All Classes and Interfaces
Class
Description
Convert a BioJava object to a CifFile.
Wrapped atoms represent individual atoms enriched with model- and chain-level information.
Abstact implementation of the
ScoresCache with the shared code used
in all objects with a variables cache.Base class for a new structure alignment CLI.
A class to represent a FATCAT aligned fragment pair (AFP)
A class that performs calculations on AFPChains
A bean to contain the core of a structure alignment.
a class to chain AFPs to an alignment
A class to convert the data in an AfpChain object to various String outputs.
does post processing after alignment chaingin
A class to listen to progress of the structure alignment calculations
A class to track the alignment results in a flat file
Methods for analyzing and manipulating AFPChains and for
other pairwise alignment utilities.
A Map<K,V> can be viewed as a function from K to V.
Low level helper methods for CE and FATCAT algorithms.
A ChemComp provider that downloads and caches the components.cif file from the wwPDB site.
A comparator to sort AlternativeAlignments based on their number of equivalent residues
and RMSD.
Implements a class which handles one possible (alternative) solution.
A
Group that represents an AminoAcid.AminoAcid inherits most from Hetatom.
Guesses an order of rotational symmetry from the angle.
Class to calculate Accessible Surface Areas based on
the rolling ball algorithm by Shrake and Rupley.
Provides programmatic access to ASTRAL representative sets.
An ASTRAL sequence-identity cutoff with an identifier such as:
A simple interface for an Atom.
A utility class that provides easy access to Structure objects.
A pair of atoms that are in contact
A set of atom-atom contacts to hold the results of intra and inter-chain contact calculations
Implementation of an Atom of a PDB file.
an iterator over all atoms of a structure / group.
A map from
ResidueNumbers to ATOM record positions in a PDB file.Used as a Predicate to indicate whether a particular Atom should be mapped
Created by douglas on 1/23/15.
Describes author attributes for author information in a PDB file.
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.
Parse binary Cif files and provide capabilities to store them locally.
SCOPe:
The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley
(http://scop.berkeley.edu/).
Container that represents a beta Bridge between two residues.
Representation of a Biological Assembly annotation as provided by the PDB.
Wrapper for the BioJava Structure Alignment Implementation
Reconstructs the quaternary structure of a protein from an asymmetric unit
The transformation needed for generation of biological assemblies
from the contents of a PDB/mmCIF file.
A Block is a Data Structure that stores aligned positions of a
MultipleAlignment with the condition that residues are in a
sequential order.General implementation of a
Block that supports any type of
sequential alignment with gaps.A BlockSet is a Data Structure to store a flexible alignment part of a
multiple alignment.
A general implementation of a BlockSet to store a flexible part of a multiple
alignment.
A simple bond -- it stores information about two atoms as well as information
about its bond order.
A simple bond -- it stores information about two atoms as well as information
about its bond order.
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.
Work in progress - NOT final!
A bounding box for short cutting some geometrical calculations.
An enum to represent the 7 Bravais lattices
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<j.
Converts full atom representations to Calpha only ones.
Utility operations on Atoms, AminoAcids, Matrices, Point3d, etc.
Utility operations on Point3d.
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).
A cartesian product between two lists A and B is the set of all ordered pairs
of the elements of both sets.
The categories found within CATH.
General API for interacting with CATH.
A class which represents a single CATH domain.
Controls global
CathDatabases being used.Represents a node in the CATH hierarchy.
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.
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.
A wrapper for
CeMain which sets default parameters to be appropriate for finding
circular permutations.Tiny wrapper for the disallowed regions of an alignment.
Provides parameters to
CeCPMainThe main class of the Java implementation of the Combinatorial Extension Algorithm (CE),
as has been originally developed by I.
Contains the parameters that can be sent to CE
Identify the symmetries in a structure by running an alignment of the
structure against itself disabling the diagonal of the identity alignment.
Iterative version of CeSymm that aims at identifying all symmetry axis of a
structure.
Provides parameters to
CeSymm.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.
This Class stores all the relevant information of an internal symmetry result
obtained with CeSymm.
process the arguments from command line
Defines the interface for a Chain.
A Chain in a PDB file.
A class to add appropriate charge information to a structure.
Properties of a chemical component.
Properties of an atom of a chemical component.
Properties of a bond in a chemical component.
Create the
ChemicalComponentDictionary from CIF data.Consumes a CCD file to create the
ChemicalComponentDictionary.Convert CifFiles to chem comps.
