom[], CECalculator) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain

Circular permutation specific code to be run after the standard CE alignment

postProcessAlignment(AFPChain, Atom[], Atom[], CECalculator, CECPParameters) - Static method in class org.biojava.nbio.structure.align.ce.CeCPMain

Circular permutation specific code to be run after the standard CE alignment

POWDER_DIFFRACTION - org.biojava.nbio.structure.ExperimentalTechnique

powerSet(Set<T>) - Method in class org.biojava.nbio.structure.symmetry.utils.PowerSet

PowerSet<T> - Class in org.biojava.nbio.structure.symmetry.utils

In mathematics, the power set (or powerset) of any set S, written P(S), is the set of all subsets of S, including the empty set and S itself.

PowerSet() - Constructor for class org.biojava.nbio.structure.symmetry.utils.PowerSet

Pr - org.biojava.nbio.structure.Element

prefetchStructure(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Download a structure, but don't parse it yet or store it in memory.

prepare() - Method in class org.biojava.nbio.structure.io.cif.ChemCompConsumerImpl

prepare() - Method in interface org.biojava.nbio.structure.io.cif.CifFileConsumer

Setup routine which initializes a new container.

prepare() - Method in class org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl

prepare() - Method in class org.biojava.nbio.structure.io.cif.MetalBondConsumerImpl

prepareGroupsForDisplay(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Rotate the Atoms/Groups so they are aligned for the 3D visualisation

print(int, int) - Method in class org.biojava.nbio.structure.jama.Matrix

Print the matrix to stdout.

print(PrintWriter, int, int) - Method in class org.biojava.nbio.structure.jama.Matrix

Print the matrix to the output stream.

print(PrintWriter, NumberFormat, int) - Method in class org.biojava.nbio.structure.jama.Matrix

Print the matrix to the output stream.

print(NumberFormat, int) - Method in class org.biojava.nbio.structure.jama.Matrix

Print the matrix to stdout.

printAboutMe() - Static method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor

printDomainsForPDB() - Method in class demo.DemoSCOP

printDSSP() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc

Generate a DSSP file format ouput String of this SS prediction.

printDSSPline(int) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

printFASTA() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc

Generate a FASTA sequence with the SS annotation letters in the aminoacid sequence order.

printFull() - Method in class org.biojava.nbio.structure.ResidueNumber

printHelixSummary() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc

Generate a summary of this SS prediction with information about the three types of helix turns in different row sequences.

printHelp() - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment

printHelp() - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor

printHelp() - Method in interface org.biojava.nbio.structure.align.ce.UserArgumentProcessor

Print help about the arguments

printScoresInLines(AFPChain, int, int, double, double, int, int, double, double, StringBuffer) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

printSecStruc(Structure) - Static method in class demo.DemoLoadSecStruc

printTimeStamps - Static variable in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner

printXMLalignment(PrettyXMLWriter, MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter

printXMLblock(PrettyXMLWriter, Block) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter

printXMLblockSet(PrettyXMLWriter, BlockSet) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter

printXMLensemble(PrettyXMLWriter, MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter

printXMLEQRInferPositions(PrettyXMLWriter, AFPChain, int, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter

printXMLheader(PrettyXMLWriter, MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter

printXMLHeader(PrettyXMLWriter, AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter

printXMLmatrix4d(PrettyXMLWriter, Matrix4d) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter

printXMLscoresCache(PrettyXMLWriter, ScoresCache) - Static method in class org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter

Prism - Class in org.biojava.nbio.structure.symmetry.geometry

Prism(int) - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Prism

PROBABILITY - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

process() - Method in class org.biojava.nbio.structure.io.FastaStructureParser

Parses the fasta file and loads it into memory.

process(String[]) - Method in class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor

process(String[]) - Method in interface org.biojava.nbio.structure.align.ce.UserArgumentProcessor

Process user arguments that have been provided from the command line

PROLATE - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass

PROTEIN_ONLY - Static variable in enum org.biojava.nbio.structure.chem.PolymerType

Convenience Set of polymer types classified as protein.

ProteinComplexSignature - Class in org.biojava.nbio.structure.symmetry.misc

ProteinComplexSignature(String, List<String>, BlastClustReader) - Constructor for class org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature

Pt - org.biojava.nbio.structure.Element

Pu - org.biojava.nbio.structure.Element

purgeTempFiles(String) - Static method in class org.biojava.nbio.structure.chem.ZipChemCompProvider

Cleanup chemical component (.cif.gz) files downloaded to tmpdir.

put(int, double) - Method in class org.biojava.nbio.structure.math.SparseVector

Setter method (should it be renamed to set?)

put(int, int, double) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix

set A[i][j] = value

put(Key, Value) - Method in class org.biojava.nbio.structure.math.SymbolTable

Put key-value pair into the symbol table.

putScore(String, Double) - Method in class org.biojava.nbio.structure.align.multiple.AbstractScoresCache

putScore(String, Double) - Method in interface org.biojava.nbio.structure.align.multiple.ScoresCache

Add a score to the list of scores.

Px - org.biojava.nbio.structure.scop.ScopCategory

Q

Q - Static variable in class org.biojava.nbio.structure.secstruc.SecStrucCalc

constant for electrostatic energy

qr() - Method in class org.biojava.nbio.structure.jama.Matrix

QR Decomposition

QRDecomposition - Class in org.biojava.nbio.structure.jama

QR Decomposition.

QRDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.QRDecomposition

QR Decomposition, computed by Householder reflections.

QsAlign - Class in org.biojava.nbio.structure.align.quaternary

Quaternary Structure Alignment (QS-Align).

QsAlign() - Constructor for class org.biojava.nbio.structure.align.quaternary.QsAlign

QsAlignParameters - Class in org.biojava.nbio.structure.align.quaternary

The parameter bean for the QsAlign algorithm.

QsAlignParameters() - Constructor for class org.biojava.nbio.structure.align.quaternary.QsAlignParameters

QsAlignResult - Class in org.biojava.nbio.structure.align.quaternary

Result of a Quaternary Structure Alignment QsAlign.

QsAlignResult(List<Subunit>, List<Subunit>) - Constructor for class org.biojava.nbio.structure.align.quaternary.QsAlignResult

The Constructor of the result takes the same inputs as the QsAlign algorithm.

QsRelation - Enum in org.biojava.nbio.structure.align.quaternary

The Quaternary Structure Relation describes the pairwise relation between two quaternary structures.

QuatSuperpositionScorer - Class in org.biojava.nbio.structure.symmetry.core

QuatSuperpositionScorer() - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSuperpositionScorer

QuatSymmetryDetector - Class in org.biojava.nbio.structure.symmetry.core

Detects the symmetry (global, pseudo, internal and local) of protein structures.

QuatSymmetryParameters - Class in org.biojava.nbio.structure.symmetry.core

The QuatSymmetryParameters specify the options used for the detection of quaternary symmetry in structures using the QuatSymmetryDetector.

QuatSymmetryParameters() - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

QuatSymmetryResults - Class in org.biojava.nbio.structure.symmetry.core

Holds the results of quaternary symmetry perception obtained with QuatSymmetryDetector.

QuatSymmetryResults(Stoichiometry, HelixLayers, SymmetryPerceptionMethod) - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

Constructor for roto-translational symmetries.

QuatSymmetryResults(Stoichiometry, RotationGroup, SymmetryPerceptionMethod) - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

Constructor for rotational symmetries.

QuatSymmetryScores - Class in org.biojava.nbio.structure.symmetry.core

QuatSymmetryScores() - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

QuatSymmetrySolver - Interface in org.biojava.nbio.structure.symmetry.core

QuatSymmetrySubunits - Class in org.biojava.nbio.structure.symmetry.core

A bean to represent information about the set of Subunits being considered for symmetry detection.

QuatSymmetrySubunits(List<SubunitCluster>) - Constructor for class org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits

Converts the List of SubunitCluster to a Subunit object.

QUESTIONMARK - org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy

Put '?' symbol for every (alphabet.length+i)-th cluster

R

R - org.biojava.nbio.structure.Element

R-group to represent generic groups that are sometimes present in MDL .sdf files.

Ra - org.biojava.nbio.structure.Element

random(int, int) - Static method in class org.biojava.nbio.structure.jama.Matrix

Generate matrix with random elements

randomPick(Collection<Number>) - Static method in class org.biojava.nbio.structure.align.util.CollectionTools

RANGE_REGEX - Static variable in class org.biojava.nbio.structure.ResidueRange

rank() - Method in class org.biojava.nbio.structure.jama.Matrix

Matrix rank

rank() - Method in class org.biojava.nbio.structure.jama.SingularValueDecomposition

Effective numerical matrix rank

RATIO_GAPS_FOR_MISMATCH - Static variable in class org.biojava.nbio.structure.io.EntityFinder

Above this ratio of mismatching residue types for same residue numbers we consider the 2 chains to have mismatching residue numbers and warn about it

RATIO_RESIDUES_TO_TOTAL - Static variable in class org.biojava.nbio.structure.StructureTools

Below this ratio of aminoacid/nucleotide residues to the sequence total, we use simple majority of aminoacid/nucleotide residues to decide the character of the chain (protein/nucleotide)

Rb - org.biojava.nbio.structure.Element

Re - org.biojava.nbio.structure.Element

read(BufferedReader) - Static method in class org.biojava.nbio.structure.jama.Matrix

Read a matrix from a stream.

readFromFile(Path) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfActions

Get a Structure object from a mmtf file.

readFromInputStream(InputStream) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfActions

Read a Biojava structure from an InputStream

readFromWeb(String) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfActions

Get a Biojava structure from the mmtf REST service.

rebuildAFPChain(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLParser

replace the PDB res nums with atom positions:

rebuildQuaternaryStructure(Structure, List<BiologicalAssemblyTransformation>, boolean, boolean) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder

Builds a Structure object containing the quaternary structure built from given asymUnit and transformations, by adding symmetry partners as new models.

RectangularPrism - Class in org.biojava.nbio.structure.symmetry.geometry

RectangularPrism(double, double, double) - Constructor for class org.biojava.nbio.structure.symmetry.geometry.RectangularPrism

reduce(Structure) - Method in class org.biojava.nbio.structure.align.client.StructureName

reduce(Structure) - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier

reduce(Structure) - Method in class org.biojava.nbio.structure.cath.CathDomain

reduce(Structure) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

reduce(Structure) - Method in class org.biojava.nbio.structure.PassthroughIdentifier

reduce(Structure) - Method in class org.biojava.nbio.structure.scop.ScopDomain

reduce(Structure) - Method in interface org.biojava.nbio.structure.StructureIdentifier

Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.

reduce(Structure) - Method in class org.biojava.nbio.structure.SubstructureIdentifier

Takes a complete structure as input and reduces it to residues present in the specified ranges

reduce(Structure) - Method in class org.biojava.nbio.structure.URLIdentifier

ReducedChemCompProvider - Class in org.biojava.nbio.structure.chem

Unlike the DownloadChemCompProvider, this ChemCompProvider does not download any chem comp definitions.

ReducedChemCompProvider() - Constructor for class org.biojava.nbio.structure.chem.ReducedChemCompProvider

reduceFragments(List<FragmentPair>, FragmentPair, Matrix) - Static method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner

In helices often many similar fragments can be found.

reduceInitialFragments() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

if this is set to false, the time spent to joint the initial fragments (step 2) is increased.

reduceToRepresentativeAtoms(Structure) - Static method in class org.biojava.nbio.structure.StructureTools

Remove all atoms but the representative atoms (C alphas or phosphates) from the given structure.

REF_RMSD - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

referenceFrames - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

ReferenceSuperimposer - Class in org.biojava.nbio.structure.align.multiple.util

Superimposes each structure in a MultipleAlignment onto a reference structure.

ReferenceSuperimposer() - Constructor for class org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer

Default Constructor.

ReferenceSuperimposer(int) - Constructor for class org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer

Constructor using a specified structure as reference.

refine(AFPChain, Atom[], int) - Method in class org.biojava.nbio.structure.symmetry.internal.GraphComponentRefiner

refine(AFPChain, Atom[], int) - Method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner

refine(AFPChain, Atom[], int) - Method in interface org.biojava.nbio.structure.symmetry.internal.SymmetryRefiner

Returns a refined symmetry alignment, where the repeat residues are aligned consistently in a MultipleAlignment.

refine(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

Refinement procedure based on superposition and dynamic programming.

RefinerFailedException - Exception in org.biojava.nbio.structure.symmetry.internal

Refinement of the self-alignment failed.

RefinerFailedException() - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException

RefinerFailedException(String) - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException

RefinerFailedException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException

RefinerFailedException(Throwable) - Constructor for exception org.biojava.nbio.structure.symmetry.internal.RefinerFailedException

refineSymmetry(Map<Integer, Integer>, int) - Static method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner

Refines a CE-Symm alignment so that it is perfectly symmetric.

refineSymmetry(AFPChain, Atom[], Atom[], int) - Static method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner

Refines a CE-Symm alignment so that it is perfectly symmetric.

REFTM_SCORE - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

relativeOrientation(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.UnitQuaternions

Calculate the relative quaternion orientation of two arrays of points.

reloadFromFile() - Method in class org.biojava.nbio.structure.domain.SerializableCache

remark800toPDB() - Method in class org.biojava.nbio.structure.Site

Provides REMARK 800 section pertaining to the site as a string.

remark800toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.Site

Appends the REMARK 800 section pertaining to the site onto the end of the StringBuffer provided.

remove() - Method in class org.biojava.nbio.structure.AtomIterator

does nothing.

remove() - Method in class org.biojava.nbio.structure.GroupIterator

does nothing .

removeAlgorithm(String) - Static method in class org.biojava.nbio.structure.align.StructureAlignmentFactory

Removes the specified algorithm from the list of options

REMOVED - org.biojava.nbio.structure.PDBStatus.Status

removeGaps(ProteinSequence) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher

Removes all gaps ('-') from a protein sequence

removeGaps(T[][]) - Static method in class org.biojava.nbio.structure.io.StructureSequenceMatcher

Creates a new list consisting of all columns of gapped where no row contained a null value.

removeInterfacesBelowArea() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

Removes from this interface list all interfaces with areas below the default cutoff area.

removeInterfacesBelowArea(double) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

Removes from this interface list all interfaces with areas below the given cutoff area.

removeModels(Structure) - Static method in class org.biojava.nbio.structure.StructureTools

Remove all models from a Structure and keep only the first

removeRotation(int) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

replaceOptAln(int[][][], AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

It replaces an optimal alignment of an AFPChain and calculates all the new alignment scores and variables.

replaceOptAln(AFPChain, Atom[], Atom[], int, int[], int[][][]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

replaceOptAln(AFPChain, Atom[], Atom[], Map<Integer, Integer>) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Takes an AFPChain and replaces the optimal alignment based on an alignment map

reset() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

reset() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

reset() - Method in interface org.biojava.nbio.structure.align.ce.ConfigStrucAligParams

Set the parameters to the default.

reset() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

reset() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

reset() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

reset() - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

reset() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

reset() - Method in class org.biojava.nbio.structure.symmetry.utils.PermutationGenerator

resetAlphas() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Reassign alpha-strings for each cluster according to the current strategy.

resetModels() - Method in interface org.biojava.nbio.structure.Structure

Resets all models of this Structure

resetModels() - Method in class org.biojava.nbio.structure.StructureImpl

ResidueGroup - Class in org.biojava.nbio.structure.symmetry.internal

A ResidueGroup is a set of residues that are part of a maximally connected component of the self-Alignment Graph in symmetry analysis.

ResidueGroup(Set<Integer>) - Constructor for class org.biojava.nbio.structure.symmetry.internal.ResidueGroup

Create a ResidueGroup object from a maximally connected component.

residueNumber - Variable in class org.biojava.nbio.structure.HetatomImpl

ResidueNumber - Class in org.biojava.nbio.structure

Everything that is needed to uniquely describe a residue position

ResidueNumber() - Constructor for class org.biojava.nbio.structure.ResidueNumber

ResidueNumber(String, Integer, Character) - Constructor for class org.biojava.nbio.structure.ResidueNumber

ResidueNumber(ResidueNumber) - Constructor for class org.biojava.nbio.structure.ResidueNumber

ResidueRange - Class in org.biojava.nbio.structure

A chainName, a start residue, and an end residue.

ResidueRange(String, String, String) - Constructor for class org.biojava.nbio.structure.ResidueRange

ResidueRange(String, ResidueNumber, ResidueNumber) - Constructor for class org.biojava.nbio.structure.ResidueRange

ResidueRangeAndLength - Class in org.biojava.nbio.structure

A chain, a start residue, and an end residue.

ResidueRangeAndLength(String, String, String, int) - Constructor for class org.biojava.nbio.structure.ResidueRangeAndLength

ResidueRangeAndLength(String, ResidueNumber, ResidueNumber, int) - Constructor for class org.biojava.nbio.structure.ResidueRangeAndLength

RESIDUES_PARAM - Static variable in class org.biojava.nbio.structure.URLIdentifier

URL parameter specifying residue ranges to include, e.g.

ResidueType - Enum in org.biojava.nbio.structure.chem

Enumerates the possible classifications of residues.

resizeArray(Object, int) - Static method in class org.biojava.nbio.structure.align.pairwise.FragmentJoiner

Reallocates an array with a new size, and copies the contents of the old array to the new array.

resizeArray(Object, int) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Reallocates an array with a new size, and copies the contents of the old array to the new array.

ResourceManager - Class in org.biojava.nbio.structure.align.util

A class that manages the Strings that are defined in the spice.properties file.

ResourceManager() - Constructor for class org.biojava.nbio.structure.align.util.ResourceManager

RG - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

RG1 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

Rh - org.biojava.nbio.structure.Element

RIGHT - org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint

RING_MAP - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

rms_dk_diag(double[], double[], int, int, int, int) - Static method in class org.biojava.nbio.structure.align.helper.AlignUtils

Given distance matrix diagonals dk1, dk2, get the rmsd of a fpair.

rmsd(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint

Calculate the RMSD of two point arrays, already superposed.

rmsd(Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.Calc

Calculate the RMSD of two Atom arrays, already superposed.

