Package org.openscience.cdk
Class CDKConstants
java.lang.Object
org.openscience.cdk.CDKConstants
An interface providing predefined values for a number of
constants used throughout the CDK. Classes using these constants should
not implement this interface, but use it like:
IBond.Order singleBondOrder = CDKConstants.BONDORDER_SINGLE;
- Source code:
- main
- Belongs to CDK module:
- core
- Keywords:
- bond order, stereochemistry
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Field Summary
Modifier and TypeFieldDescriptionstatic final String
Atom number/label that can be applied using the Manual Numbering Tool in ACD/ChemSketch.static final String
A set of all rings computed for this molecule.static final String
A List of annotation remarks.static final String
static final String
The IUPAC compatible name generated with AutoNom.static final String
The Beilstein Registry Number.static final IBond.Order
Deprecated.static final IBond.Order
Deprecated.UseIBond.Order
QUADRUPLE directly.static final IBond.Order
Deprecated.UseIBond.Order
SINGLE directly.static final IBond.Order
Deprecated.UseIBond.Order
TRIPLE directly.static final String
The CAS Registry Number.static final String
Used as property key for indicating the chemical group of a certain atom type.static final String
Property key to store the CIP descriptor label for an atom / bond.static final String
A String comment.static final String
Key to store/fetch CTab Sgroups from Molfiles.static final String
A description for a IChemObject.static final int
Flag used for JUnit testing the pointer functionality.static final String
The essential rings computed for this molecule.static final int[]
static final String
The Molecular Formula Identifier.static final int
A geometry of neighboring atoms when an s orbital is hybridized with one p orbital.static final int
A geometry of neighboring atoms when an s orbital is hybridized with two p orbitals.static final int
A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals.static final int
A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with one d orbital.static final int
A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with two d orbitals.static final int
A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with three d orbitals.static final int
A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with four d orbitals.static final int
A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with five d orbitals.static final int
A undefined hybridization.static final String
The IUPAC International Chemical Identifier.static final int
Sets to true if the atom is an hydrogen bond acceptor.static final int
Sets to true if the atom is an hydrogen bond donor.static final int
Flag is set if an atom could be typed.static final int
Flag that is set if a chemobject is part of an aliphatic chain.static final int
Flag is set if chemobject is part of an aromatic system.static final int
Flag is set if chemobject is part of a conjugated system.static final int
Flag that is set when the chemobject is part of a ring.static final int
Flag that is set when the chemobject is part of a ring.static final String
The Isotropic Shielding, usually calculated by a quantum chemistry program like Gaussian.static final int
Flag that is set if the chemobject is placed (somewhere).static final String
Used as property key for indicating the HOSE code for a certain atom type.static final int
Flag is set if a chemobject is mapped to another chemobject.static final int
Maximum flags array index.static final int
Maximum pointers array index.static final String
A List of names.static final String
Carbon NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.static final String
Deuterium NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.static final String
Fluorine NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.static final String
Hydrogen NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.static final String
Nitrogen NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.static final String
Phosphorus NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.static final String
Sulfur NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.static final String
NMR signal intensity constant for use as a key in the IChemObject.physicalProperties hashtable.static final String
NMR signal multiplicity constant for use as a key in the IChemObject.physicalProperties hashtable.static final String
NMR spectrum type constant for use as key for an arbitrary 1-dimensional NMR experiment.static final String
NMR spectrum type constant for use as key for a 1-dimensional DEPT135 NMR experiment.static final String
NMR spectrum type constant for use as key for a 1-dimensional DEPT90 NMR experiment.static final String
NMR spectrum type constant for use as key for a 2-dimensional H,H-COSY NMR experiment.static final String
NMR spectrum type constant for use as key for a 2-dimensional HMBC NMR experiment.static final String
NMR spectrum type constant for use as key for a 2-dimensional HSQC NMR experiment.static final String
NMR spectrum type constant for use as key for a 2-dimensional INADEQUATE NMR experiment.static final String
Used as property key for indicating the ring size of a certain atom type.static final String