Properties of the chemical component descriptor.
Interface that is implemented by all classes that can provide
ChemComp definitions.A representation of the Chemical Component Dictionary.
Cholesky Decomposition.
Flag for BioJava beans that resemble categories defined by the mmCIF schema.
Convert a chain to a
CifFile.Defines a rather generic interface which allows to populate some data structure with data parsed from a CIF file.
Parse text Cif files and provide capabilities to store them locally.
Create a CifFile instance for a given container of structure data.
Defines the categories to consume during CIF parsing.
An implementation of a CifFileConsumer for BioJava.
Convert BioJava structures to CifFiles and vice versa.
Convert a structure to a CifFile.
Utilities for autoconfiguring javabeans based on command line arguments.
A class that clusters alternative alignments according to their
similarity.
Utilities for working with collections.
A simple class to store contacts in the form of pairs of indices and a distance associated to them.
Superimposes the core aligned residues of every structure in a
MultipleAlignment onto a reference structure.A class containing methods to find interfaces in a given crystallographic Structure by
reconstructing the crystal lattice through application of symmetry operators
A crystal cell's parameters.
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.
Represents revision records for use by
PDBHeader.A class to represent database cross references.
Example of how to load PDB files using the AtomCache class.
A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP
An example for how to access CATH data.
Example of how to run a structure alignment using the CE algorithm.
Quick demo of how to call CE-Symm programmatically.
This demo shows how to use an alternative ChemCompProvider.
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).
Example for how to load protein structures (from PDB files).
An example of how to read MMcif files
An example of how to convert mmCIF file to PDB file
Class to show how to read a Biojava structure using MMTF
Demo for running the MultipleMC Algorithm on a protein family.
Demo on how to use programatically
QsAlign for the alignment of
quaternary structures.A class demonstrating the use of the SCOP parsing tools
Demonstration on how to use the Secondary Structure Prediction (DSSP)
implementation in BioJava and obtain different SS representations and
outputs.
A demo on how to use the quaternary symmetry detection algorithms.
Decomposes a structure from the PDB into representative domains
This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web
site.
Class to parse a DSSP file (output of the DSSP program),
that contains the secondary structure assignment of a structure.
General API for interacting with 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).
Controls global
EcodDatabases being used.Provides access to the Evolutionary Classification of Protein Domains (ECOD).
Eigenvalues and eigenvectors of a real matrix.
Element is an enumeration of the elements of the periodic table.
ElementType is an enumeration of the types of elements found in the periodic table.
Heuristical finding of Entities (called Compounds in legacy PDB format)
in a given Structure.
An object to contain the info from the PDB header for a Molecule.
An enum to represent the experimental technique of a PDB structure
A collection of static utilities to convert between
AFPChains and FastaSequences.Reads a protein sequence from a fasta file and attempts to match it to a
3D structure.
A class that does calculations on an AFPChain
Methods to convert a structure object into different file formats.
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.Joins the initial Fragments together to larger Fragments
a pair of fragments of two protein structures
a class to perform Gotoh algorithm
The GraphOrderDetector transforms the self-alignment into a Graph and
extracts its maximally connected Components.
The GraphRefiner transforms the self-alignment into a Graph and extracts its
maximally connected Components.
A grid to be used for calculating atom contacts through a spatial hashing algorithm.
A grid cell to be used in contact calculation via spatial hashing algorithm.
This is the data structure for a single Group of atoms.
A class to store the results of ASA calculations, it can
hold ASA values per atom present in
GroupA pair of residues that are in contact
A set of residue-residue contacts.
An iterator over all groups of a structure.
This contains basic categories for Group types.
A class to wrap some of the strucutre.gui classes using Reflection
Container that represents a hidrogen bond.
Generic Implementation of a Group interface.
Behaviors for how to balance memory vs.
Represents an even coverage of quaternion space by 60 points.
A class containing methods to find interfaces in a given structure.
A utility class that defines which set of atoms are considered
to be on equivalent positions.
PDB-specific
A Ladder is a set of one or more consecutive bridges of identical type.
Superclass for classes which download and interact with the PDB's FTP server,
specifically
PDBFileReader and CifFileReader.Controls when the class should fetch files from the ftp server
Behaviors for when an obsolete structure is requested.
Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures.
Classes which implement ScopDatabase in a way which allows them to serve queries
without accessing the internet should implement this interface instead.
LU Decomposition.
Matrices contains static methods to operate and transform matrices used in 3D
geometry (transformation matrices and rotation matrices).