RMSD - Static variable in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

rmsdMin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint

rmsdThr - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

rmsdThrJoin - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

Rn - org.biojava.nbio.structure.Element

rna - org.biojava.nbio.structure.chem.PolymerType

polyribonucleotide

RNA_ONLY - Static variable in enum org.biojava.nbio.structure.chem.PolymerType

Convenience Set of polymer types classified as RNA.

rna3PrimeTerminus - org.biojava.nbio.structure.chem.ResidueType

rna5PrimeTerminus - org.biojava.nbio.structure.chem.ResidueType

rnaLinking - org.biojava.nbio.structure.chem.ResidueType

rotate(Atom[], double) - Method in class org.biojava.nbio.structure.align.util.RotationAxis

rotate(Atom[], Matrix) - Static method in class org.biojava.nbio.structure.Calc

rotate(Atom, double[][]) - Static method in class org.biojava.nbio.structure.Calc

Rotate a single Atom aroud a rotation matrix.

rotate(Atom, Matrix) - Static method in class org.biojava.nbio.structure.Calc

Rotate an Atom around a Matrix object.

rotate(Group, double[][]) - Static method in class org.biojava.nbio.structure.Calc

Rotate a Group.

rotate(Group, Matrix) - Static method in class org.biojava.nbio.structure.Calc

Rotate a group object.

rotate(Structure, double[][]) - Static method in class org.biojava.nbio.structure.Calc

Rotate a structure.

rotate(Structure, Matrix) - Static method in class org.biojava.nbio.structure.Calc

Rotate a structure object.

Rotation - Class in org.biojava.nbio.structure.symmetry.core

Rotation() - Constructor for class org.biojava.nbio.structure.symmetry.core.Rotation

ROTATION - org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod

RotationAxis - Class in org.biojava.nbio.structure.align.util

Calculates the rotation axis for an alignment

RotationAxis(Matrix4d) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis

Create a rotation axis from a Matrix4d containing a rotational component and a translational component.

RotationAxis(AFPChain) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis

Calculate the rotation axis for the first block of an AFPChain

RotationAxis(Atom, Atom, double) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis

Create a rotation axis from a vector, a point, and an angle.

RotationAxis(Matrix, Atom) - Constructor for class org.biojava.nbio.structure.align.util.RotationAxis

Determine the location of the rotation axis based on a rotation matrix and a translation vector

RotationAxisAligner - Class in org.biojava.nbio.structure.symmetry.axis

RotationAxisAligner(QuatSymmetryResults) - Constructor for class org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner

RotationGroup - Class in org.biojava.nbio.structure.symmetry.core

RotationGroup() - Constructor for class org.biojava.nbio.structure.symmetry.core.RotationGroup

RotationSolver - Class in org.biojava.nbio.structure.symmetry.core

RotationSolver(QuatSymmetrySubunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.RotationSolver

rotMatrixToString(Matrix4d) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

ROTO_TRANSLATION - org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod

Ru - org.biojava.nbio.structure.Element

run() - Method in class org.biojava.nbio.structure.chem.AllChemCompProvider

Do the actual loading of the dictionary in a thread.

runOptimization(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer

run the optimization

S

S - org.biojava.nbio.structure.Element

s_min - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues

saccharide - org.biojava.nbio.structure.chem.ResidueType

Sb - org.biojava.nbio.structure.Element

Sc - org.biojava.nbio.structure.Element

scalarProduct(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Scalar product (dot product).

scale(double) - Method in class org.biojava.nbio.structure.math.SparseVector

Calculates alpha * a

scale(Atom, double) - Static method in class org.biojava.nbio.structure.Calc

Multiply elements of a by s

scaleAdd(double, Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Perform linear transformation s*X+B, and store the result in b

scaleEquals(Atom, double) - Static method in class org.biojava.nbio.structure.Calc

Multiply elements of a by s (in place)

SCOP - org.biojava.nbio.structure.align.client.StructureName.Source

SCOP_DOWNLOAD - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation

SCOP_DOWNLOAD_ALTERNATE - Static variable in class org.biojava.nbio.structure.scop.ScopInstallation

ScopCategory - Enum in org.biojava.nbio.structure.scop

The various categories provided by SCOP.

ScopDatabase - Interface in org.biojava.nbio.structure.scop

General API how to interact with SCOP

ScopDescription - Class in org.biojava.nbio.structure.scop

Contains data from dir.des.scop.txt_1.75

ScopDescription() - Constructor for class org.biojava.nbio.structure.scop.ScopDescription

ScopDomain - Class in org.biojava.nbio.structure.scop

Container for the information for a domain.

ScopDomain() - Constructor for class org.biojava.nbio.structure.scop.ScopDomain

ScopFactory - Class in org.biojava.nbio.structure.scop

Controls the global ScopDatabase being used.

ScopFactory() - Constructor for class org.biojava.nbio.structure.scop.ScopFactory

ScopInstallation - Class in org.biojava.nbio.structure.scop

This class provides access to the SCOP protein structure classification.

ScopInstallation() - Constructor for class org.biojava.nbio.structure.scop.ScopInstallation

Create a new SCOP installation, downloading the file to "the right place".

ScopInstallation(String) - Constructor for class org.biojava.nbio.structure.scop.ScopInstallation

Create a new SCOP installation.

ScopIOException - Exception in org.biojava.nbio.structure.scop

Indicates that an I/O error occurred with SCOP lazy initialization.

ScopIOException() - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException

ScopIOException(String) - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException

ScopIOException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException

ScopIOException(Throwable) - Constructor for exception org.biojava.nbio.structure.scop.ScopIOException

ScopMirror - Class in org.biojava.nbio.structure.scop

Helper class to store paths to the four SCOP files The string "%s" is replaced with the version number.

ScopMirror() - Constructor for class org.biojava.nbio.structure.scop.ScopMirror

Use default MRC location

ScopMirror(String) - Constructor for class org.biojava.nbio.structure.scop.ScopMirror

ScopMirror(String, String, String, String) - Constructor for class org.biojava.nbio.structure.scop.ScopMirror

Specify all keys individually

ScopMirror(String, String, String, String, String) - Constructor for class org.biojava.nbio.structure.scop.ScopMirror

Specify a common root URL which is concatenated with individual filenames

ScopNode - Class in org.biojava.nbio.structure.scop

ScopNode() - Constructor for class org.biojava.nbio.structure.scop.ScopNode

ScoresCache - Interface in org.biojava.nbio.structure.align.multiple

Interface for classes which implement a temporary cache for various numeric scores, e.g.

scoringStrategy - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

scoringStrategy - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

Se - org.biojava.nbio.structure.Element

SEC_STRUC - Static variable in interface org.biojava.nbio.structure.Group

Group property key for secondary structure annotation

SecStrucCalc - Class in org.biojava.nbio.structure.secstruc

Calculate and assign the secondary structure (SS) to the Groups of a Structure object.

SecStrucCalc() - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucCalc

SecStrucElement - Class in org.biojava.nbio.structure.secstruc

A secondary structure element (SSE) is an object representing a block of sequential residues that share the same secondary structure type.

SecStrucElement(SecStrucType, ResidueNumber, ResidueNumber, int, int, String) - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucElement

Create a new SSE object.

SecStrucInfo - Class in org.biojava.nbio.structure.secstruc

Container for the secondary structure information of a single residue.

SecStrucInfo(Group, String, SecStrucType) - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucInfo

SecStrucState - Class in org.biojava.nbio.structure.secstruc

This class extends the basic container for secondary structure annotation, including all the information used in the DSSP algorithm.

SecStrucState(Group, String, SecStrucType) - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucState

SecStrucTools - Class in org.biojava.nbio.structure.secstruc

This class contains methods for obtaining and converting secondary structure information from BioJava Structures.

SecStrucTools() - Constructor for class org.biojava.nbio.structure.secstruc.SecStrucTools

SecStrucType - Enum in org.biojava.nbio.structure.secstruc

This enum contains all of the secondary structure types found in the DSSP output.

Segment - Class in org.biojava.nbio.structure.domain.pdp

Segment() - Constructor for class org.biojava.nbio.structure.domain.pdp.Segment

SegmentComparator - Class in org.biojava.nbio.structure.domain.pdp

SegmentComparator() - Constructor for class org.biojava.nbio.structure.domain.pdp.SegmentComparator

SeqMisMatch - Interface in org.biojava.nbio.structure

Created by andreas on 9/11/15.

SeqMisMatchImpl - Class in org.biojava.nbio.structure

Created by andreas on 9/11/15.

SeqMisMatchImpl() - Constructor for class org.biojava.nbio.structure.SeqMisMatchImpl

SeqRes2AtomAligner - Class in org.biojava.nbio.structure.io

Aligns the SEQRES residues to the ATOM residues.

SeqRes2AtomAligner() - Constructor for class org.biojava.nbio.structure.io.SeqRes2AtomAligner

SEQRESRECORD - Static variable in interface org.biojava.nbio.structure.AminoAcid

Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.

SEQUENCE - org.biojava.nbio.structure.cluster.SubunitClustererMethod

The SEQUENCE clustering method uses the residue sequence of the Subunit to calculate sequence alignments.

SEQUENCE_CONSERVATION - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

SEQUENCE_FUNCTION - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod

SEQUENCE_FUNCTION - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod

SEQUENCE_STRUCTURE - org.biojava.nbio.structure.cluster.SubunitClustererMethod

The SEQUENCE_STRUCTURE clustering method uses the residue sequence and the coordinates of its Atom representatives of the Subunit to calculate sequence and structure alignments.

SequenceFamily - org.biojava.nbio.structure.cath.CathCategory

SequenceFunctionOrderDetector - Class in org.biojava.nbio.structure.symmetry.internal

Calls Spencer's method for determining order.

SequenceFunctionOrderDetector() - Constructor for class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector

SequenceFunctionOrderDetector(int, float) - Constructor for class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector

SequenceFunctionRefiner - Class in org.biojava.nbio.structure.symmetry.internal

Creates a refined alignment with the CE-Symm alternative self-alignment.

SequenceFunctionRefiner() - Constructor for class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner

seqWeight - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

SerializableCache<K,V> - Class in org.biojava.nbio.structure.domain

A class that provides all that is necessary to create a Serializable Cache

SerializableCache(String) - Constructor for class org.biojava.nbio.structure.domain.SerializableCache

set cacheFileName to null to disable caching

serialize(File) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

serializedCache - Variable in class org.biojava.nbio.structure.domain.SerializableCache

serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathDomain

serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathFragment

serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathNode

serialVersionUID - Static variable in class org.biojava.nbio.structure.cath.CathSegment

serialVersionUID - Static variable in exception org.biojava.nbio.structure.io.PDBParseException

serialVersionUID - Static variable in exception org.biojava.nbio.structure.StructureException

serverBaseUrl - Static variable in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

The base URL to which the full path specified via DownloadChemCompProvider.setChemCompPathUrlTemplate(String) is appended.

set(int, int, double) - Method in class org.biojava.nbio.structure.jama.Matrix

Set a single element.

setA(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setAbsoluteMinimumSequenceLength(int) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.

setAccept1(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setAccept2(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setAcceptedAtomNames(String[]) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

By default the parser will read in all atoms (unless using the CAonly switch).

setAfpAftIndex(int[][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpBefIndex(int[][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpChainLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpChainList(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpChainTwiBin(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpChainTwiList(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpChainTwiNum(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpDisCut(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setAfpDisCut0(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setAfpIndex(int[][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAfpSet(List<AFP>) - Method in class org.biojava.nbio.structure.align.model.AFPChain

Set the set of AFPs for this alignment.

setAlgorithmName(String) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setAlgorithmName(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain

Caution has to be made when changing the algorithmName of an AFPChain, since downstream analysis methods (scores, display, etc) behave differently if the alignment is flexible (created with FatCat).

setAlgorithmName(String) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Set the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.

setAlgorithmName(String) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setAligMat(int, int, AligMatEl) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setAligMat(AligMatEl[][]) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setAligMat(AligMatEl[][]) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setAlign_se1(int[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setAlign_se1(int[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setAlign_se2(int[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setAlign_se2(int[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

The alignment that specifies the residue equivalencies of the equivalent Subunits.

setAlignments(AlternativeAlignment[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

we only keep the first alternative...

setAlignPairs(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setAlignRes(List<List<Integer>>) - Method in interface org.biojava.nbio.structure.align.multiple.Block

Set the double List containing the aligned residues for each structure.

setAlignRes(List<List<Integer>>) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

setAlignScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlignScoreUpdate(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlignSeqRes(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Define if the SEQRES in the structure should be aligned with the ATOM records if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.

setAllAtoms(List<Atom>) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

setAllChains(List<Chain>) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

setAlnbeg1(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlnbeg2(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlnLength(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlnseq1(char[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlnseq2(char[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlnsymb(char[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setAlpha(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setAlpha(String) - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

A letter that is assigned to this cluster in stoichiometry.

setAlphabet(String) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Change alphabet used for string representation of a stoichiometry.

setAltAligNumber(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setAltAtomId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setAltLoc(Character) - Method in interface org.biojava.nbio.structure.Atom

Set alternate Location.

setAltLoc(Character) - Method in class org.biojava.nbio.structure.AtomImpl

setAltShortSymbol(String) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setAminoType(Character) - Method in interface org.biojava.nbio.structure.AminoAcid

Set the name of the AA, in single letter code .

setAminoType(Character) - Method in class org.biojava.nbio.structure.AminoAcidImpl

Set the name of the AA, in single letter code .

setAngleDiff(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setAngleThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setArchitectureId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setArchitectureName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setAsaC(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa

setAsaU(double) - Method in class org.biojava.nbio.structure.asa.GroupAsa

setAssemblyId(Long) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setAtcc(String) - Method in class org.biojava.nbio.structure.EntityInfo

setAtomArrays(List<Atom[]>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Sets the List of Atom arrays.

setAtomArrays(List<Atom[]>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setAtomAsaCs(List<Double>) - Method in class org.biojava.nbio.structure.asa.GroupAsa

setAtomAsaUs(List<Double>) - Method in class org.biojava.nbio.structure.asa.GroupAsa

setAtomCache(AtomCache) - Static method in class org.biojava.nbio.structure.StructureIO

setAtomCaThreshold(int) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.

setAtomGroups(List<Group>) - Method in interface org.biojava.nbio.structure.Chain

Set all Groups with observed density in the chain, i.e.

setAtomGroups(List<Group>) - Method in class org.biojava.nbio.structure.ChainImpl

setAtomId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setAtomId1(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond

setAtomId2(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond

setAtomInfo(String, int, char, float, float, float, float, float, String, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

setAtoms(List<Atom>) - Method in interface org.biojava.nbio.structure.Group

Set the atoms of this group.

setAtoms(List<Atom>) - Method in class org.biojava.nbio.structure.HetatomImpl

Set the atoms of this group.

setAtoms(List<ChemCompAtom>) - Method in class org.biojava.nbio.structure.chem.ChemComp

setAtoms(Atom[]) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setAtomType1(String) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

setAtomType2(String) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

setAuthorList(List<Author>) - Method in class org.biojava.nbio.structure.JournalArticle

setAuthors(String) - Method in class org.biojava.nbio.structure.PDBHeader

setAutoFetch(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setAverageScore(double) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

setAxes(SymmetryAxes) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setAxisAngle(AxisAngle4d) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setAxisTypes(int[]) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setB(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setBadRmsd(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setBbs(Structure, Matrix4d[], boolean) - Method in class org.biojava.nbio.structure.xtal.UnitCellBoundingBox

setBend(boolean) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setBeta(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setBinaryOperators(List<OrderedPair<String>>) - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver

setBioAssemblies(Map<Integer, BioAssemblyInfo>) - Method in class org.biojava.nbio.structure.PDBHeader

setBioAssemblyTrans(int, int[], double[], String) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

setBiologicalAssembly(boolean) - Method in interface org.biojava.nbio.structure.Structure

Set a flag to indicate if this structure is a biological assembly

setBiologicalAssembly(boolean) - Method in class org.biojava.nbio.structure.StructureImpl

Sets a flag to indicate if this structure is a biological assembly

setBiologicalUnit(String) - Method in class org.biojava.nbio.structure.EntityInfo

setBlock2Afp(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockGap(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockNum(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockNumClu(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockNumIni(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockNumSpt(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockResList(int[][][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockResSize(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockRmsd(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockRotationMatrix(Matrix[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlocks(List<Block>) - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Set the List of alignment Blocks of the BlockSet.

setBlocks(List<Block>) - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

setBlockScore(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockSet(BlockSet) - Method in interface org.biojava.nbio.structure.align.multiple.Block

Set the back-reference to its parent BlockSet.

setBlockSet(BlockSet) - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

setBlockSets(List<BlockSet>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Sets the List of BlockSet List of the specified alignment.

setBlockSets(List<BlockSet>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

setBlockShiftVector(Atom[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBlockSize(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setBonds(List<Bond>) - Method in interface org.biojava.nbio.structure.Atom

Sets the bonds

setBonds(List<Bond>) - Method in class org.biojava.nbio.structure.AtomImpl

Sets the bonds

setBonds(List<ChemCompBond>) - Method in class org.biojava.nbio.structure.chem.ChemComp

setBravLattice(BravaisLattice) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setBridge1(BetaBridge) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setBridge2(BetaBridge) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setC(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setC1(int) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

setCa1(Atom[]) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setCa1Length(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setCa2Length(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setCache(AtomCache) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setCacheFilePath(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setCacheFilePath(String) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

setCacheLocation(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setCacheLocation(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

Set an alternate download location for files

setCacheLocation(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

setCachePath(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

set the location at which utility data should be cached.

setCalculationTime(long) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setCalculationTime(long) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setCalculationTime(Long) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Set the running time spent to calculate this alignment.

setCalculationTime(Long) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setCategory(ScopCategory) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setCath(CathDatabase) - Static method in class org.biojava.nbio.structure.cath.CathFactory

Sets the default (singleton) CathDatabase.