Used as property key for indicating the HOSE code for a certain atom type.static final String
Property for reaction objects where the conditions of reactions can be placed.static final String
Property used for reactions when converted to/from molecules.static final String
Property used for reactions when converted to/from molecules.static final int
Flag is set if a chemobject has reactive center.static final String
The relevant rings computed for this molecule.static final String
A remark for a IChemObject.static final String
A property to indicate RestH being true or false.static final String
This property indicates how many ring bonds are connected to the given atom.static final String
This property will contain an ArrayList of Integers.static final String
Used as property key for indicating the number of single electrons on the atom type.static final int
Flag used for marking uncertainty of the bond order.static final String
A smallest set of smallest rings computed for this molecule.static final String
The Daylight SMILES.static final String
Used as property key for indicating the HOSE code for a certain atom type.static final String
Enumeration of all valid radical values.static final int
A negative atom parity.static final int
A positive atom parity.static final int
A undefined atom parity.static final String
The title for a IChemObject.static final String
static final String
static final Object
static final int
Flag is set if chemobject has been visited. -
Constructor Summary
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Method Summary
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Field Details
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UNSET
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BONDORDER_SINGLE
Deprecated.UseIBond.Order
SINGLE directly.A bond of degree 1.0. -
BONDORDER_DOUBLE
Deprecated.UseIBond.Order
DOUBLE directly.A bond of degree 2.0. -
BONDORDER_TRIPLE
Deprecated.UseIBond.Order
TRIPLE directly.A bond of degree 3.0. -
BONDORDER_QUADRUPLE
Deprecated.UseIBond.Order
QUADRUPLE directly.A bond of degree 4.0. -
STEREO_ATOM_PARITY_PLUS
public static final int STEREO_ATOM_PARITY_PLUSA positive atom parity.- See Also:
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STEREO_ATOM_PARITY_MINUS
public static final int STEREO_ATOM_PARITY_MINUSA negative atom parity.- See Also:
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STEREO_ATOM_PARITY_UNDEFINED
public static final int STEREO_ATOM_PARITY_UNDEFINEDA undefined atom parity.- See Also:
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HYBRIDIZATION_UNSET
public static final int HYBRIDIZATION_UNSETA undefined hybridization.- See Also:
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HYBRIDIZATION_SP1
public static final int HYBRIDIZATION_SP1A geometry of neighboring atoms when an s orbital is hybridized with one p orbital.- See Also:
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HYBRIDIZATION_SP2
public static final int HYBRIDIZATION_SP2A geometry of neighboring atoms when an s orbital is hybridized with two p orbitals.- See Also:
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HYBRIDIZATION_SP3
public static final int HYBRIDIZATION_SP3A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals.- See Also:
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HYBRIDIZATION_SP3D1
public static final int HYBRIDIZATION_SP3D1A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with one d orbital.- See Also:
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HYBRIDIZATION_SP3D2
public static final int HYBRIDIZATION_SP3D2A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with two d orbitals.- See Also:
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HYBRIDIZATION_SP3D3
public static final int HYBRIDIZATION_SP3D3A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with three d orbitals.- See Also:
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HYBRIDIZATION_SP3D4
public static final int HYBRIDIZATION_SP3D4A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with four d orbitals.- See Also:
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HYBRIDIZATION_SP3D5
public static final int HYBRIDIZATION_SP3D5A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with five d orbitals.- See Also:
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NMRSHIFT_CARBON
Carbon NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.- See Also:
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org.openscience.cdk.ChemObject
- Constant Field Values
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NMRSHIFT_HYDROGEN
Hydrogen NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.- See Also:
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org.openscience.cdk.ChemObject
- Constant Field Values
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NMRSHIFT_NITROGEN
Nitrogen NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.- See Also:
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org.openscience.cdk.ChemObject
- Constant Field Values
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NMRSHIFT_PHOSPORUS
Phosphorus NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.- See Also:
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org.openscience.cdk.ChemObject
- Constant Field Values
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NMRSHIFT_FLUORINE
Fluorine NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.- See Also:
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org.openscience.cdk.ChemObject
- Constant Field Values
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NMRSHIFT_DEUTERIUM
Deuterium NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.- See Also:
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org.openscience.cdk.ChemObject
- Constant Field Values
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NMRSHIFT_SULFUR
Sulfur NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.- See Also:
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org.openscience.cdk.ChemObject
- Constant Field Values
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NMRSIGNAL_MULTIPLICITY
NMR signal multiplicity constant for use as a key in the IChemObject.physicalProperties hashtable.- See Also:
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org.openscience.cdk.ChemObject
- Constant Field Values
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NMRSIGNAL_INTENSITY
NMR signal intensity constant for use as a key in the IChemObject.physicalProperties hashtable.- See Also:
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org.openscience.cdk.ChemObject
- Constant Field Values
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NMRSPECTYPE_1D
NMR spectrum type constant for use as key for an arbitrary 1-dimensional NMR experiment.- See Also:
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NMRSPECTYPE_1D_DEPT90
NMR spectrum type constant for use as key for a 1-dimensional DEPT90 NMR experiment.- See Also:
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NMRSPECTYPE_1D_DEPT135
NMR spectrum type constant for use as key for a 1-dimensional DEPT135 NMR experiment.- See Also:
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NMRSPECTYPE_2D_HSQC
NMR spectrum type constant for use as key for a 2-dimensional HSQC NMR experiment.- See Also:
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NMRSPECTYPE_2D_HHCOSY
NMR spectrum type constant for use as key for a 2-dimensional H,H-COSY NMR experiment.- See Also:
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NMRSPECTYPE_2D_INADEQUATE
NMR spectrum type constant for use as key for a 2-dimensional INADEQUATE NMR experiment.- See Also:
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NMRSPECTYPE_2D_HMBC
NMR spectrum type constant for use as key for a 2-dimensional HMBC NMR experiment.- See Also:
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CIP_DESCRIPTOR
Property key to store the CIP descriptor label for an atom / bond. The label is a string.- See Also:
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ISPLACED
public static final int ISPLACEDFlag that is set if the chemobject is placed (somewhere).- See Also:
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ISINRING
public static final int ISINRINGFlag that is set when the chemobject is part of a ring.- See Also:
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ISNOTINRING
public static final int ISNOTINRINGFlag that is set when the chemobject is part of a ring.- See Also:
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ISALIPHATIC
public static final int ISALIPHATICFlag that is set if a chemobject is part of an aliphatic chain.- See Also:
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VISITED
public static final int VISITEDFlag is set if chemobject has been visited.- See Also:
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ISAROMATIC
public static final int ISAROMATICFlag is set if chemobject is part of an aromatic system.- See Also:
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ISCONJUGATED
public static final int ISCONJUGATEDFlag is set if chemobject is part of a conjugated system.- See Also:
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MAPPED
public static final int MAPPEDFlag is set if a chemobject is mapped to another chemobject. It is used for example in subgraph isomorphism search.- See Also:
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IS_HYDROGENBOND_DONOR
public static final int IS_HYDROGENBOND_DONORSets to true if the atom is an hydrogen bond donor.- See Also:
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IS_HYDROGENBOND_ACCEPTOR
public static final int IS_HYDROGENBOND_ACCEPTORSets to true if the atom is an hydrogen bond acceptor.- See Also:
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REACTIVE_CENTER
public static final int REACTIVE_CENTERFlag is set if a chemobject has reactive center. It is used for example in reaction.- See Also:
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IS_TYPEABLE
public static final int IS_TYPEABLEFlag is set if an atom could be typed.- See Also:
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SINGLE_OR_DOUBLE
public static final int SINGLE_OR_DOUBLEFlag used for marking uncertainty of the bond order. If used on anIAtomContainer
it means that one or several of the bonds have this flag raised (which may indicate aromaticity).IBond
it means that it's unclear whether the bond is a single or double bond.IAtom