Jama = Java Matrix class.
Consume metal bond data.
Created by andreas on 6/9/16.
Created by andreas on 6/6/16.
A bean that contains cutoffs for correctly detecting metal bonds.
This class allows for finding inter-strand base pairs that are not necessarily canonical Watson-Crick pairs.
A class of functions for reading and writing Biojava structures using MMTF
A class to read MMTF files and cache them locally.
A biojava specific structure inflator for MMTF.
Class to take Biojava structure data and covert to the DataApi for encoding.
Class to store the summary data for a given structure.
A utils class of functions needed for Biojava to read and write to mmtf.
An internal utility class for StructureImpl to make it easier to manage poly and nonpoly chains.
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.
A MultipleAlignment is a Data Structure to store the core information of a
multiple structure alignment, as a return type.
Utility functions to generalize the visualization of MultipleAlignments in
molecular viewers.
A MultipleAlignmentEnsemble is a collection of
MultipleAlignments
that share the same structures (Atoms) and creation properties (algorithm,
version, creation time, etc.).A general implementation of a
MultipleAlignmentEnsemble.A general implementation of a
MultipleAlignment.Utility class for calculating common scores of
MultipleAlignments.Utility functions for working with
MultipleAlignment.This class contains functions for the conversion of
MultipleAlignment
to various String outputs.Helper methods to convert all the hierarchy levels of a MultipleAlignment
into an XML format.
Parse an XML file representing a
MultipleAlignmentEnsemble, so
that the original alignment can be recovered.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.
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.
Contains the parameters to be sent to the MC optimization.
Interface for the Multiple Structure Alignment Algorithms.
Interface for Multiple Alignment superposition algorithms.
A class that can change one amino acid to another.
A nucleotide group is almost the same as a Hetatm group.
A class to resolve the operators for transformations
A wrapper for
CeMain which sets default parameters to be appropriate for finding
circular permutations.Contains the parameters that can be sent to CE
A method to decide the order of symmetry (number of subunits)
given a structure self-alignment, calculated by CE-Symm.
An ordered pair represents a component of a cartesian product.
A Pair of objects.
A stub StructureIdentifier, representing the full structure in all cases.
Parses REMARK 350 records in a PDB file and creates transformations to
construct the quaternary structure of a protein from an asymmetric unit
A class to hold crystallographic information about a PDB structure.
This class implements the actual PDB file parsing.
The wrapper class for parsing a PDB file.
A class that contains PDB Header information.
A wrapper class for the PDB identifier.
A pair for structure alignment.
An exception during the parsing of a PDB file.
An interface implemented by all classes that represent PDB records.
Methods for getting the status of a PDB file (current, removed, unreleased)
and for accessing different versions of the structure.
Represents a simplified 3 state status of PDB IDs.
Internal use only.
Temporary data storage for LINK records.
Enumerates the classification of polymers.
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.
QR Decomposition.
Quaternary Structure Alignment (QS-Align).
The parameter bean for the
QsAlign algorithm.Result of a Quaternary Structure Alignment
QsAlign.The Quaternary Structure Relation describes the pairwise relation between two
quaternary structures.
Detects the symmetry (global, pseudo, internal and local) of protein
structures.
The QuatSymmetryParameters specify the options used for the detection of
quaternary symmetry in structures using the
QuatSymmetryDetector.Holds the results of quaternary symmetry perception obtained with
QuatSymmetryDetector.A bean to represent information about the set of
Subunits being
considered for symmetry detection.Unlike the
DownloadChemCompProvider, this ChemCompProvider does not download any chem comp
definitions.Superimposes each structure in a
MultipleAlignment onto a reference
structure.Refinement of the self-alignment failed.
A ResidueGroup is a set of residues that are part of a maximally connected
component of the self-Alignment Graph in symmetry analysis.
Everything that is needed to uniquely describe a residue position
A chainName, a start residue, and an end residue.
A chain, a start residue, and an end residue.
Enumerates the possible classifications of residues.
A class that manages the Strings that are defined in the spice.properties file.
Calculates the rotation axis for an alignment
The various categories provided by SCOP.
General API how to interact with SCOP
Contains data from
dir.des.scop.txt_1.75
Container for the information for a domain.
Controls the global ScopDatabase being used.
This class provides access to the SCOP protein structure classification.
Indicates that an I/O error occurred with SCOP lazy initialization.
Helper class to store paths to the four SCOP files
The string "%s" is replaced with the version number.