setCATH(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setCathDownloadUrl(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setCathVersion(String) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setCell(String) - Method in class org.biojava.nbio.structure.EntityInfo

setCellLine(String) - Method in class org.biojava.nbio.structure.EntityInfo

setCellularLocation(String) - Method in class org.biojava.nbio.structure.EntityInfo

setCenter1(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setCenter2(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setCentered(boolean) - Method in class org.biojava.nbio.structure.geometry.SuperPositionAbstract

setChain(Chain) - Method in interface org.biojava.nbio.structure.Group

Sets the back-reference to its parent Chain.

setChain(Chain) - Method in class org.biojava.nbio.structure.HetatomImpl

Sets the back-reference to its parent Chain.

setChain1(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setChain2(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setChainId(String) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier

setChainId(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setChainId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setChainId(String) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Sets the chain identifier (asym id) that this transformation should be applied to.

setChainID1(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setChainID2(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setChainIdToIndexMap(Map<String, Integer>) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

setChainInfo(String, String, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

setChainLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setChainName(String) - Method in class org.biojava.nbio.structure.DBRef

The name of the corresponding chain.

setChainName(String) - Method in class org.biojava.nbio.structure.ResidueNumber

setChainOrigNamesMap(Map<String, String>) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

Sets a map with mapping from NCS chain names to original chain names.

setChainRmsd(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

The RMSD of the chain of AFPs.

setChains(int, List<Chain>) - Method in interface org.biojava.nbio.structure.Structure

Set the chains for a model

setChains(int, List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the chains for a model

setChains(List<Chain>) - Method in class org.biojava.nbio.structure.EntityInfo

Set the chains for this EntityInfo

setChains(List<Chain>) - Method in class org.biojava.nbio.structure.Model

setChains(List<Chain>) - Method in interface org.biojava.nbio.structure.Structure

Set the chains of a structure, if this is a NMR structure, this will only set model 0.

setChains(List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the chains of a structure, if this is a NMR structure, this will only set model 0.

setCharge(int) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setCharge(short) - Method in interface org.biojava.nbio.structure.Atom

Set the charge of this atom

setCharge(short) - Method in class org.biojava.nbio.structure.AtomImpl

setChemComp(ChemComp) - Method in interface org.biojava.nbio.structure.Group

Set the Chemical Component that closer describes this group.

setChemComp(ChemComp) - Method in class org.biojava.nbio.structure.HetatomImpl

setChemCompPathUrlTemplate(String) - Static method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

Set the path to append to the serverBaseUrl (settable in DownloadChemCompProvider.setServerBaseUrl(String)).

setChemCompProvider(ChemCompProvider) - Static method in class org.biojava.nbio.structure.chem.ChemCompGroupFactory

The new ChemCompProvider will be set in the static variable, so this provider will be used from now on until it is changed again.

setChildren(List<Integer>) - Method in class org.biojava.nbio.structure.scop.ScopNode

setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

Set the radius of a circumscribed sphere, that goes through all vertices

setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

Set the radius of a circumscribed sphere, that goes through all vertices

setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

Set the radius of a circumscribed sphere, that goes through all vertices

setCirumscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

Set the radius of a circumscribed sphere, that goes through all vertices

setClassId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setClassId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setClassification(String) - Method in class org.biojava.nbio.structure.PDBHeader

setClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setClassificationId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setCluster(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

set the number of the cluster this alignment belongs to.

setCluster(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setCluster(StructureInterfaceCluster) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setClustererMethod(SubunitClustererMethod) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Method to cluster subunits.

setClusters(List<SubunitCluster>) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

setCol(short) - Method in class org.biojava.nbio.structure.align.helper.IndexPair

setComment(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond

setCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

setCompositionId(String) - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature

setConn(Double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setContacts(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setContacts(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setContacts(AtomContactSet) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setContig(int) - Method in class org.biojava.nbio.structure.align.helper.AligMatEl

setConvergenceSteps(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setCoords(double[]) - Method in interface org.biojava.nbio.structure.Atom

Set the coordinates.

setCoords(double[]) - Method in class org.biojava.nbio.structure.AtomImpl

Set the coordinates.

setCovered(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setCPPoint(Integer) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

setCreate_co(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setCreateAtomBonds(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should we create bonds between atoms when parsing a file.

setCreateAtomCharges(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should we create charges on atoms when parsing a file?

setCrystalCell(CrystalCell) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Set the crystal cell

setCrystallographicInfo(PDBCrystallographicInfo) - Method in class org.biojava.nbio.structure.PDBHeader

setCrystallographicInfo(PDBCrystallographicInfo) - Method in interface org.biojava.nbio.structure.Structure

Set crystallographic information for this structure

setCrystallographicInfo(PDBCrystallographicInfo) - Method in class org.biojava.nbio.structure.StructureImpl

Sets crystallographic information for this structure

setCustomStringGenerator(Function<List<SubunitCluster>, String>) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Let a user-defined function handle the entire string representation of a stoichiometry.

setCut_sites(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.CutSites

setCutoff(double) - Method in class org.biojava.nbio.structure.contact.InterfaceFinder

Set the contact distance cutoff.

setData(TreeMap<Integer, SpaceGroup>) - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper

setDatabase(String) - Method in class org.biojava.nbio.structure.DBRef

Specifies the database value.

setDate(Date) - Method in class org.biojava.nbio.structure.cath.CathDomain

setDbAccession(String) - Method in class org.biojava.nbio.structure.DBRef

Sequence database accession code.

setDbIdCode(String) - Method in class org.biojava.nbio.structure.DBRef

Sequence database identification code.

setDBRefs(List<DBRef>) - Method in interface org.biojava.nbio.structure.Structure

Set the list of database references for this structure

setDBRefs(List<DBRef>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the list of database references for this structure

setDbSeqBegin(int) - Method in class org.biojava.nbio.structure.DBRef

Initial sequence number of the database seqment.

setDbSeqEnd(int) - Method in class org.biojava.nbio.structure.DBRef

The begin of the sequence position in the database

setdCutoff(double) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters

The maximum allowed distance between the centroids of two equivalent Subunits, in A.

setDefault() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

setDefaultSuperPosition(SuperPositionAbstract) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions

setDensityCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDepDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader

The deposition date of the structure in the PDB

setDescription(String) - Method in class org.biojava.nbio.structure.cath.CathNode

setDescription(String) - Method in class org.biojava.nbio.structure.EntityInfo

setDescription(String) - Method in class org.biojava.nbio.structure.PDBHeader

Deprecated.
will be removed later. Use PDBHeader.getKeywords() if you use description to keep the keywords.

setDescription(String) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setDescription(String) - Method in class org.biojava.nbio.structure.Site

sets the REMARK 800 description of the site

setDescription2(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain

Set the textual description for protein 2.

setDescriptor(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

setDescriptors(List<ChemCompDescriptor>) - Method in class org.biojava.nbio.structure.chem.ChemComp

setDetails(String) - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord

setDetails(String) - Method in class org.biojava.nbio.structure.EntityInfo

setDetails(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setDetails(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setDiagonalDistance(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDiagonalDistance2(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDirection(int) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setDisCut(double) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

setDisCut(Double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setDisFilter(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setDisSmooth(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setDist(int[][]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

setDist1(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setDist1(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setDist2(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setDist2(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setDisTable1(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setDisTable2(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setDistance(double) - Method in class org.biojava.nbio.structure.contact.AtomContact

setDistanceCutoff(Double) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setDistanceCutoff(Double) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setDistanceIncrement(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setDistanceMatrix(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFPChain

A matrix with ca1length rows and ca2length columns.

setDistanceMatrix(Matrix) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

The distance matrix this alignment is based on

setDoAngleCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDoDensityCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDoDistanceCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDoi(String) - Method in class org.biojava.nbio.structure.JournalArticle

Set the value of doi

setDomainCounter(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setDomainId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setDomainId(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setDomainName(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setDomainSplit(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setDonor1(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setDonor2(HBond) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setDoRMSCheck(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setDownloadAll(boolean) - Method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

By default this provider will download only some of the ChemComp files.

setDuplicationHint(CECPParameters.DuplicationHint) - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

setDuplicationHint(CECPParameters.DuplicationHint) - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

setDVar(Double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setEcNums(List<String>) - Method in class org.biojava.nbio.structure.EntityInfo

setEcodDatabase(String) - Static method in class org.biojava.nbio.structure.ecod.EcodFactory

Updates the default version

setEditorList(List<Author>) - Method in class org.biojava.nbio.structure.JournalArticle

setElement(Element) - Method in interface org.biojava.nbio.structure.Atom

Set element of the atom name, e.g.

setElement(Element) - Method in class org.biojava.nbio.structure.AtomImpl

Set element of the atom name, e.g.

setElement1(T) - Method in class org.biojava.nbio.structure.quaternary.OrderedPair

Sets the first element of an ordered pair.

setElement2(T) - Method in class org.biojava.nbio.structure.quaternary.OrderedPair

Sets the second element of an ordered pair.

setEnd(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

setEnergy(double) - Method in class org.biojava.nbio.structure.secstruc.HBond

setEngineered(String) - Method in class org.biojava.nbio.structure.EntityInfo

setEnsemble(MultipleAlignmentEnsemble) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Set the back-reference to its parent Ensemble.

setEnsemble(MultipleAlignmentEnsemble) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

setEntityId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

setEntityInfo(int[], String, String, String) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

setEntityInfo(EntityInfo) - Method in interface org.biojava.nbio.structure.Chain

Sets the Entity information

setEntityInfo(EntityInfo) - Method in class org.biojava.nbio.structure.ChainImpl

setEntityInfos(List<EntityInfo>) - Method in interface org.biojava.nbio.structure.Structure

Set the EntityInfo

setEntityInfos(List<EntityInfo>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the EntityInfo

setEvalCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setEvCode(String) - Method in class org.biojava.nbio.structure.Site

sets the REMARK 800 EVIDENCE CODE for the site.

setExperimentalTechnique(String) - Method in class org.biojava.nbio.structure.PDBHeader

Adds the experimental technique to the set of experimental techniques of this header.

setExpressionSystem(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemAtccNumber(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemCell(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemCellLine(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemCellularLocation(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemGene(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemOrgan(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemOrganelle(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemOtherDetails(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemPlasmid(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemStrain(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemTaxId(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemTissue(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemVariant(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemVector(String) - Method in class org.biojava.nbio.structure.EntityInfo

setExpressionSystemVectorType(String) - Method in class org.biojava.nbio.structure.EntityInfo

setFamilyId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setFetchBehavior(LocalPDBDirectory.FetchBehavior) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Set the behavior for fetching files from the server

setFetchBehavior(LocalPDBDirectory.FetchBehavior) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

setFetchBehavior(LocalPDBDirectory.FetchBehavior) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Set the behavior for fetching files from the server.

setFGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setFGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setFile1(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setFile2(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setFileFormat(String) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

setFileLocation(String) - Static method in class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider

setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

setFileParsingParameters(FileParsingParameters) - Method in class org.biojava.nbio.structure.io.PDBFileParser

setFileParsingParameters(FileParsingParameters) - Method in interface org.biojava.nbio.structure.io.StructureProvider

Set the parameters that should be used for file parsing

setFileParsingParams(FileParsingParameters) - Method in class org.biojava.nbio.structure.align.util.AtomCache

setFiletype(StructureFiletype) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Set the file type that will be parsed.

setFirstGroupAsa(GroupAsa) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setFirstGroupAsas(Map<ResidueNumber, GroupAsa>) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setFirstRepeat(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

setFlexible(boolean) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

setFocusAfpList(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setFocusAfpn(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setFocusRes1(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setFocusRes2(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setFocusResn(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setFold(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setFold(int) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setFoldId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setFormat(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setFormula(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setFormulaWeight(double) - Method in class org.biojava.nbio.structure.chem.ChemComp

setFragCompat(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setFragLen(int) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

setFragLen(int) - Method in class org.biojava.nbio.structure.align.model.AFP

setFragLen(Integer) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setFragLenSq(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setFragment(String) - Method in class org.biojava.nbio.structure.EntityInfo

setFragmentId(Integer) - Method in class org.biojava.nbio.structure.cath.CathFragment

setFragmentLength(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setFragmentMiniDistance(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setFragmentPairs(FragmentPair[]) - Method in class org.biojava.nbio.structure.align.StructurePairAligner

setFragScore(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setFrom(Integer) - Method in class org.biojava.nbio.structure.domain.pdp.Segment

setGamma(double) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

setGapCreate(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setGapExtCol(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setGapExtCol(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setGapExtend(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setGapExtend(short) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

setGapExtend(Short) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

setGapExtension(double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

setGapExtension(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setGapExtension(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setGapExtension(Double) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setGapExtRow(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setGapExtRow(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setGapLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setGapOpen(double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

setGapOpen(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setGapOpen(short) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

setGapOpen(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setGapOpen(Double) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setGapOpen(Short) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

setGapOpenCol(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setGapOpenCol(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setGapOpenRow(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setGapOpenRow(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setGaps(Boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setGene(String) - Method in class org.biojava.nbio.structure.EntityInfo

setGroup(Group) - Method in interface org.biojava.nbio.structure.Atom

Set the back-reference to its parent Group.

setGroup(Group) - Method in class org.biojava.nbio.structure.AtomImpl

Set the back-reference to its parent Group.

setGroupBond(int, int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

setGroupInfo(String, int, char, String, int, int, char, int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

setGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setGroups(List<Group>) - Method in class org.biojava.nbio.structure.Site

setHeaderInfo(float, float, float, String, String, String, String[]) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

setHeaderOnly(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Parse only the PDB file header out of the files

setHeaderVars(String) - Method in class org.biojava.nbio.structure.EntityInfo

setHeight(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

setHelixRmsdThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setHelixRmsdToRiseRatio(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setHetAtomInFile(boolean) - Method in interface org.biojava.nbio.structure.Group

Sets the field isHetAtomInFile which is intented only for helping in infering if a polymeric group is in a ligand chain or in a polymeric chain.

setHetAtomInFile(boolean) - Method in class org.biojava.nbio.structure.HetatomImpl

setHGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setHGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setHomologyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setIclose(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

setId(int) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setId(int) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

setId(int) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

setId(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setId(long) - Method in class org.biojava.nbio.structure.align.model.AFP

setId(long) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setId(long) - Method in class org.biojava.nbio.structure.HetatomImpl

the Hibernate database ID

setId(Long) - Method in class org.biojava.nbio.structure.DBRef

Set the ID used by Hibernate.

setId(Long) - Method in class org.biojava.nbio.structure.EntityInfo

set the ID used by Hibernate

setId(String) - Method in interface org.biojava.nbio.structure.Chain

Set the 'private' asymId (internal chain IDs in mmCif) for this chain.

setId(String) - Method in class org.biojava.nbio.structure.ChainImpl

setId(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setId(String) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

setId(String) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Sets the identifier for this biological assembly transformation.

setIdbnsBegin(char) - Method in class org.biojava.nbio.structure.DBRef

Insertion code of initial residue of the segment, if PDB is the reference.

setIdbnsEnd(char) - Method in class org.biojava.nbio.structure.DBRef

Insertion code of the ending residue of the segment, if PDB is the reference.

setIdCode(String) - Method in class org.biojava.nbio.structure.DBRef

Set the idCode for this entry.

setIdCode(String) - Method in class org.biojava.nbio.structure.PDBHeader

Deprecated.
use PDBHeader.setPdbId(PdbId)

setIdenticalSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setIdentity(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setIdxlist(List<int[]>) - Method in class org.biojava.nbio.structure.align.helper.JointFragments

Stores the alignment between the residues of several fragments.

setIndex(int) - Method in class org.biojava.nbio.structure.align.helper.GapArray

setInitialK(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setInitials(String) - Method in class org.biojava.nbio.structure.Author

setInsCode(Character) - Method in class org.biojava.nbio.structure.ResidueNumber

setInsCode(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setInsCode(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setInsCode1(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setInsCode2(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

Sets the radius of an inscribed sphere, that is tangent to each of the icosahedron's faces

setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

Sets the radius of an inscribed sphere, that is tangent to each of the octahedron's faces

setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Prism

Sets the radius of an inscribed sphere, that is tangent to each of the icosahedron's faces

setInscribedRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

Sets the radius of an inscribed sphere, that is tangent to each of the tetrahedron's faces

setInsertBegin(char) - Method in class org.biojava.nbio.structure.DBRef

Initial insertion code of the PDB sequence segment.

setInsertEnd(char) - Method in class org.biojava.nbio.structure.DBRef

Ending insertion code of the PDB sequence segment.

setInstalledDomainDescription(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setInstalledDomainList(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setInstalledDomall(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setInstalledNodeList(AtomicBoolean) - Method in class org.biojava.nbio.structure.cath.CathInstallation

setInterGroupBond(int, int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

setInternalSymmetry(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

The internal symmetry option divides each Subunit of each SubunitCluster into its internally symmetric repeats.

setIoTime(long) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setIoTime(long) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setIoTime(Long) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Set the IO time to load this object

setIoTime(Long) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setIsPublished(Boolean) - Method in class org.biojava.nbio.structure.JournalArticle

Sets the publication state of a JournalArticle - TO BE PUBLISHED == false

setJclose(int[]) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

setJoinFast(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setJoinPlo(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setJoinRMSCutoff(double) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setJournalArticle(JournalArticle) - Method in class org.biojava.nbio.structure.PDBHeader

Set the associated publication as defined by the JRNL records in a PDB file.

setJournalArticle(JournalArticle) - Method in interface org.biojava.nbio.structure.Structure

Set the associated publication as defined by the JRNL records in a PDB file.

setJournalArticle(JournalArticle) - Method in class org.biojava.nbio.structure.StructureImpl

set the associated publication as defined by the JRNL records in a PDB file.

setJournalName(String) - Method in class org.biojava.nbio.structure.JournalArticle

setKappa(float) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setKeywords(List<String>) - Method in class org.biojava.nbio.structure.PDBHeader

Sets the KEYWODS record of the structure.

setLcmp(int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setLcmp(int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setLength(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setLength(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setLength(Integer) - Method in class org.biojava.nbio.structure.cath.CathFragment

setLength(Integer) - Method in class org.biojava.nbio.structure.cath.CathSegment

setLength1(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setLength2(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setLevel(int) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

setLigands(Set<String>) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setLikeSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setLocalTimeLimit(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setLowerLimit(float) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

setM(Matrix) - Method in class org.biojava.nbio.structure.align.model.AFP

setMacromolecularSize(int) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

setMacromolecularSizes() - Method in class org.biojava.nbio.structure.io.PDBBioAssemblyParser

Set the macromolecularSize fields of the parsed bioassemblies.

setManual(Boolean) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setMapProperty(TreeMap<Integer, SpaceGroup>) - Method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot

setMatMatrix(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setMatMatrix(double[][]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setMatrix(int[], int[], Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Set a submatrix.

setMatrix(int[], int, int, Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Set a submatrix.

setMatrix(int, int, int[], Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Set a submatrix.

setMatrix(int, int, int, int, Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Set a submatrix.

setMatTransform(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

setMaxAtoms(int) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

The maximum numbers of atoms to load in a protein structure (prevents memory overflows)

setMaxGap(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setMaxGapFrag(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setMaxGapSize(int) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

CE specific parameter: set the Max gap size parameter G (during AFP extension).

setMaxGapSize(Integer) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Set the Max gap size parameter.

setMaximumLocalCombinations(int) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMaxIter(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setMaxNrIterationsForOptimization(int) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Set the maximum nr of times the (slow) optimiziation of alignment should iterate.

setMaxOptRMSD(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

set the maximum RMSD cutoff to be applied during alignment optimization.

setMaxOptRMSD(Double) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

(jCE specific): maximum RMSD that shall be calculated for the alignment.

setMaxOrientationAngle(double) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters

The maximum orientation angle between two equivalent Subunits, in radians.

setMaxPenalty(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setMaxPropeller(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method sets the maximum propeller allowed for a base pair, prior to analyze() call

setMaxPropeller(double) - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

This method sets the maximum propeller allowed for a base pair, prior to analyze() call

setMaxrefine(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setMaxRmsd(double) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignParameters

The maximum allowed RMSD of the alignment, in A.

setMaxRmsd(double) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

setMaxRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setMaxRmsd(Double) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

setMaxShear(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method sets the maximum shear allowed for a base pair, prior to analyze() call

setMaxStagger(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method sets the maximum stagger allowed for a base pair, prior to analyze() call

setMaxStagger(double) - Method in class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

This method sets the maximum stagger allowed for a base pair, prior to analyze() call

setMaxStretch(double) - Method in class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

This method sets the maximum stretch allowed for a base pair, prior to analyze() call.

setMaxSymmOrder(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setMaxTm(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setMaxTra(int) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

setMaxTra(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

Set the maximum number of Twists that are allowed...

setMaxTra(Integer) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

set the maximum number of Twists that are allowed...

setMembers(List<StructureInterface>) - Method in class org.biojava.nbio.structure.contact.StructureInterfaceCluster

setMethod(String) - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage

setMidRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Icosahedron

Sets the radius of radius of a sphere, that is tangent to each of the icosahedron's edges

setMidRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Octahedron

Sets the radius of radius of a sphere, that is tangent to each of the octahedron's edges

setMidRadius(double) - Method in class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

Sets the radius of radius of a sphere, that is tangent to each of the tetrahedron's edges

setMinAlignedStructures(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setMinBlockLen(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setMinCoreLength(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setMinCPLength(Integer) - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

setMinCPLength(Integer) - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

setMinimumHelixAngle(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMinimumHelixRise(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setMinimumSequenceLength(int) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Set the minimum number of residues of a subunits to be considered in the clusters.

setMinimumSequenceLengthFraction(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.

setMinLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setMinLen(int) - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

setMinLen(Integer) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

setMinRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setMinTm(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setMisCut(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setMisLen(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setMisScore(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setModDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader

The latest modification date of the structure.

setModel(int, List<Chain>) - Method in interface org.biojava.nbio.structure.Structure

A convenience function if one wants to edit and replace the models in a structure.

setModel(int, List<Chain>) - Method in class org.biojava.nbio.structure.StructureImpl

A convenience function if one wants to edit and replace the models in a structure.

setModelCartnX(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setModelCartnY(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setModelCartnZ(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setModelInfo(int, int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

setMoleculeIds(Pair<String>) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setMolecules(Pair<Atom[]>) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setMolId(int) - Method in class org.biojava.nbio.structure.EntityInfo

Set the molecule identifier, called entity_id in mmCIF dictionary.

setMonNstdFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setMonNstdParentCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setMultipleAlignment(MultipleAlignment) - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Set the back-reference to its parent MultipleAlignment.

setMultipleAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

setMultipleAlignment(MultipleAlignment) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setMultipleAlignments(List<MultipleAlignment>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Set the List of MultipleAlignments in the ensemble.

setMultipleAlignments(List<MultipleAlignment>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setMultiplicity(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setMutation(String) - Method in class org.biojava.nbio.structure.EntityInfo

setName(String) - Method in interface org.biojava.nbio.structure.Atom

Set atom name, e.g.

setName(String) - Method in class org.biojava.nbio.structure.AtomImpl

Set atom name, e.g.

setName(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setName(String) - Method in interface org.biojava.nbio.structure.Chain

Set the 'public' authId (chain ID in PDB file)

setName(String) - Method in class org.biojava.nbio.structure.ChainImpl

setName(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setName(String) - Method in class org.biojava.nbio.structure.cluster.Subunit

The Name of a Subunit is a free-text field, user defined.

setName(String) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setName(String) - Method in interface org.biojava.nbio.structure.Structure

Set biological name of Structure .

setName(String) - Method in class org.biojava.nbio.structure.StructureImpl

Set biological name of Structure .

setName1(String) - Method in class org.biojava.nbio.structure.align.client.PdbPair

setName1(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setName2(String) - Method in class org.biojava.nbio.structure.align.client.PdbPair

setName2(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setnAtom(int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

setnAtom(int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

setNaturalPos(Integer) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setNclose(int) - Method in class org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix

setNcsOperators(Matrix4d[]) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Set the NCS operators.

setNcuts(int) - Method in class org.biojava.nbio.structure.domain.pdp.CutSites

setNodeId(String) - Method in class org.biojava.nbio.structure.cath.CathNode

setNonStandardCoordFrameConvention(boolean) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Set the non-standard coordinate frame convention field

setNonStandardSg(boolean) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Set the non-standard space group field

setNormAlignScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setNotObserved(Boolean) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setNrCPU(int) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setNrThreads(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setNseg(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

setnStart(int) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setNumBonds(int) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfSummaryDataBean

setNumCells(int) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder

Set the number of neighboring crystal cells that will be used in the search for contacts

setNumRepeats(int) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setNumRes(String) - Method in class org.biojava.nbio.structure.EntityInfo

setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior) - Method in class org.biojava.nbio.structure.align.util.AtomCache

[Optional] This method changes the behavior when obsolete entries are requested.

setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

[Optional] This method changes the behavior when obsolete entries are requested.

setOccupancy(float) - Method in interface org.biojava.nbio.structure.Atom

Set occupancy.

setOccupancy(float) - Method in class org.biojava.nbio.structure.AtomImpl

setOmega(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setOneLetterCode(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setOnTheFly(boolean) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

On-the-fly Jmol bioassembly generation.

setOperator(Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis

setOptAln(int[][][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setOptimization(Boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setOptimizationSteps(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setOptimizeAlignment(boolean) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Whether the CE algorithm should extend the best found trace with dynamic programming, while keeping RMSD at about the same level.

setOptimizeAlignment(boolean) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.

setOptimizeAlignment(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.

setOptLen(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setOptLength(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

The length of the optimal alignment.

setOptRmsd(double[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setOrderDetectorMethod(CESymmParameters.OrderDetectorMethod) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setOrgan(String) - Method in class org.biojava.nbio.structure.EntityInfo

setOrganelle(String) - Method in class org.biojava.nbio.structure.EntityInfo

setOrganismCommon(String) - Method in class org.biojava.nbio.structure.EntityInfo

setOrganismScientific(String) - Method in class org.biojava.nbio.structure.EntityInfo

setOrganismTaxId(String) - Method in class org.biojava.nbio.structure.EntityInfo

setOrigGroup(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setOrigGroup(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setORmsdThr(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Set the Original RMSD threshold from which the alignment optimization is started

setOrthologousSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setOutFile(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setOutFile(SynchronizedOutFile) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setOutputDir(File) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setOutputPDB(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

When writing the results to a file, don;t write as XML but write aligned PDB file

setP1(int) - Method in class org.biojava.nbio.structure.align.model.AFP

setP2(int) - Method in class org.biojava.nbio.structure.align.model.AFP

setPair(PdbPair) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setPair(Pair<Atom>) - Method in class org.biojava.nbio.structure.contact.AtomContact

setPair(Pair<Group>) - Method in class org.biojava.nbio.structure.contact.GroupContact

setPairs(SortedSet<PdbPair>) - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.AbstractStructureAlignment

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.BioJavaStructureAlignment

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.CallableStructureAlignment

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.ce.CeMain

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.ce.CeSideChainMain

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPMain

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatFlexible

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatRigid

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain

setParameters(ConfigStrucAligParams) - Method in interface org.biojava.nbio.structure.align.MultipleStructureAligner

Set the parameters for this algorithm to use.

setParameters(ConfigStrucAligParams) - Method in class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner

setParameters(ConfigStrucAligParams) - Method in interface org.biojava.nbio.structure.align.StructureAlignment

Set the default parameters for this algorithm to use

setParams(StrucAligParameters) - Method in class org.biojava.nbio.structure.align.StructurePairAligner

set the parameters to be used for the algorithm

setParams(CESymmParameters) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setParent(Structure) - Method in class org.biojava.nbio.structure.DBRef

Set the structure object that this DBRef relates to.

setParentId(String) - Method in class org.biojava.nbio.structure.cath.CathNode

setParentSunid(int) - Method in class org.biojava.nbio.structure.scop.ScopNode

setParseBioAssembly(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should the biological assembly info (REMARK 350) be parsed from the PDB file?

setParseCAOnly(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Flag if only the C-alpha atoms of the structure should be parsed.

setParseSecStruc(boolean) - Method in class org.biojava.nbio.structure.io.FileParsingParameters

A flag to tell the parser to parse the Author's secondary structure assignment from the file default is set to false, i.e.

setPartner(int) - Method in class org.biojava.nbio.structure.secstruc.HBond

setPath(String) - Method in class org.biojava.nbio.structure.align.util.AtomCache

Set the path that is used to cache PDB files.

setPath(String) - Method in class org.biojava.nbio.structure.io.LocalPDBDirectory

Sets the path for the directory where PDB files are read/written

setPath(IndexPair[]) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setPath(IndexPair[]) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setPathSize(int) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setPathSize(int) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setPdb1(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

mandatory argument to set the first PDB (and optionally chain ID) to be aligned.

setPdb1(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setPdb2(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

mandatory argument to set the second PDB (and optionally chain ID) to be aligned.

setPdb2(String) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

setPdbAln(String[][][]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setPDBCode(String) - Method in interface org.biojava.nbio.structure.Structure

Deprecated.
use #setPDBCode(PdbId)

setPDBCode(String) - Method in class org.biojava.nbio.structure.StructureImpl

Deprecated.
use #setPDBCode(PdbId)

setPdbFilePath(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

mandatory argument to set the location of PDB files.

setPdbFilePath(String) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

setPDBFlag(boolean) - Method in interface org.biojava.nbio.structure.Group

Flag if group has 3D data .

setPDBFlag(boolean) - Method in class org.biojava.nbio.structure.HetatomImpl

setPdbGroup(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setPdbGroup(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setPDBHeader(PDBHeader) - Method in interface org.biojava.nbio.structure.Structure

Set the the header information for this PDB file

setPDBHeader(PDBHeader) - Method in class org.biojava.nbio.structure.StructureImpl

Set the the header information for this PDB file

setPdbId(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setPdbId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setPdbId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain

Deprecated.
use ScopDomain.setPdbId(PdbId)

setPdbId(PdbId) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setPdbId(PdbId) - Method in class org.biojava.nbio.structure.PDBHeader

Sets the PDB identifier code for this protein structure.

setPdbId(PdbId) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setPdbId(PdbId) - Method in interface org.biojava.nbio.structure.Structure

Sets the PdbId identifier associated with this structure.

setPdbId(PdbId) - Method in class org.biojava.nbio.structure.StructureImpl

Sets the PdbId identifier associated with this structure.

setPDBName(String) - Method in class org.biojava.nbio.structure.AminoAcidImpl

set three character name of AminoAcid.

setPDBName(String) - Method in interface org.biojava.nbio.structure.Group

Set the PDB 3-letter name for this group.

setPDBName(String) - Method in class org.biojava.nbio.structure.HetatomImpl

setPdbResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setPdbResNum(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setPdbResNum(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setPdbResNum(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setPDBresnum1(String[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setPDBresnum2(String[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setPdbSerial(int) - Method in class org.biojava.nbio.structure.contact.AtomIdentifier

setPDBserial(int) - Method in interface org.biojava.nbio.structure.Atom

Set PDB atom number.

setPDBserial(int) - Method in class org.biojava.nbio.structure.AtomImpl

Set PDB atom number.

setPdbxAlign(int) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxAmbiguousFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxAromaticFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxAromaticFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond

setPdbxComponentAtomId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxComponentCompId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxComponentId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxFormalCharge(int) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxIdealCoordinatesDetails(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxIdealCoordinatesMissingFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxInitialDate(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxLeavingAtomFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxModelCartnXIdeal(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxModelCartnYIdeal(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxModelCartnZIdeal(double) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxModelCoordinatesDbCode(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxModelCoordinatesDetails(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxModelCoordinatesMissingFlag(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxModifiedDate(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxOrdinal(int) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxOrdinal(int) - Method in class org.biojava.nbio.structure.chem.ChemCompBond

setPdbxPolymerType(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxProcessingSite(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxRefId(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxReleaseStatus(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxReplacedBy(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxReplaces(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxResidueNumbering(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxStereoConfig(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setPdbxStereoConfig(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond

setPdbxSubcomponentList(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxSynonyms(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPdbxType(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPercId(int) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setPermutation(List<Integer>) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setPermutationSize(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setPhi(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setPmid(String) - Method in class org.biojava.nbio.structure.JournalArticle

Set the value of pmid

setPolymerType(PolymerType) - Method in class org.biojava.nbio.structure.chem.ChemComp

setPos1(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setPos2(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setPrimitiveMultiplicity(int) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setPrintCE(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

Display the output string in CE style

setPrintConnections(boolean) - Method in class org.biojava.nbio.structure.io.FileConvert

enable/disable printing of connections connections are sometimes buggy in PDB files so there are some cases where one might turn this off.

setPrintFatCat(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setPrintXML(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setProbability(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setProgram(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

setProgramVersion(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

setProperties(Map<String, Object>) - Method in interface org.biojava.nbio.structure.Group

Properties of this amino acid.

setProperties(Map<String, Object>) - Method in class org.biojava.nbio.structure.HetatomImpl

Properties of this amino acid.

setProperty(String, Object) - Method in interface org.biojava.nbio.structure.Group

Set a single property .

setProperty(String, Object) - Method in class org.biojava.nbio.structure.HetatomImpl

setPsi(double) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

setPublicationDate(int) - Method in class org.biojava.nbio.structure.JournalArticle

setPublished(boolean) - Method in class org.biojava.nbio.structure.JournalArticle

setPublisher(String) - Method in class org.biojava.nbio.structure.JournalArticle

setPx(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setRandomSeed(Integer) - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

setRange(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setRanges(List<String>) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setRecordType(String) - Method in interface org.biojava.nbio.structure.AminoAcid

Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.

setRecordType(String) - Method in class org.biojava.nbio.structure.AminoAcidImpl

Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.

setReduceInitialFragments(boolean) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setRef(String) - Method in class org.biojava.nbio.structure.JournalArticle

Set the value of the ref.

setRefChainId(String) - Method in class org.biojava.nbio.structure.EntityInfo

Return the ref chain id value.

setRefined(boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setRefinedScoreThreshold(Double) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setRefineMethod(CESymmParameters.RefineMethod) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setRefineResult(boolean) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

Deprecated.

setRefn(String) - Method in class org.biojava.nbio.structure.JournalArticle

Set the value of the refn

setRelation(QsRelation) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

The quaternary structure relation QsRelation between the two groups of Subunits.

setRelDate(Date) - Method in class org.biojava.nbio.structure.PDBHeader

The release date of the structure in the PDB.

setRemoveCif(boolean) - Method in class org.biojava.nbio.structure.chem.ZipChemCompProvider

Remove downloaded .cif.gz after adding to zip archive? Default is true.

setRepeatUnits(List<List<Integer>>) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setRepresentative(String) - Method in class org.biojava.nbio.structure.cath.CathNode

setResidueNumber(String, Integer, Character) - Method in interface org.biojava.nbio.structure.Group

Utility method to temporarily set a chainID for a group, if a parent chain object does not exist yet.

setResidueNumber(String, Integer, Character) - Method in class org.biojava.nbio.structure.HetatomImpl

setResidueNumber(ResidueNumber) - Method in interface org.biojava.nbio.structure.Group

Sets the ResidueNumber for this Group

setResidueNumber(ResidueNumber) - Method in class org.biojava.nbio.structure.HetatomImpl

setResidues(List<SiftsResidue>) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

setResidueType(ResidueType) - Method in class org.biojava.nbio.structure.chem.ChemComp

setResNames(String) - Method in class org.biojava.nbio.structure.EntityInfo

setResnum1(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setResnum2(String) - Method in class org.biojava.nbio.structure.io.SSBondImpl

setResolution(float) - Method in class org.biojava.nbio.structure.PDBHeader

setResolution(Double) - Method in class org.biojava.nbio.structure.cath.CathDomain

setResScore(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setRevisionRecords(List<DatabasePDBRevRecord>) - Method in class org.biojava.nbio.structure.PDBHeader

setRevNum(String) - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord

setRfree(float) - Method in class org.biojava.nbio.structure.PDBHeader

setRise(double) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setRms(double) - Method in class org.biojava.nbio.structure.align.helper.JointFragments

setRms(double) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

the rms in the structurally equivalent regions

setRms(double) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setRmsd(double) - Method in class org.biojava.nbio.structure.align.model.AFP

setRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setRmsdCenters(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setRmsdCut(Double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