Interface for classes which implement a temporary cache for various numeric
scores, e.g.
Calculate and assign the secondary structure (SS) to the
Groups of a Structure object.
A secondary structure element (SSE) is an object representing a block of
sequential residues that share the same secondary structure type.
Container for the secondary structure information of a single residue.
This class extends the basic container for secondary structure annotation,
including all the information used in the DSSP algorithm.
This class contains methods for obtaining and converting secondary structure
information from BioJava
Structures.This enum contains all of the secondary structure types found in the DSSP
output.
Created by andreas on 9/11/15.
Created by andreas on 9/11/15.
Aligns the SEQRES residues to the ATOM residues.
Calls Spencer's method for determining order.
Creates a refined alignment with the CE-Symm alternative self-alignment.
A class that provides all that is necessary to create a Serializable Cache
An entry in the chain-level SIFTS mapping between UniProt and the PDB.
A mapping between UniProt entries and PDB chains.
Singular Value Decomposition.
Holds the data of sites presented in PDB files.
Provides a 3D superimposition of two structures based on their sequence
alignment.
A crystallographic space group.
A sparse, square matrix, implementing using two arrays of sparse
vectors, one representation for the rows and one for the columns.
A sparse vector, implemented using a symbol table.
Sample possible orientations.
A simple bean to store disulfide bridge information, the SSBOND records in the PDB files.
A class that provides a set of standard amino acids.
A simple bean that contains the parameters that can get set at startup
A utility object that describes Stoichiometry (composition of a protein assembly),
determined via clustering procedure
SubunitClusterer,
and implements human-readable representation using various strategies.What to do when the number of
SubunitCluster exceeds the length of the alphabet.A class that contains all the parameters of the structure alignment algorithm.
Interface for a structure object.
An exception during the parsing of a PDB file.
An enum of supported file formats.
An identifier that uniquely identifies a whole
Structure or
arbitrary substructure.Implementation of a PDB Structure.
An interface between 2 molecules (2 sets of atoms).
A list of interfaces between 2 molecules (2 sets of atoms)
A class that provides static access methods for easy lookup of protein structure related components
StructureIOFile extends StructureProvider with methods specific to
parsing files from the filesystem.
A utility class that makes working with names of structures, domains and ranges easier.
Perform a pairwise protein structure superimposition.
A class that can provide a protein structure object from somewhere.
A utility class with methods for matching ProteinSequences with
Structures.
A class that provides some tool methods.
This is the canonical way to identify a part of a structure.
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.
A SubunitCluster contains a set of equivalent
QuatSymmetrySubunits,
the set of equivalent residues (EQR) between Subunit and a
Subunit representative.The SubunitClusterer takes as input a collection of
Subunit and
returns a collection of SubunitCluster.The SubunitClustererMethod ennummerates all methods that can be used to
cluster
Subunit in the SubunitCluster.The SubunitClustererParameters specifies the options used for the clustering
of the subunits in structures using the
SubunitClusterer.The SuperPosition interface defines and documents the required methods for
any superpostion algorithm implementation, so that the input and expected
output are uniform.
The SuperPositionAbstract contains common code shared by all SuperPosition
algorithm implementations.
Implementation of the Quaternion-Based Characteristic Polynomial algorithm
for RMSD and Superposition calculations.
The SuperPositionQuat implements a quaternion based algorithm to superpose
arrays of Points in 3D.
SuperPositions is a Class that provides static helper methods and an easy
access to the whole family of
SuperPosition algorithms.A class that calculates the superposition between two sets of points using an
SVD Matrix Decomposition.
Sorted symbol table implementation using a java.util.TreeMap.
Data Structure that stores all the symmetry axis that describe
the symmetry of a structure.
Represents an axis of symmetry
Method used for symmetry perception in the
QuatSymmetryDetector.Interface for all symmetry refinement implementations.
Utility methods for symmetry (quaternary and internal) detection and result
manipulation.
Optimizes a symmetry alignment by a Monte Carlo score optimization of the
repeat multiple alignment.
A class containing static methods to parse the symop.lib file from the
CCP4 package.
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.
A class to contain the BoundingBoxes of all polymeric molecules in a full unit cell.
UnitQuaternions is a static Class that contains methods for calculating and
using unit quaternions.
A class that takes care about opening URLConnections and sets the proper timeouts
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
A container to persist config to the file system
This chemical component provider retrieves and caches chemical component definition files from a
zip archive specified in its construction.