The cutoff to be used during AFP detection

setRmsdCut(Double) - Method in class org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams

setRmsdIntra(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setRmsdThr(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setRmsdThreshold(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

setRMSDThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Structure similarity threshold (measured with RMSD) to consider for the structural subunit clustering.

setRmsdThrJoin(Double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setRndSeed(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setRot(Matrix) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setRotationMatrix(double[][]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

setRow(short) - Method in class org.biojava.nbio.structure.align.helper.IndexPair

setRwork(float) - Method in class org.biojava.nbio.structure.PDBHeader

setSaveOutputDir(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setScopDatabase(String) - Static method in class org.biojava.nbio.structure.scop.ScopFactory

Set the default scop version

setScopDatabase(ScopDatabase) - Static method in class org.biojava.nbio.structure.scop.ScopFactory

Set the default scop version and instance

setScopId(String) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setScopVersion(String) - Method in interface org.biojava.nbio.structure.scop.ScopDatabase

Sets the scop version used.

setScopVersion(String) - Method in class org.biojava.nbio.structure.scop.ScopInstallation

setScore(double) - Method in class org.biojava.nbio.structure.align.model.AFP

setScore(double) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

setScore(double) - Method in class org.biojava.nbio.structure.domain.pdp.Segment

setScore(float) - Method in interface org.biojava.nbio.structure.align.pairwise.Alignable

setScore(float) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

setScore(float) - Method in class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

setScores(QuatSymmetryScores) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setScores(QuatSymmetryScores) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setScoringStrategy(CeParameters.ScoringStrategy) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Set the scoring strategy to use.

setScoringStrategy(CeParameters.ScoringStrategy) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

setSearchFile(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setSecondGroupAsa(GroupAsa) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setSecondGroupAsas(Map<ResidueNumber, GroupAsa>) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setSecretion(String) - Method in class org.biojava.nbio.structure.EntityInfo

setSecStructType(Group, int) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Get the secondary structure as defined by DSSP.

setSeedFragmentLength(int) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setSeedRmsdCutoff(float) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setSegId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

setSegmentId(Integer) - Method in class org.biojava.nbio.structure.cath.CathSegment

setSegments(List<CathSegment>) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSegments(List<Segment>) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

setSegments(List<SiftsSegment>) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

setSelfAlignment(AFPChain) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setSeqBegin(int) - Method in class org.biojava.nbio.structure.DBRef

Initial sequence number of the PDB sequence segment.

setSeqEnd(int) - Method in class org.biojava.nbio.structure.DBRef

Ending sequence number of the PDB sequence segment.

setSeqIdRange(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setSeqMisMatches(List<SeqMisMatch>) - Method in interface org.biojava.nbio.structure.Chain

Sets annotated sequence mismatches for this chain.

setSeqMisMatches(List<SeqMisMatch>) - Method in class org.biojava.nbio.structure.ChainImpl

setSeqNum(Integer) - Method in class org.biojava.nbio.structure.ResidueNumber

setSeqNum(Integer) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setSeqNum(Integer) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setSeqResGroups(List<Group>) - Method in interface org.biojava.nbio.structure.Chain

Sets the list of SeqResGroups for this chain.

setSeqResGroups(List<Group>) - Method in class org.biojava.nbio.structure.ChainImpl

setSeqResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setSequence(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSequence(String) - Method in class org.biojava.nbio.structure.cath.CathSegment

setSequenceCoverageThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

The minimum coverage of the sequence alignment between two subunits to be clustered together.

setSequenceFamilyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSequenceHeader(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSequenceHeader(String) - Method in class org.biojava.nbio.structure.cath.CathSegment

setSequenceIdentityThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Sequence identity threshold to consider for the sequence subunit clustering.

setSequentialAlignment(boolean) - Method in class org.biojava.nbio.structure.align.model.AFPChain

Set whether this alignment has the normal topology, ie the residues aligned in each block increase sequentially over the original protein.

setSeqWeight(double) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.

setSerNum(int) - Method in class org.biojava.nbio.structure.io.SSBondImpl

get serial number of this SSBOND in PDB file

setServerBaseUrl(String) - Static method in class org.biojava.nbio.structure.chem.DownloadChemCompProvider

Set the base URL for the location of all chemical component CIF files, to which the chemCompPathUrlTemplate is appended, settable in DownloadChemCompProvider.setChemCompPathUrlTemplate(String).

setShortAlign(boolean) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setShortSymbol(String) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setShow3d(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setShowAFPRanges(boolean) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setShowAFPRanges(boolean) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

setShowDBresult(String) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setShowMenu(boolean) - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

setSimilarity(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setSiteID(String) - Method in class org.biojava.nbio.structure.Site

setSites(List<Site>) - Method in interface org.biojava.nbio.structure.Structure

setSites(List<Site>) - Method in class org.biojava.nbio.structure.StructureImpl

setSize(int) - Method in class org.biojava.nbio.structure.domain.pdp.Domain

setSOLID(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSource(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setSpaceGroup(SpaceGroup) - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

Set the SpaceGroup

setSparse(int) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setSpeciesId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setSSBonds(List<Bond>) - Method in interface org.biojava.nbio.structure.Structure

Set the list of SSBonds for this structure

setSSBonds(List<Bond>) - Method in class org.biojava.nbio.structure.StructureImpl

Set the list of SSBonds for this structure

setSSEThreshold(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setStart(String) - Method in class org.biojava.nbio.structure.cath.CathFragment

setStart(String) - Method in class org.biojava.nbio.structure.cath.CathSegment

setStart(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

setStartPage(String) - Method in class org.biojava.nbio.structure.JournalArticle

setStop(String) - Method in class org.biojava.nbio.structure.cath.CathFragment

setStop(String) - Method in class org.biojava.nbio.structure.cath.CathSegment

setStrain(String) - Method in class org.biojava.nbio.structure.EntityInfo

setStrategy(Stoichiometry.StringOverflowStrategy) - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Change string representation of a stoichiometry in case number of clusters exceeds number of letters in the alphabet.

setStructure(Structure) - Method in interface org.biojava.nbio.structure.Chain

Sets the back-reference to its parent Structure.

setStructure(Structure) - Method in class org.biojava.nbio.structure.ChainImpl

setStructure(Structure) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

setStructureCoverageThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

The minimum coverage of the structure alignment between two subunits to be clustered together.

setStructureId(StructureIdentifier) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setStructureIdentifier(StructureIdentifier) - Method in interface org.biojava.nbio.structure.Structure

Set the identifier corresponding to this structure

setStructureIdentifier(StructureIdentifier) - Method in class org.biojava.nbio.structure.StructureImpl

setStructureIdentifiers(List<StructureIdentifier>) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Set the List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).

setStructureIdentifiers(List<StructureIdentifier>) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setSubstitutionMatrix(SubstitutionMatrix<AminoAcidCompound>) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.

setSubunitMap(Map<Integer, Integer>) - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

Map of Subunit equivalencies from the first to the second group.

setSubunitRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setSunid(int) - Method in class org.biojava.nbio.structure.scop.ScopNode

setSunid(Integer) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setSunID(int) - Method in class org.biojava.nbio.structure.scop.ScopDescription

setSuperfamilyId(int) - Method in class org.biojava.nbio.structure.scop.ScopDomain

setSuperpositionAlgorithm(String) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Method to cluster subunits.

setSurname(String) - Method in class org.biojava.nbio.structure.Author

setSymDeviation(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setSymmetryDeviation(double) - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

setSymmetryDeviation(double) - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

setSymmGroup(String) - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

setSymmLevels(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setSymmType(CESymmParameters.SymmetryType) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setSynonyms(List<String>) - Method in class org.biojava.nbio.structure.EntityInfo

setSynthetic(String) - Method in class org.biojava.nbio.structure.EntityInfo

setT(double[]) - Method in class org.biojava.nbio.structure.align.model.AFP

setTempFactor(float) - Method in interface org.biojava.nbio.structure.Atom

Set temp factor .

setTempFactor(float) - Method in class org.biojava.nbio.structure.AtomImpl

setTGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setThreeLetterCode(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setTissue(String) - Method in class org.biojava.nbio.structure.EntityInfo

setTitle(String) - Method in class org.biojava.nbio.structure.EntityInfo

setTitle(String) - Method in class org.biojava.nbio.structure.JournalArticle

Set the value of title

setTitle(String) - Method in class org.biojava.nbio.structure.PDBHeader

setTm(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setTmIntra(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

setTMScore(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setTMThreshold(double) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Structure similarity threshold (measured with TMScore) to consider for the structural subunit clustering.

setTo(Integer) - Method in class org.biojava.nbio.structure.domain.pdp.Segment

setTopologyId(Integer) - Method in class org.biojava.nbio.structure.cath.CathDomain

setTorsionPenalty(double) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

setTotalArea(double) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setTotalLenIni(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setTotalLenOpt(int) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setTotalRmsdIni(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

this is the init-RMSD, not the final RMSD after refinement.

setTotalRmsdOpt(double) - Method in class org.biojava.nbio.structure.align.model.AFPChain

The RMSD of the final alignment.

setTraceRmsd(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setTraceTmScoreMin(double) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setTrans(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setTransfAlgebraic(List<String>) - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

setTransformation(Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.core.Helix

setTransformation(Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

setTransformationMatrix(Matrix4d) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Sets the transformation using a 4x4 transformation matrix

setTransformations(List<Matrix4d>) - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Set a new superposition for the structures.

setTransformations(List<Matrix4d>) - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

setTransformId(int) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

setTransforms(List<BiologicalAssemblyTransformation>) - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

setTransforms(Pair<CrystalTransform>) - Method in class org.biojava.nbio.structure.contact.StructureInterface

setTranslation(double[]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

setTryAllCPs(Boolean) - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

setTurn(char, int) - Method in class org.biojava.nbio.structure.secstruc.SecStrucState

Set the turn column corresponding to 3,4 or 5 helix patterns.

setTwi(int[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setTwistedGroups(Group[]) - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner

setType(String) - Method in class org.biojava.nbio.structure.chem.ChemComp

setType(String) - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

setType(String) - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord

setType(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

setType(EntityType) - Method in class org.biojava.nbio.structure.EntityInfo

Set the type of entity this EntityInfo describes.

setType(SecStrucType) - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo

setTypeSymbol(String) - Method in class org.biojava.nbio.structure.chem.ChemCompAtom

setUid(Long) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setUnaryOperators(List<String>) - Method in class org.biojava.nbio.structure.quaternary.OperatorResolver

setUniProtAccessionId(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setUniProtId(String) - Method in interface org.biojava.nbio.structure.SeqMisMatch

setUniProtId(String) - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

setUniProtPos(Integer) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setUniProtResName(String) - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

setUnitv(Atom) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setUnrefinedScoreThreshold(Double) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setUpdateFrequency(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

The "latest" version will be re-downloaded if it is older than EcodInstallation.getUpdateFrequency() days.

setUpperLimit(float) - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

setUrl(String) - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

Specify a different mirror for the ECOD server.

setUsed(int) - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

setUsedAtomNames(String[]) - Method in class org.biojava.nbio.structure.align.StrucAligParameters

setUseEntityIdForSeqIdentityDetermination(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Whether to use the entity id of subunits to infer that sequences are identical.

setUseGlobalMetrics(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use metrics calculated relative to the whole sequence or structure, rather than the aligned part only

setUseRMSD(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use RMSD for evaluating structure similarity

setUserOrder(Integer) - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

setUseSequenceCoverage(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use sequence coverage for evaluating sequence similarity

setUseStructureCoverage(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use structure coverage for evaluating sequence similarity

setUseTMScore(boolean) - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Use TMScore for evaluating structure similarity

setValue(int) - Method in class org.biojava.nbio.structure.align.helper.AligMatEl

setValue(int) - Method in class org.biojava.nbio.structure.align.helper.GapArray

setValueOrder(String) - Method in class org.biojava.nbio.structure.chem.ChemCompBond

setVariant(String) - Method in class org.biojava.nbio.structure.EntityInfo

setVersion(String) - Method in class org.biojava.nbio.structure.align.model.AFPChain

setVersion(String) - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Sets the version of the algorithm used to generate the MultipleAlignment objects.

setVersion(String) - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

setVersion(String) - Method in class org.biojava.nbio.structure.cath.CathDomain

setVolume(String) - Method in class org.biojava.nbio.structure.JournalArticle

setWinSize(int) - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

setWinSize(Integer) - Method in class org.biojava.nbio.structure.align.ce.CeParameters

setX(double) - Method in interface org.biojava.nbio.structure.Atom

Set the X coordinate.

setX(double) - Method in class org.biojava.nbio.structure.AtomImpl

setXGroup(Integer) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setXGroupName(String) - Method in class org.biojava.nbio.structure.ecod.EcodDomain

setXtalInfo(String, float[], double[][]) - Method in class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader

setY(double) - Method in interface org.biojava.nbio.structure.Atom

Set the Y coordinate.

setY(double) - Method in class org.biojava.nbio.structure.AtomImpl

setZ(double) - Method in interface org.biojava.nbio.structure.Atom

Set the Z coordinate.

setZ(double) - Method in class org.biojava.nbio.structure.AtomImpl

shift(Atom[], Atom) - Static method in class org.biojava.nbio.structure.Calc

Shift an array of atoms at once.

shift(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Shift a vector.

shift(Group, Atom) - Static method in class org.biojava.nbio.structure.Calc

Shift a Group with a vector.

shift(Structure, Atom) - Static method in class org.biojava.nbio.structure.Calc

shift a structure with a vector.

shiftCA2(AFPChain, Atom[], Matrix, Atom, Group[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

only shift CA positions.

SHORTER - org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint

ShortSegmentRemover - Class in org.biojava.nbio.structure.domain.pdp

ShortSegmentRemover() - Constructor for class org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover

shouldCreateAtomBonds() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should we create bonds between atoms when parsing a file?

shouldCreateAtomCharges() - Method in class org.biojava.nbio.structure.io.FileParsingParameters

Should we create charges on atoms when parsing a file?

showAFPRanges - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

showAFPRanges - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

showAlignmentGUI() - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

showAlignmentImage(AFPChain, Atom[], Atom[], Object) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

showStructure(Structure) - Static method in class org.biojava.nbio.structure.align.ce.GuiWrapper

Shows a structure in Jmol

Si - org.biojava.nbio.structure.Element

SIDE_CHAIN_ANGLE_SCORING - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

SIDE_CHAIN_SCORING - org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

sideChainScoringType - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

SiftsChainEntry - Class in org.biojava.nbio.structure.io.sifts

An entry in the chain-level SIFTS mapping between UniProt and the PDB.

SiftsChainEntry(String, String, String, String, String, String, String, String, String) - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

SiftsChainToUniprotMapping - Class in org.biojava.nbio.structure.io.sifts

A mapping between UniProt entries and PDB chains.

SiftsEntity - Class in org.biojava.nbio.structure.io.sifts

SiftsEntity() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsEntity

SiftsEntity(String, String) - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsEntity

SiftsMappingProvider - Class in org.biojava.nbio.structure.io.sifts

SiftsMappingProvider() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsMappingProvider

SiftsResidue - Class in org.biojava.nbio.structure.io.sifts

SiftsResidue() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsResidue

SiftsSegment - Class in org.biojava.nbio.structure.io.sifts

SiftsSegment() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsSegment

SiftsSegment(String, String, String) - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsSegment

SiftsXMLParser - Class in org.biojava.nbio.structure.io.sifts

SiftsXMLParser() - Constructor for class org.biojava.nbio.structure.io.sifts.SiftsXMLParser

SigEva - Class in org.biojava.nbio.structure.align.fatcat.calc

SigEva() - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.SigEva

SingularValueDecomposition - Class in org.biojava.nbio.structure.jama

Singular Value Decomposition.

SingularValueDecomposition(Matrix) - Constructor for class org.biojava.nbio.structure.jama.SingularValueDecomposition

Construct the singular value decomposition.

Site - Class in org.biojava.nbio.structure

Holds the data of sites presented in PDB files.

Site() - Constructor for class org.biojava.nbio.structure.Site

Site(String, List<Group>) - Constructor for class org.biojava.nbio.structure.Site

site2 - Variable in class org.biojava.nbio.structure.domain.pdp.CutValues

SIXBAR - org.biojava.nbio.structure.xtal.TransformType

SIXFOLD - org.biojava.nbio.structure.xtal.TransformType

SIXFOLDSCREW - org.biojava.nbio.structure.xtal.TransformType

size() - Method in interface org.biojava.nbio.structure.align.multiple.Block

Returns the number of aligned structures (rows) in the Block.

size() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

size() - Method in interface org.biojava.nbio.structure.align.multiple.BlockSet

Returns the number of aligned structures in the BlockSet.

size() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

size() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Returns the number of aligned structures in the MultipleAlignment.

size() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble

Returns the number of aligned structures in the MultipleAlignments.

size() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

size() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

size() - Method in class org.biojava.nbio.structure.chem.ChemicalComponentDictionary

Returns the number of ChemComps in this dictionary

size() - Method in class org.biojava.nbio.structure.cluster.Subunit

The size of a Subunit is the number of residues it contains.

size() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

size() - Method in class org.biojava.nbio.structure.contact.AtomContactSet

size() - Method in class org.biojava.nbio.structure.contact.GroupContactSet

size() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

size() - Method in interface org.biojava.nbio.structure.Group

Get number of atoms.

size() - Method in class org.biojava.nbio.structure.HetatomImpl

Get number of atoms.

size() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

Returns the number of mapped entries.

size() - Method in class org.biojava.nbio.structure.math.SparseVector

size() - Method in class org.biojava.nbio.structure.math.SymbolTable

How many keys are in the table?

size() - Method in class org.biojava.nbio.structure.Model

Returns the total number of chains in this model: polymeric, non-polymeric and water

size() - Method in interface org.biojava.nbio.structure.Structure

Return number of polymer Chains in this Structure for first model.

size() - Method in class org.biojava.nbio.structure.StructureImpl

size() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

size(int) - Method in interface org.biojava.nbio.structure.Structure

Return number of chains of model.

size(int) - Method in class org.biojava.nbio.structure.StructureImpl

return number of chains of model.

Sm - org.biojava.nbio.structure.Element

SmithWaterman3Daligner - Class in org.biojava.nbio.structure.align.seq

Provides a 3D superimposition of two structures based on their sequence alignment.

SmithWaterman3Daligner() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner

SmithWaterman3DParameters - Class in org.biojava.nbio.structure.align.seq

SmithWaterman3DParameters() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

SmithWatermanStartupParams() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

SmithWatermanUserArgumentProcessor - Class in org.biojava.nbio.structure.align.seq

SmithWatermanUserArgumentProcessor() - Constructor for class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor

SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams - Class in org.biojava.nbio.structure.align.seq

Sn - org.biojava.nbio.structure.Element

SOLID_STATE_NMR - org.biojava.nbio.structure.ExperimentalTechnique

SOLUTION_NMR - org.biojava.nbio.structure.ExperimentalTechnique

SOLUTION_SCATTERING - org.biojava.nbio.structure.ExperimentalTechnique

solve(Matrix) - Method in class org.biojava.nbio.structure.jama.CholeskyDecomposition

Solve A*X = B

solve(Matrix) - Method in class org.biojava.nbio.structure.jama.LUDecomposition

Solve A*X = B

solve(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Solve A*X = B

solve(Matrix) - Method in class org.biojava.nbio.structure.jama.QRDecomposition

Least squares solution of A*X = B

solveTranspose(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Solve X*A = B, which is also A'*X' = B'

sort() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

Sorts the interface list and reassigns ids based on new sorting

sortAfps(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator

sortBlocks(List<Block>, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Sort blocks so that the specified row is in sequential order.

sortByFoldDecending() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

SpaceGroup - Class in org.biojava.nbio.structure.xtal

A crystallographic space group.

SpaceGroup(int, int, int, String, String, BravaisLattice) - Constructor for class org.biojava.nbio.structure.xtal.SpaceGroup

SpaceGroupMapElements - Class in org.biojava.nbio.structure.xtal.io

SpaceGroupMapElements(Integer, SpaceGroup) - Constructor for class org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements

SpaceGroupMapRoot - Class in org.biojava.nbio.structure.xtal.io

SpaceGroupMapRoot() - Constructor for class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot

SparseSquareMatrix - Class in org.biojava.nbio.structure.math

A sparse, square matrix, implementing using two arrays of sparse vectors, one representation for the rows and one for the columns.

SparseSquareMatrix(int) - Constructor for class org.biojava.nbio.structure.math.SparseSquareMatrix

initialize an N-by-N matrix of all 0s

SparseVector - Class in org.biojava.nbio.structure.math

A sparse vector, implemented using a symbol table.

SparseVector(int) - Constructor for class org.biojava.nbio.structure.math.SparseVector

Constructor.

Species - org.biojava.nbio.structure.scop.ScopCategory

SphereSampler - Class in org.biojava.nbio.structure.symmetry.geometry

Sample possible orientations.

splitBlocksByTopology(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Sr - org.biojava.nbio.structure.Element

SSBondImpl - Class in org.biojava.nbio.structure.io

A simple bean to store disulfide bridge information, the SSBOND records in the PDB files.

SSBondImpl() - Constructor for class org.biojava.nbio.structure.io.SSBondImpl

STANDARD_BASES - Static variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

StandardAminoAcid - Class in org.biojava.nbio.structure

A class that provides a set of standard amino acids.

startingAlignment(String, Atom[], String, Atom[]) - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener

StartupParameters - Class in org.biojava.nbio.structure.align.ce

A simple bean that contains the parameters that can get set at startup

StartupParameters() - Constructor for class org.biojava.nbio.structure.align.ce.StartupParameters

STATUS_ENDPOINT - Static variable in class org.biojava.nbio.structure.PDBStatus

STATUS_LIST_ENDPOINT - Static variable in class org.biojava.nbio.structure.PDBStatus

stepParameters - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

Stoichiometry - Class in org.biojava.nbio.structure.symmetry.core

A utility object that describes Stoichiometry (composition of a protein assembly), determined via clustering procedure SubunitClusterer, and implements human-readable representation using various strategies.

Stoichiometry(List<SubunitCluster>) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Constructor for Stoichiometry.

Stoichiometry(List<SubunitCluster>, boolean) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Constructor for Stoichiometry.

Stoichiometry(List<SubunitCluster>, Function<List<SubunitCluster>, String>) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Constructor for Stoichiometry.

Stoichiometry(List<SubunitCluster>, Stoichiometry.StringOverflowStrategy) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Constructor for Stoichiometry.

Stoichiometry(List<SubunitCluster>, Stoichiometry.StringOverflowStrategy, boolean) - Constructor for class org.biojava.nbio.structure.symmetry.core.Stoichiometry

Constructor for Stoichiometry.

Stoichiometry.StringOverflowStrategy - Enum in org.biojava.nbio.structure.symmetry.core

What to do when the number of SubunitCluster exceeds the length of the alphabet.

storeUnAlignedSeqRes(Structure, List<Chain>, boolean) - Static method in class org.biojava.nbio.structure.io.SeqRes2AtomAligner

Storing unaligned SEQRES groups in a Structure.

StrCompAlignment - Class in org.biojava.nbio.structure.align.pairwise

StrCompAlignment(int, int) - Constructor for class org.biojava.nbio.structure.align.pairwise.StrCompAlignment

StrucAligParameters - Class in org.biojava.nbio.structure.align

A class that contains all the parameters of the structure alignment algorithm.

StrucAligParameters() - Constructor for class org.biojava.nbio.structure.align.StrucAligParameters

structure - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

Structure - Interface in org.biojava.nbio.structure

Interface for a structure object.

STRUCTURE - org.biojava.nbio.structure.cluster.SubunitClustererMethod

The STRUCTURE clustering method uses the residue sequence and the coordinates of its Atom representatives of the Subunit to calculate sequence and structure alignments.

StructureAlignment - Interface in org.biojava.nbio.structure.align

StructureAlignmentFactory - Class in org.biojava.nbio.structure.align

StructureAlignmentFactory() - Constructor for class org.biojava.nbio.structure.align.StructureAlignmentFactory

StructureAlignmentOptimizer - Class in org.biojava.nbio.structure.align.fatcat.calc

StructureAlignmentOptimizer(int, int, Atom[], int, int, Atom[], int, int[][]) - Constructor for class org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer

optimize the structural alignment by update the equivalent residues and then run dynamic programming input: len1 the length of structure 1; c1: the structure information of 1 len2 the length of structure 2; c2: the structure information of 2 iniLen and iniSet is the length and list of initial equivalent residues

StructureException - Exception in org.biojava.nbio.structure

An exception during the parsing of a PDB file.

StructureException(String) - Constructor for exception org.biojava.nbio.structure.StructureException

Constructs a StructureException object.

StructureException(String, Throwable) - Constructor for exception org.biojava.nbio.structure.StructureException

Constructs a StructureException object.

StructureException(Throwable) - Constructor for exception org.biojava.nbio.structure.StructureException

Constructs a StructureException object.

StructureFiletype - Enum in org.biojava.nbio.structure.io

An enum of supported file formats.

StructureIdentifier - Interface in org.biojava.nbio.structure

An identifier that uniquely identifies a whole Structure or arbitrary substructure.

StructureImpl - Class in org.biojava.nbio.structure

Implementation of a PDB Structure.

StructureImpl() - Constructor for class org.biojava.nbio.structure.StructureImpl

Constructs a StructureImpl object.

StructureImpl(Chain) - Constructor for class org.biojava.nbio.structure.StructureImpl

Construct a Structure object that contains a particular chain

StructureImpl(Group) - Constructor for class org.biojava.nbio.structure.StructureImpl

Construct a Structure object that only contains a single group

StructureInterface - Class in org.biojava.nbio.structure.contact

An interface between 2 molecules (2 sets of atoms).

StructureInterface() - Constructor for class org.biojava.nbio.structure.contact.StructureInterface

Constructs an empty StructureInterface

StructureInterface(Atom[], Atom[], String, String, AtomContactSet, CrystalTransform, CrystalTransform) - Constructor for class org.biojava.nbio.structure.contact.StructureInterface

Constructs a StructureInterface

StructureInterfaceCluster - Class in org.biojava.nbio.structure.contact

StructureInterfaceCluster() - Constructor for class org.biojava.nbio.structure.contact.StructureInterfaceCluster

StructureInterfaceList - Class in org.biojava.nbio.structure.contact

A list of interfaces between 2 molecules (2 sets of atoms)

StructureInterfaceList() - Constructor for class org.biojava.nbio.structure.contact.StructureInterfaceList

StructureIO - Class in org.biojava.nbio.structure

A class that provides static access methods for easy lookup of protein structure related components

StructureIO() - Constructor for class org.biojava.nbio.structure.StructureIO

StructureIOFile - Interface in org.biojava.nbio.structure.io

StructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem.

StructureName - Class in org.biojava.nbio.structure.align.client

A utility class that makes working with names of structures, domains and ranges easier.

StructureName(String) - Constructor for class org.biojava.nbio.structure.align.client.StructureName

Create a new StructureName from the given identifier, which may be a domain name, a substructure identifier, etc.

StructureName.Source - Enum in org.biojava.nbio.structure.align.client

StructurePairAligner - Class in org.biojava.nbio.structure.align

Perform a pairwise protein structure superimposition.

StructurePairAligner() - Constructor for class org.biojava.nbio.structure.align.StructurePairAligner

StructureProvider - Interface in org.biojava.nbio.structure.io

A class that can provide a protein structure object from somewhere.

StructureSequenceMatcher - Class in org.biojava.nbio.structure.io

A utility class with methods for matching ProteinSequences with Structures.

StructureSequenceMatcher() - Constructor for class org.biojava.nbio.structure.io.StructureSequenceMatcher

StructureTools - Class in org.biojava.nbio.structure

A class that provides some tool methods.

StructureTools() - Constructor for class org.biojava.nbio.structure.StructureTools

substitutionMatrix - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

SubstructureIdentifier - Class in org.biojava.nbio.structure

This is the canonical way to identify a part of a structure.

SubstructureIdentifier(String) - Constructor for class org.biojava.nbio.structure.SubstructureIdentifier

Create a new identifier from a string.

SubstructureIdentifier(String, List<ResidueRange>) - Constructor for class org.biojava.nbio.structure.SubstructureIdentifier

Create a new identifier based on a set of ranges.

SubstructureIdentifier(PdbId, List<ResidueRange>) - Constructor for class org.biojava.nbio.structure.SubstructureIdentifier

Create a new identifier based on a set of ranges.

subtract(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

subtract two atoms ( a - b).

Subunit - Class in org.biojava.nbio.structure.cluster

A Subunit consists of a set of residues from a Structure, which may correspond to an entire Chain, a Domain, or any subset or combination of residues from them.

Subunit(Atom[], String, StructureIdentifier, Structure) - Constructor for class org.biojava.nbio.structure.cluster.Subunit

A Subunit is solely defined by the coordinates of the representative Atoms of its residues.

SubunitCluster - Class in org.biojava.nbio.structure.cluster

A SubunitCluster contains a set of equivalent QuatSymmetrySubunits, the set of equivalent residues (EQR) between Subunit and a Subunit representative.

SubunitCluster(Subunit) - Constructor for class org.biojava.nbio.structure.cluster.SubunitCluster

A constructor from a single Subunit.

SubunitCluster(SubunitCluster, List<Integer>) - Constructor for class org.biojava.nbio.structure.cluster.SubunitCluster

A copy constructor with the possibility of removing subunits.

SubunitClusterer - Class in org.biojava.nbio.structure.cluster

The SubunitClusterer takes as input a collection of Subunit and returns a collection of SubunitCluster.

SubunitClustererMethod - Enum in org.biojava.nbio.structure.cluster

The SubunitClustererMethod ennummerates all methods that can be used to cluster Subunit in the SubunitCluster.

SubunitClustererParameters - Class in org.biojava.nbio.structure.cluster

The SubunitClustererParameters specifies the options used for the clustering of the subunits in structures using the SubunitClusterer.

SubunitClustererParameters() - Constructor for class org.biojava.nbio.structure.cluster.SubunitClustererParameters

Initialize with "local" metrics by default.

SubunitClustererParameters(boolean) - Constructor for class org.biojava.nbio.structure.cluster.SubunitClustererParameters

"Local" metrics are scoring SubunitClustererMethod.SEQUENCE: sequence identity of a local alignment (normalised by the number of aligned residues) sequence coverage of the alignment (normalised by the length of the longer sequence) SubunitClustererMethod.STRUCTURE: RMSD of the aligned substructures and structure coverage of the alignment (normalised by the length of the larger structure) Two thresholds for each method are required.

SubunitExtractor - Class in org.biojava.nbio.structure.cluster

The SubunitExtractor extracts the information of each protein Chain in a Structure and converts them into a List of Subunit.

suggestDomains(Atom[]) - Static method in class org.biojava.nbio.structure.domain.LocalProteinDomainParser

Suggest domains for a set of Calpha atoms

suggestDomains(Structure) - Static method in class org.biojava.nbio.structure.domain.LocalProteinDomainParser

Suggest domains for a protein structure

SULFUR_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

Superfamily - org.biojava.nbio.structure.scop.ScopCategory

superimpose(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer

superimpose(MultipleAlignment) - Method in interface org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer

Superimpose all structures from a MultipleAlignment.

superimpose(MultipleAlignment) - Method in class org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer

superpose(Point3d[], Point3d[]) - Method in interface org.biojava.nbio.structure.geometry.SuperPosition

Obtain the superposition matrix that minimizes the RMSD between two arrays of equivalent points.

superpose(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP

superpose(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQuat

superpose(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions

Use the SuperPosition.superpose(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.

superpose(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionSVD

superposeAfterRmsd() - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP

The QCP method can be used as a two-step calculation: first compute the RMSD (fast) and then compute the superposition.

superposeAndTransform(Point3d[], Point3d[]) - Method in interface org.biojava.nbio.structure.geometry.SuperPosition

Transform an array of points so that the coordinates of its points minimize the RMSD to the other array of equivalent points, and return the transformation matrix applied.

superposeAndTransform(Point3d[], Point3d[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionAbstract

superposeAndTransform(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions

Use the SuperPosition.superposeAndTransform(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.

superposeAndTransformAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions

Use the SuperPosition.superposeAndTransform(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.

superposeAtOrigin(Point3d[], Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.SuperPositions

Use the SuperPosition.superpose(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.

SuperPosition - Interface in org.biojava.nbio.structure.geometry

The SuperPosition interface defines and documents the required methods for any superpostion algorithm implementation, so that the input and expected output are uniform.

SuperPositionAbstract - Class in org.biojava.nbio.structure.geometry

The SuperPositionAbstract contains common code shared by all SuperPosition algorithm implementations.

SuperPositionAbstract(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionAbstract

SuperPositionQCP - Class in org.biojava.nbio.structure.geometry

Implementation of the Quaternion-Based Characteristic Polynomial algorithm for RMSD and Superposition calculations.

SuperPositionQCP(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionQCP

Default constructor for the quaternion based superposition algorithm.

SuperPositionQCP(boolean, double, double) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionQCP

Constructor with option to set the precision values.

SuperPositionQuat - Class in org.biojava.nbio.structure.geometry

The SuperPositionQuat implements a quaternion based algorithm to superpose arrays of Points in 3D.

SuperPositionQuat(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionQuat

Constructor for the quaternion based superposition algorithm.

SuperPositions - Class in org.biojava.nbio.structure.geometry

SuperPositions is a Class that provides static helper methods and an easy access to the whole family of SuperPosition algorithms.

SuperPositionSVD - Class in org.biojava.nbio.structure.geometry

A class that calculates the superposition between two sets of points using an SVD Matrix Decomposition.

SuperPositionSVD(boolean) - Constructor for class org.biojava.nbio.structure.geometry.SuperPositionSVD

Constructor for the SVD superposition algorithm.

svd() - Method in class org.biojava.nbio.structure.jama.Matrix

Singular Value Decomposition

SYM_CHAIN_ID_SEPARATOR - Static variable in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder

The character separating the original chain identifier from the operator id.

SymbolTable<Key extends Comparable<Key>,Value> - Class in org.biojava.nbio.structure.math

Sorted symbol table implementation using a java.util.TreeMap.

SymbolTable() - Constructor for class org.biojava.nbio.structure.math.SymbolTable

Create an empty symbol table.

SYMMETRIC - org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass

SymmetryAxes - Class in org.biojava.nbio.structure.symmetry.internal

Data Structure that stores all the symmetry axis that describe the symmetry of a structure.

SymmetryAxes() - Constructor for class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Constructor.

SymmetryAxes.Axis - Class in org.biojava.nbio.structure.symmetry.internal

Represents an axis of symmetry

symmetryCoefficient() - Method in class org.biojava.nbio.structure.geometry.MomentsOfInertia

SymmetryPerceptionMethod - Enum in org.biojava.nbio.structure.symmetry.core

Method used for symmetry perception in the QuatSymmetryDetector.

SymmetryRefiner - Interface in org.biojava.nbio.structure.symmetry.internal

Interface for all symmetry refinement implementations.

SymmetryTools - Class in org.biojava.nbio.structure.symmetry.utils

Utility methods for symmetry (quaternary and internal) detection and result manipulation.

SymmOptimizer - Class in org.biojava.nbio.structure.symmetry.internal

Optimizes a symmetry alignment by a Monte Carlo score optimization of the repeat multiple alignment.

SymmOptimizer(CeSymmResult) - Constructor for class org.biojava.nbio.structure.symmetry.internal.SymmOptimizer

Constructor with a seed MultipleAligment storing a refined symmetry alignment of the repeats.

SymoplibParser - Class in org.biojava.nbio.structure.xtal

A class containing static methods to parse the symop.lib file from the CCP4 package.

SymoplibParser() - Constructor for class org.biojava.nbio.structure.xtal.SymoplibParser

SynchronizedOutFile - Class in org.biojava.nbio.structure.align.util

SynchronizedOutFile(File) - Constructor for class org.biojava.nbio.structure.align.util.SynchronizedOutFile

create a thread safe wrapper for working with this file

SynchronizedOutFile(File, boolean) - Constructor for class org.biojava.nbio.structure.align.util.SynchronizedOutFile

Create a thread safe wrapper for writing to this file, the file will be gzip compressed.

SystematicSolver - Class in org.biojava.nbio.structure.symmetry.core

SystematicSolver(QuatSymmetrySubunits, QuatSymmetryParameters) - Constructor for class org.biojava.nbio.structure.symmetry.core.SystematicSolver

T

T - org.biojava.nbio.structure.Element

Tritium

Ta - org.biojava.nbio.structure.Element

Tb - org.biojava.nbio.structure.Element

Tc - org.biojava.nbio.structure.Element

TD - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

TD1 - Static variable in class org.biojava.nbio.structure.domain.pdp.PDPParameters

Te - org.biojava.nbio.structure.Element

techniquesToStringArray(Set<ExperimentalTechnique>) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfUtils

Converts the set of experimental techniques to an array of strings.

TertiaryBasePairParameters - Class in org.biojava.nbio.structure.basepairs

This class also finds the base pairing and base-pair step parameters but has a broader definition of a base pair so that non-canonical-WC base pairs will be detected and reported.

TertiaryBasePairParameters(Structure, boolean, boolean) - Constructor for class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

TETRAGONAL - org.biojava.nbio.structure.xtal.BravaisLattice

TETRAHEDRAL_CARBON_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

TETRAHEDRAL_NITROGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

Tetrahedron - Class in org.biojava.nbio.structure.symmetry.geometry

Tetrahedron() - Constructor for class org.biojava.nbio.structure.symmetry.geometry.Tetrahedron

Th - org.biojava.nbio.structure.Element

THREEBAR - org.biojava.nbio.structure.xtal.TransformType

THREEFOLD - org.biojava.nbio.structure.xtal.TransformType

THREEFOLDSCREW - org.biojava.nbio.structure.xtal.TransformType

THROW_EXCEPTION - org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior

Throw a StructureException for obsolete entries.

Ti - org.biojava.nbio.structure.Element

times(double) - Method in class org.biojava.nbio.structure.jama.Matrix

Multiply a matrix by a scalar, C = s*A

times(Matrix) - Method in class org.biojava.nbio.structure.jama.Matrix

Linear algebraic matrix multiplication, A * B

times(SparseVector) - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix

timesEquals(double) - Method in class org.biojava.nbio.structure.jama.Matrix

Multiply a matrix by a scalar in place, A = s*A

Tl - org.biojava.nbio.structure.Element

Tm - org.biojava.nbio.structure.Element

TMP_DIR - Static variable in class org.biojava.nbio.structure.align.util.UserConfiguration

TMScore(Point3d[], Point3d[], int) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint

Returns the TM-Score for two superimposed sets of coordinates Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)

to3DFormat(MultipleAlignment, int, int) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Outputs a pairwise alignment in I-TASSER's 3D Format for target-template alignment.

toAlignedPairs(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

Prints the alignment in the simplest form: a list of aligned residues.

toAlignedResidues(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Converts the alignment to its simplest form: a list of groups of aligned residues.

toAtomSite() - Static method in class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier

Collects AbstractCifFileSupplier.WrappedAtom instances into one AtomSite.

toBinary(Structure) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert a structure to BCIF format.

toBinaryFile(Structure, Path) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Write a structure to a BCIF file.

toCanonical() - Method in class org.biojava.nbio.structure.align.client.StructureName

toCanonical() - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier

toCanonical() - Method in class org.biojava.nbio.structure.cath.CathDomain

toCanonical() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

toCanonical() - Method in class org.biojava.nbio.structure.PassthroughIdentifier

toCanonical() - Method in class org.biojava.nbio.structure.scop.ScopDomain

toCanonical() - Method in interface org.biojava.nbio.structure.StructureIdentifier

Convert to a canonical SubstructureIdentifier.

toCanonical() - Method in class org.biojava.nbio.structure.SubstructureIdentifier

Return itself.

toCanonical() - Method in class org.biojava.nbio.structure.URLIdentifier

toCE(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

toCE(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

toCifFile(Chain) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert Chain to CifFile

toCifFile(Structure) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert Structure to CifFile.

toConciseAlignmentString(Map<S, T>, Map<T, S>) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

Print an alignment map in a concise representation.

toConciseAlignmentString(Map<T, T>) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

toDASStructure(XMLWriter) - Method in class org.biojava.nbio.structure.io.FileConvert

Convert a protein Structure to a DAS Structure XML response .

toDBSearchResult() - Method in class org.biojava.nbio.structure.align.model.AFPChain

toDBSearchResult(AFPChain) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

toDoubleArray(Collection<Number>) - Static method in class org.biojava.nbio.structure.align.util.CollectionTools

toExtendedId(String) - Static method in class org.biojava.nbio.structure.PdbId

Converts shortId to the PDB ID extended format.

toFASTA(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Converts the MultipleAlignment into a multiple sequence alignment String in FASTA format.

toFatcat(Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.model.AFPChain

toFatCat(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

toFatCat(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Converts the MultipleAlignment into a FatCat String format.

toFatCatCore(AFPChain, Atom[], Atom[], boolean, boolean, boolean, boolean) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

Output in FatCatCore format

toFullAlignment(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Method that converts a repeats symmetric alignment into an alignment of whole structures.

toIntArray(Collection<Number>) - Static method in class org.biojava.nbio.structure.align.util.CollectionTools

toMMCIF() - Method in interface org.biojava.nbio.structure.Chain

Convert this Chain to a String in mmCIF format

toMMCIF() - Method in class org.biojava.nbio.structure.ChainImpl

toMMCIF() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Return a String representing the 2 molecules of this interface in mmCIF format.

toMMCIF() - Method in class org.biojava.nbio.structure.io.FileConvert

Convert this structure to its CIF representation.

toMMCIF() - Method in interface org.biojava.nbio.structure.Structure

Create a String that contains this Structure's contents in MMCIF file format.

toMMCIF() - Method in class org.biojava.nbio.structure.StructureImpl

Create a String that contains this Structure's contents in MMCIF file format.

toMMCIF(Chain) - Static method in class org.biojava.nbio.structure.io.FileConvert

Convert a chain to its CIF representation.

toMultimodelStructure(MultipleAlignment, List<Atom[]>) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

toPDB() - Method in class org.biojava.nbio.structure.AtomImpl

toPDB() - Method in interface org.biojava.nbio.structure.Chain

Convert this Chain to a String in PDB format

toPDB() - Method in class org.biojava.nbio.structure.ChainImpl

toPDB() - Method in class org.biojava.nbio.structure.contact.StructureInterface

Return a String representing the 2 molecules of this interface in PDB format.

toPDB() - Method in class org.biojava.nbio.structure.DBRef

Convert the DBRef object to a DBREF record as it is used in PDB files

toPDB() - Method in class org.biojava.nbio.structure.io.FileConvert

Convert a structure into a PDB file.

toPDB() - Method in class org.biojava.nbio.structure.io.SSBondImpl

toPDB() - Method in class org.biojava.nbio.structure.PDBHeader

Return a PDB representation of the PDB Header

toPDB() - Method in interface org.biojava.nbio.structure.PDBRecord

Returns a PDB file like representation of this record.

toPDB() - Method in class org.biojava.nbio.structure.ResidueNumber

toPDB() - Method in class org.biojava.nbio.structure.Site

toPDB() - Method in interface org.biojava.nbio.structure.Structure

Create a String that contains this Structure's contents in PDB file format.

toPDB() - Method in class org.biojava.nbio.structure.StructureImpl

Create a String that contains this Structure's contents in PDB file format.

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.AtomImpl

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.DBRef

Append the PDB representation of this DBRef to the provided StringBuffer

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.io.SSBondImpl

Append the PDB representation of this SSBOND to the provided StringBuffer

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.PDBHeader

Appends a PDB representation of the PDB header to the provided StringBuffer

toPDB(StringBuffer) - Method in interface org.biojava.nbio.structure.PDBRecord

Appends a PDB file like representation of this record to the provided StringBuffer.

toPDB(StringBuffer) - Method in class org.biojava.nbio.structure.Site

toPDB(Atom) - Static method in class org.biojava.nbio.structure.io.FileConvert

Prints the content of an Atom object as a PDB formatted line.

toPDB(Atom, String) - Static method in class org.biojava.nbio.structure.io.FileConvert

toPDB(Atom, StringBuffer) - Static method in class org.biojava.nbio.structure.io.FileConvert

toPDB(Atom, StringBuffer, String) - Static method in class org.biojava.nbio.structure.io.FileConvert

Print ATOM record in the following syntax

toPDB(Chain) - Static method in class org.biojava.nbio.structure.io.FileConvert

Convert a Chain object to PDB representation

toPDB(Group) - Static method in class org.biojava.nbio.structure.io.FileConvert

Convert a Group object to PDB representation

toPDB(Structure, Structure) - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

converts the alignment to a PDB file each of the structures will be represented as a model.

Topolgy - org.biojava.nbio.structure.cath.CathCategory

toPrettyAlignment(AFPChain, Atom[], Atom[], boolean, boolean) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

toProteinMSA(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Convert a MultipleAlignment into a MultipleSequenceAlignment of AminoAcid residues.

toRepeatsAlignment(CeSymmResult) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Method that converts a symmetry alignment into an alignment of the repeats only, as new independent structures.

toRotMat() - Method in class org.biojava.nbio.structure.align.model.AFPChain

toRotMat(AFPChain) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

torsionAngle(Atom, Atom, Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Calculate the torsion angle, i.e.

toScoresList(AFPChain) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

toSDF() - Method in interface org.biojava.nbio.structure.Group

Function to get the Group as an MDL molblock

toSDF() - Method in class org.biojava.nbio.structure.HetatomImpl

toShortId(String) - Static method in class org.biojava.nbio.structure.PdbId

Converts extendedId to the PDB ID short format.

toSsBond(Bond) - Static method in class org.biojava.nbio.structure.io.SSBondImpl

Converts the given Bond object into a SSBondImpl.

toString() - Method in enum org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint

toString() - Method in class org.biojava.nbio.structure.align.ce.CECPParameters

toString() - Method in class org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams

toString() - Method in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

toString() - Method in class org.biojava.nbio.structure.align.ce.CeParameters

toString() - Method in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

toString() - Method in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

toString() - Method in class org.biojava.nbio.structure.align.ce.StartupParameters

toString() - Method in class org.biojava.nbio.structure.align.client.PdbPair

toString() - Method in class org.biojava.nbio.structure.align.client.StructureName

toString() - Method in class org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

toString() - Method in class org.biojava.nbio.structure.align.fatcat.FatCat

toString() - Method in class org.biojava.nbio.structure.align.helper.AligMatEl

toString() - Method in class org.biojava.nbio.structure.align.helper.IndexPair

toString() - Method in class org.biojava.nbio.structure.align.helper.JointFragments

toString() - Method in class org.biojava.nbio.structure.align.model.AFP

toString() - Method in class org.biojava.nbio.structure.align.model.AFPChain

toString() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

toString() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

toString() - Method in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

toString() - Method in interface org.biojava.nbio.structure.align.multiple.MultipleAlignment

Return a summary of the MultipleAlignment, containing the structures, the lengths and the cached scores.

toString() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

toString() - Method in class org.biojava.nbio.structure.align.pairwise.AlignmentResult

toString() - Method in class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

print the idx positions of this alignment

toString() - Method in class org.biojava.nbio.structure.align.pairwise.FragmentPair

toString() - Method in class org.biojava.nbio.structure.align.quaternary.QsAlignResult

toString() - Method in class org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

toString() - Method in class org.biojava.nbio.structure.align.StrucAligParameters

toString() - Method in class org.biojava.nbio.structure.align.xml.PdbPairsMessage

toString() - Method in class org.biojava.nbio.structure.AminoAcidImpl

string representation.

toString() - Method in class org.biojava.nbio.structure.AtomImpl

toString() - Method in class org.biojava.nbio.structure.Author

toString() - Method in class org.biojava.nbio.structure.basepairs.BasePairParameters

toString() - Method in class org.biojava.nbio.structure.BioAssemblyIdentifier

toString() - Method in class org.biojava.nbio.structure.BondImpl

toString() - Method in enum org.biojava.nbio.structure.cath.CathCategory

toString() - Method in class org.biojava.nbio.structure.cath.CathDomain

toString() - Method in class org.biojava.nbio.structure.cath.CathNode

toString() - Method in class org.biojava.nbio.structure.cath.CathSegment

toString() - Method in interface org.biojava.nbio.structure.Chain

toString() - Method in class org.biojava.nbio.structure.ChainImpl

toString() - Method in class org.biojava.nbio.structure.chem.ChemComp

toString() - Method in class org.biojava.nbio.structure.chem.ChemCompDescriptor

toString() - Method in class org.biojava.nbio.structure.chem.MetalBondDistance

toString() - Method in class org.biojava.nbio.structure.cluster.Subunit

toString() - Method in class org.biojava.nbio.structure.cluster.SubunitCluster

toString() - Method in class org.biojava.nbio.structure.cluster.SubunitClustererParameters

toString() - Method in class org.biojava.nbio.structure.contact.AtomIdentifier

toString() - Method in class org.biojava.nbio.structure.contact.BoundingBox

toString() - Method in class org.biojava.nbio.structure.contact.GridCell

toString() - Method in class org.biojava.nbio.structure.contact.GroupContact

toString() - Method in class org.biojava.nbio.structure.contact.Pair

toString() - Method in class org.biojava.nbio.structure.contact.StructureInterface

toString() - Method in class org.biojava.nbio.structure.contact.StructureInterfaceList

toString() - Method in class org.biojava.nbio.structure.DatabasePDBRevRecord

toString() - Method in class org.biojava.nbio.structure.DBRef

String representation of a DBRef.

toString() - Method in class org.biojava.nbio.structure.domain.pdp.CutSites

toString() - Method in class org.biojava.nbio.structure.domain.pdp.CutValues

toString() - Method in class org.biojava.nbio.structure.domain.pdp.Domain

toString() - Method in class org.biojava.nbio.structure.domain.pdp.Segment

toString() - Method in class org.biojava.nbio.structure.ecod.EcodDomain

toString() - Method in class org.biojava.nbio.structure.ecod.EcodInstallation

toString() - Method in class org.biojava.nbio.structure.EntityInfo

toString() - Method in enum org.biojava.nbio.structure.ExperimentalTechnique

toString() - Method in enum org.biojava.nbio.structure.GroupType

toString() - Method in class org.biojava.nbio.structure.HetatomImpl

toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainEntry

toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsEntity

toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsResidue

toString() - Method in class org.biojava.nbio.structure.io.sifts.SiftsSegment

toString() - Method in class org.biojava.nbio.structure.io.SSBondImpl

toString() - Method in class org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord

toString() - Method in class org.biojava.nbio.structure.jama.Matrix

toString() - Method in class org.biojava.nbio.structure.JournalArticle

toString() - Method in class org.biojava.nbio.structure.math.SparseSquareMatrix

toString() - Method in class org.biojava.nbio.structure.math.SparseVector

toString() - Method in class org.biojava.nbio.structure.Model

toString() - Method in class org.biojava.nbio.structure.NucleotideImpl

toString() - Method in class org.biojava.nbio.structure.PDBCrystallographicInfo

toString() - Method in class org.biojava.nbio.structure.PDBHeader

String representation

toString() - Method in class org.biojava.nbio.structure.PdbId

toString() - Method in class org.biojava.nbio.structure.quaternary.BioAssemblyInfo

toString() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

toString() - Method in class org.biojava.nbio.structure.quaternary.OrderedPair

toString() - Method in class org.biojava.nbio.structure.ResidueNumber

toString() - Method in class org.biojava.nbio.structure.ResidueRange

toString() - Method in enum org.biojava.nbio.structure.scop.Astral.AstralSet

toString() - Method in enum org.biojava.nbio.structure.scop.ScopCategory

toString() - Method in class org.biojava.nbio.structure.scop.ScopDescription

toString() - Method in class org.biojava.nbio.structure.scop.ScopDomain

toString() - Method in class org.biojava.nbio.structure.scop.ScopNode

toString() - Method in enum org.biojava.nbio.structure.secstruc.BridgeType

toString() - Method in class org.biojava.nbio.structure.secstruc.HBond

toString() - Method in class org.biojava.nbio.structure.secstruc.SecStrucCalc

toString() - Method in class org.biojava.nbio.structure.secstruc.SecStrucElement

toString() - Method in class org.biojava.nbio.structure.secstruc.SecStrucInfo

toString() - Method in enum org.biojava.nbio.structure.secstruc.SecStrucType

toString() - Method in interface org.biojava.nbio.structure.SeqMisMatch

toString() - Method in class org.biojava.nbio.structure.SeqMisMatchImpl

toString() - Method in class org.biojava.nbio.structure.Site

toString() - Method in interface org.biojava.nbio.structure.Structure

String representation of object.

toString() - Method in class org.biojava.nbio.structure.StructureImpl

String representation.

toString() - Method in class org.biojava.nbio.structure.SubstructureIdentifier

toString() - Method in class org.biojava.nbio.structure.symmetry.core.Helix

toString() - Method in class org.biojava.nbio.structure.symmetry.core.HelixLayers

toString() - Method in class org.biojava.nbio.structure.symmetry.core.PermutationGroup

toString() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

toString() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

toString() - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores

toString() - Method in class org.biojava.nbio.structure.symmetry.core.Rotation

toString() - Method in class org.biojava.nbio.structure.symmetry.core.RotationGroup

toString() - Method in class org.biojava.nbio.structure.symmetry.core.Stoichiometry

toString() - Method in class org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus

toString() - Method in class org.biojava.nbio.structure.symmetry.internal.CESymmParameters

toString() - Method in class org.biojava.nbio.structure.symmetry.internal.CeSymmResult

toString() - Method in class org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector

toString() - Method in class org.biojava.nbio.structure.symmetry.misc.ChainSignature

toString() - Method in class org.biojava.nbio.structure.xtal.CrystalCell

toString() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

toString() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

toString(List<? extends ResidueRange>) - Static method in class org.biojava.nbio.structure.ResidueRange

toStrings(List<? extends ResidueRange>) - Static method in class org.biojava.nbio.structure.ResidueRange

toText(Chain) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert a chain to mmCIF format.

toText(Structure) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Convert a structure to mmCIF format.

toTextFile(Structure, Path) - Static method in class org.biojava.nbio.structure.io.cif.CifStructureConverter

Write a structure to a CIF file.

toTransformMatrices(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Converts the transformation Matrices of the alignment into a String output.

toWebSiteDisplay(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.

toWebSiteDisplay(AFPChain, Atom[], Atom[], boolean) - Static method in class org.biojava.nbio.structure.align.model.AfpChainWriter

Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.

toXML() - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

toXML() - Method in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot

toXML() - Method in class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper

toXML() - Method in class org.biojava.nbio.structure.xtal.SpaceGroup

toXML(PrintWriter) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

convert Configuration to an XML file so it can be serialized

toXML(PrettyXMLWriter) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

toXML(XMLWriter) - Method in class org.biojava.nbio.structure.align.util.UserConfiguration

convert Configuration to an XML file so it can be serialized add to an already existing xml file.

toXML(AFPChain) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter

toXML(AFPChain, StringWriter, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter

Write the XML representation to a StringWriter

toXML(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.xml.AFPChainXMLConverter

Convert an afpChain to a simple XML representation

toXML(MultipleAlignmentEnsemble) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter

Converts all the information of a multiple alignment ensemble into an XML String format.

toXYZString() - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

Expresses this transformation in terms of x,y,z fractional coordinates.

trace() - Method in class org.biojava.nbio.structure.jama.Matrix

Matrix trace.

trace1 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

trace1 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

trace2 - Variable in class org.biojava.nbio.structure.align.ce.CECalculator

trace2 - Variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

traceFragmentMatrix(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

traceFragmentMatrix(AFPChain, Atom[], Atom[]) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

TransfAlgebraicAdapter - Class in org.biojava.nbio.structure.xtal.io

TransfAlgebraicAdapter() - Constructor for class org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter

transform(Matrix4d, Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint

Transform all points with a 4x4 transformation matrix.

transform(Atom[], Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transform an array of atoms at once.

transform(Atom, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transforms an atom object, given a Matrix4d (i.e.

transform(Chain, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transforms a chain object, given a Matrix4d (i.e.

transform(Group, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transforms a group object, given a Matrix4d (i.e.

transform(Structure, Matrix4d) - Static method in class org.biojava.nbio.structure.Calc

Transforms a structure object, given a Matrix4d (i.e.

transformAtoms(MultipleAlignment) - Static method in class org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools

Transforms atoms according to the superposition stored in the alignment.

transformPoint(double[]) - Method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Applies the transformation to given point.

TransformType - Enum in org.biojava.nbio.structure.xtal

transfToCrystal(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Transform given Matrix4d in orthonormal basis to the crystal basis using the PDB axes convention (NCODE=1)

transfToCrystal(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Transforms the given orthonormal basis coordinates into crystal coordinates.

transfToOriginCell(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Converts the coordinates in pt so that they occur within the (0,0,0) unit cell

transfToOriginCell(Tuple3d[], Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Converts a set of points so that the reference point falls in the unit cell.

transfToOriginCellCrystal(Matrix4d[], Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

transfToOriginCellOrthonormal(Matrix4d[], Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

transfToOrthonormal(Matrix4d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Transform given Matrix4d in crystal basis to the orthonormal basis using the PDB axes convention (NCODE=1)

transfToOrthonormal(Tuple3d) - Method in class org.biojava.nbio.structure.xtal.CrystalCell

Transforms the given crystal basis coordinates into orthonormal coordinates.

TRANSITION_METAL - org.biojava.nbio.structure.ElementType

translate(Matrix4d, Vector3d) - Method in class org.biojava.nbio.structure.xtal.CrystalBuilder

translate(Point3i) - Method in class org.biojava.nbio.structure.xtal.CrystalTransform

translate(Vector3d) - Method in class org.biojava.nbio.structure.contact.BoundingBox

translate(Vector3d, Point3d[]) - Static method in class org.biojava.nbio.structure.geometry.CalcPoint

Translate all points with a translation vector.

translate(Atom, Vector3d) - Static method in class org.biojava.nbio.structure.Calc

Translates an atom object, given a Vector3d (i.e.

translate(Chain, Vector3d) - Static method in class org.biojava.nbio.structure.Calc

Translates a chain object, given a Vector3d (i.e.

translate(Group, Vector3d) - Static method in class org.biojava.nbio.structure.Calc

Translates a group object, given a Vector3d (i.e.

translate(Structure, Vector3d) - Static method in class org.biojava.nbio.structure.Calc

Translates a Structure object, given a Vector3d (i.e.

translVecToString(Matrix4d) - Static method in class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

transpose() - Method in class org.biojava.nbio.structure.jama.Matrix

Matrix transpose.

traverseHierarchy() - Method in class demo.DemoSCOP

Traverse throught the SCOP hierarchy

TreeMapSpaceGroupWrapper - Class in org.biojava.nbio.structure.xtal.io

TreeMapSpaceGroupWrapper() - Constructor for class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper

TRICLINIC - org.biojava.nbio.structure.xtal.BravaisLattice

TRIGONAL - org.biojava.nbio.structure.xtal.BravaisLattice

TRIGONAL_CARBON_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

TRIGONAL_NITROGEN_VDW - Static variable in class org.biojava.nbio.structure.asa.AsaCalculator

trimToSize() - Method in interface org.biojava.nbio.structure.Group

Attempts to reduce the memory imprint of this group by trimming all internal Collection objects to the required size.

trimToSize() - Method in class org.biojava.nbio.structure.HetatomImpl

trimToValidResidues(ResidueRange) - Method in class org.biojava.nbio.structure.AtomPositionMap

Trims a residue range so that both endpoints are contained in this map.

tryAllCPs - Variable in class org.biojava.nbio.structure.align.ce.OptimalCECPParameters

If true, ignores OptimalCECPParameters.cpPoint and tries all possible cp points.

turn - org.biojava.nbio.structure.secstruc.SecStrucType

twistOptimized(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.AFPTwister

superimposing according to the optimized alignment

twistPDB(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.AFPTwister

calculate the total rmsd of the blocks output a merged pdb file for both proteins protein 1, in chain A protein 2 is twisted according to the twists detected, in chain B

TWOBAR - org.biojava.nbio.structure.xtal.TransformType

TWOFOLD - org.biojava.nbio.structure.xtal.TransformType

TWOFOLDSCREW - org.biojava.nbio.structure.xtal.TransformType

type - Static variable in class org.biojava.nbio.structure.AminoAcidImpl

this is an Amino acid.

type - Static variable in class org.biojava.nbio.structure.HetatomImpl

The GroupType is HETATM

type - Static variable in class org.biojava.nbio.structure.NucleotideImpl

this is a "nucleotide", a special occurance of a Hetatom.

type - Variable in enum org.biojava.nbio.structure.secstruc.BridgeType

type - Variable in class org.biojava.nbio.structure.secstruc.SecStrucInfo

type - Variable in enum org.biojava.nbio.structure.secstruc.SecStrucType

U

U - org.biojava.nbio.structure.Element

uminus() - Method in class org.biojava.nbio.structure.jama.Matrix

Unary minus

UNDEFINED - org.biojava.nbio.structure.BondType

UNDERSCORE - Static variable in class org.biojava.nbio.structure.align.util.AtomCache

uniProtEntrySet() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

UnitCellBoundingBox - Class in org.biojava.nbio.structure.xtal

A class to contain the BoundingBoxes of all polymeric molecules in a full unit cell.

UnitCellBoundingBox(int, int) - Constructor for class org.biojava.nbio.structure.xtal.UnitCellBoundingBox

UnitQuaternions - Class in org.biojava.nbio.structure.geometry

UnitQuaternions is a static Class that contains methods for calculating and using unit quaternions.

unitVector(Atom) - Static method in class org.biojava.nbio.structure.Calc

Returns the unit vector of vector a .

unknown - org.biojava.nbio.structure.chem.PolymerType

if all else fails...

UNKNOWN - org.biojava.nbio.structure.ElementType

UNKNOWN - org.biojava.nbio.structure.io.StructureFiletype

UNKNOWN_ALGORITHM - Static variable in class org.biojava.nbio.structure.align.model.AFPChain

UNKNOWN_GROUP_LABEL - Static variable in class org.biojava.nbio.structure.StructureTools

The character to use for unknown compounds in sequence strings

unmarshal(String[]) - Method in class org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter

UNRELEASED - org.biojava.nbio.structure.PDBStatus.Status

updateAtomArrays() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

Force the atom arrays to regenerate based on MultipleAlignmentEnsembleImpl.getStructureIdentifiers().

updateAxis(Integer, Matrix4d) - Method in class org.biojava.nbio.structure.symmetry.internal.SymmetryAxes

Updates an axis of symmetry, after the superposition changed.

updateCache() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

updateCache() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

Updates all cached properties

updateCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockImpl

updateCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

updateCoreLength() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

Force recalculation of the core length (ungapped columns) based on the BlockSet core lengths.

updateDistanceMatrix() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

Force recalculation of the distance matrices.

updateLength() - Method in class org.biojava.nbio.structure.align.multiple.BlockSetImpl

updateLength() - Method in class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

Force recalculation of the length (aligned columns) based on the BlockSet lengths.

updateMatrixWithSequenceConservation(double[][], Atom[], Atom[], CeParameters) - Static method in class org.biojava.nbio.structure.align.ce.CECalculator

Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.

updateMatrixWithSequenceConservation(double[][], Atom[], Atom[], CeParameters) - Static method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.

updateScore(FatCatParameters, AFPChain) - Static method in class org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer

to update the chaining score after block delete and merge processed the blockScore value is important for significance evaluation

updateSuperposition(AFPChain, Atom[], Atom[]) - Static method in class org.biojava.nbio.structure.align.util.AlignmentTools

After the alignment changes (optAln, optLen, blockNum, at a minimum), many other properties which depend on the superposition will be invalid.

updateSymmetryScores(MultipleAlignment) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Update the scores (TM-score and RMSD) of a symmetry multiple alignment.

updateSymmetryTransformation(SymmetryAxes, MultipleAlignment) - Static method in class org.biojava.nbio.structure.symmetry.utils.SymmetryTools

Calculates the set of symmetry operation Matrices (transformations) of the new alignment, based on the symmetry relations in the SymmetryAxes object.

URL - org.biojava.nbio.structure.align.client.StructureName.Source

URLConnectionTools - Class in org.biojava.nbio.structure.align.util

A class that takes care about opening URLConnections and sets the proper timeouts

URLConnectionTools() - Constructor for class org.biojava.nbio.structure.align.util.URLConnectionTools

URLIdentifier - Class in org.biojava.nbio.structure

Represents a structure loaded from a URL (including a file URL) A few custom query parameters are supported: format=[pdb|cif] Specify the file format (will otherwise be guessed from the extension) pdbId=[String] Specify the PDB ID (also guessed from the filename) chainID=[String] A single chain from the structure residues=[String] Residue ranges, in a form understood by SubstructureIdentifier

URLIdentifier(String) - Constructor for class org.biojava.nbio.structure.URLIdentifier

URLIdentifier(URL) - Constructor for class org.biojava.nbio.structure.URLIdentifier

useLocalTimeLimit(double) - Method in class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

USER_INPUT - org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod

UserArgumentProcessor - Interface in org.biojava.nbio.structure.align.ce

UserConfiguration - Class in org.biojava.nbio.structure.align.util

A container to persist config to the file system

UserConfiguration() - Constructor for class org.biojava.nbio.structure.align.util.UserConfiguration

Default UserConfiguration: split directory autofetch files default download location.

useRNA - Variable in class org.biojava.nbio.structure.basepairs.BasePairParameters

V

V - org.biojava.nbio.structure.Element

value - Variable in class org.biojava.nbio.structure.align.helper.GapArray

value - Variable in class org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements

valueOf(String) - Static method in enum org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.align.client.StructureName.Source

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.align.quaternary.QsRelation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.BondType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.cath.CathCategory

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.chem.PolymerType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.chem.ResidueType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.cluster.SubunitClustererMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.Element

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.ElementType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.EntityType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.GroupType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.io.StructureFiletype

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.PDBStatus.Status

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.scop.Astral.AstralSet

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.scop.ScopCategory

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.structure.xtal.TransformType

Returns the enum constant of this type with the specified name.

valueOfIgnoreCase(String) - Static method in enum org.biojava.nbio.structure.Element

Returns the Element that corresponds to the specified element symbol.

values() - Static method in enum org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.align.client.StructureName.Source

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.align.quaternary.QsRelation

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.BondType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.cath.CathCategory

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.chem.PolymerType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.chem.ResidueType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.cluster.SubunitClustererMethod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.Element

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.ElementType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.EntityType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.ExperimentalTechnique

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.geometry.MomentsOfInertia.SymmetryClass

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.GroupType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Method in class org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

values() - Static method in enum org.biojava.nbio.structure.io.StructureFiletype

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.PDBStatus.Status

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.scop.Astral.AstralSet

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.scop.ScopCategory

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.secstruc.BridgeType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.secstruc.SecStrucType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.symmetry.core.Stoichiometry.StringOverflowStrategy

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.symmetry.core.SymmetryPerceptionMethod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.xtal.BravaisLattice

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.structure.xtal.TransformType

Returns an array containing the constants of this enum type, in the order they are declared.

VANDERWAALS - org.biojava.nbio.structure.BondType

vectorProduct(Atom, Atom) - Static method in class org.biojava.nbio.structure.Calc

Vector product (cross product).

verbose - Static variable in class org.biojava.nbio.structure.domain.pdp.CutDomain

version - Static variable in class org.biojava.nbio.structure.align.ce.CeCPMain

version history: 1.5 - Added more parameters to the command line, including -maxOptRMSD 1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain 1.3 - Short CPs are now discarded 1.2 - now supports check AlignmentTools.isSequentialAlignment.

version - Static variable in class org.biojava.nbio.structure.align.ce.CeMain

version history: 1.2 - Added more parameters to the command line, including -maxOptRMSD 1.1 - Additional parameters 1.0 - Initial port from C code

version - Static variable in class org.biojava.nbio.structure.align.ce.OptimalCECPMain

version history: 1.0 - Initial version

version - Static variable in class org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain

Version history:

version - Static variable in class org.biojava.nbio.structure.symmetry.internal.CeSymm

Version History:

VERSION - Static variable in class org.biojava.nbio.structure.align.fatcat.FatCat

version history: 1.1 - Added more parameters to the command line 1.0 - Initial version

VERSION_1_55 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_57 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_59 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_61 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_63 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_65 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_67 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_69 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_71 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_73 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_75 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_75A - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_75B - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_1_75C - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_1 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_2 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_3 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_4 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_5 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_6 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_7 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_2_0_8 - Static variable in class org.biojava.nbio.structure.scop.ScopFactory

VERSION_3_5_0 - Static variable in class org.biojava.nbio.structure.cath.CathFactory

VERSION_4_0_0 - Static variable in class org.biojava.nbio.structure.cath.CathFactory

VERSION_4_1_0 - Static variable in class org.biojava.nbio.structure.cath.CathFactory

VERSION_4_2_0 - Static variable in class org.biojava.nbio.structure.cath.CathFactory

W

W - org.biojava.nbio.structure.Element

WATER - org.biojava.nbio.structure.EntityType

Water

WATERNAMES - Static variable in enum org.biojava.nbio.structure.GroupType

The 3-letter codes used in the PDB to identify water molecules

weightedSuperpose(Point3d[], Point3d[], double[]) - Method in class org.biojava.nbio.structure.geometry.SuperPositionQCP

Weighted superposition.

winSize - Variable in class org.biojava.nbio.structure.align.ce.CeParameters

winSize - Variable in class org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams

WrappedAtom(int, String, String, Atom, int) - Constructor for class org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier.WrappedAtom

Construct a new atoms.

write(String) - Method in class org.biojava.nbio.structure.align.util.SynchronizedOutFile

writeToFile(Structure, Path) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfActions

Write a Structure object to a file.

writeToOutputStream(Structure, OutputStream) - Static method in class org.biojava.nbio.structure.io.mmtf.MmtfActions

Write a Structure object to an OutputStream

X

Xe - org.biojava.nbio.structure.Element

xmax - Variable in class org.biojava.nbio.structure.contact.BoundingBox

xmin - Variable in class org.biojava.nbio.structure.contact.BoundingBox

XRAY_DIFFRACTION - org.biojava.nbio.structure.ExperimentalTechnique

XTALTRANSL - org.biojava.nbio.structure.xtal.TransformType

Y

Y - org.biojava.nbio.structure.Element

Yb - org.biojava.nbio.structure.Element

ymax - Variable in class org.biojava.nbio.structure.contact.BoundingBox

ymin - Variable in class org.biojava.nbio.structure.contact.BoundingBox

Z

ZipChemCompProvider - Class in org.biojava.nbio.structure.chem

This chemical component provider retrieves and caches chemical component definition files from a zip archive specified in its construction.

ZipChemCompProvider(String, String) - Constructor for class org.biojava.nbio.structure.chem.ZipChemCompProvider

ZipChemCompProvider is a Chemical Component provider that stores chemical components in a zip archive.

zmax - Variable in class org.biojava.nbio.structure.contact.BoundingBox

zmin - Variable in class org.biojava.nbio.structure.contact.BoundingBox

Zn - org.biojava.nbio.structure.Element

Zr - org.biojava.nbio.structure.Element

zStrAlign(int, int, double, int) - Method in class org.biojava.nbio.structure.align.ce.CECalculator

zStrAlign(int, int, double, int) - Method in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

zThr - Static variable in class org.biojava.nbio.structure.align.ce.CECalculator

zThr - Static variable in class org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced

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