it is a way for the Smiles parser to indicate that this atom was written with a lower case letter, e.g. 'c' rather than 'C'
- See Also:
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MAX_FLAG_INDEX
public static final int MAX_FLAG_INDEXMaximum flags array index. Please update this if the value exceeds 16 - the flags are currently stored as a single short value (16-bit) in the ChemObject implementations (default, silent and query).- See Also:
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FLAG_MASKS
public static final int[] FLAG_MASKS -
DUMMY_POINTER
public static final int DUMMY_POINTERFlag used for JUnit testing the pointer functionality.- See Also:
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MAX_POINTER_INDEX
public static final int MAX_POINTER_INDEXMaximum pointers array index.- See Also:
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TITLE
The title for a IChemObject.- See Also:
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REMARK
A remark for a IChemObject.- See Also:
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COMMENT
A String comment.- See Also:
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NAMES
A List of names.- See Also:
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ANNOTATIONS
A List of annotation remarks.- See Also:
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DESCRIPTION
A description for a IChemObject.- See Also:
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SMILES
The Daylight SMILES.- See Also:
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INCHI
The IUPAC International Chemical Identifier.- See Also:
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FORMULA
The Molecular Formula Identifier.- See Also:
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AUTONOMNAME
The IUPAC compatible name generated with AutoNom.- See Also:
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BEILSTEINRN
The Beilstein Registry Number.- See Also:
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CASRN
The CAS Registry Number.- See Also:
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ALL_RINGS
A set of all rings computed for this molecule.- See Also:
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SMALLEST_RINGS
A smallest set of smallest rings computed for this molecule.- See Also:
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ESSENTIAL_RINGS
The essential rings computed for this molecule. The concept of Essential Rings is defined in SSSRFinder- See Also:
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RELEVANT_RINGS
The relevant rings computed for this molecule. The concept of relevant Rings is defined in SSSRFinder- See Also:
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REACTION_ROLE
Property used for reactions when converted to/from molecules. It defines what role and atom has an a reaction. Used in. ReactionManipulator.toMolecule and ReactionManipulator.toReaction.- See Also:
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REACTION_GROUP
Property used for reactions when converted to/from molecules. It defines fragment grouping, for example when handling ionic components. Used in. ReactionManipulator.toMolecule and ReactionManipulator.toReaction.- See Also:
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RING_SIZES
This property will contain an ArrayList of Integers. Each element of the list indicates the size of the ring the given atom belongs to (if it is a ring atom at all).- See Also:
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RING_CONNECTIONS
This property indicates how many ring bonds are connected to the given atom.- See Also:
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TOTAL_CONNECTIONS
- See Also:
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TOTAL_H_COUNT
- See Also:
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ISOTROPIC_SHIELDING
The Isotropic Shielding, usually calculated by a quantum chemistry program like Gaussian. This is a property used for calculating NMR chemical shifts by subtracting the value from the isotropic shielding value of a standard (e.g. TMS).- See Also:
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REST_H
A property to indicate RestH being true or false. RestH is a term used in RGroup queries: "if this property is applied ('on'), sites labelled with Rgroup rrr may only be substituted with a member of the Rgroup or with H"- See Also:
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ATOM_ATOM_MAPPING
- See Also:
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ACDLABS_LABEL
Atom number/label that can be applied using the Manual Numbering Tool in ACD/ChemSketch.- See Also:
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CTAB_SGROUPS
Key to store/fetch CTab Sgroups from Molfiles. Important! - Use at your own risk, property is transitive and may be removed in future with a more specific accessor.- See Also:
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SPIN_MULTIPLICITY
Enumeration of all valid radical values.- See Also:
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REACTION_CONDITIONS
Property for reaction objects where the conditions of reactions can be placed.- See Also:
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PART_OF_RING_OF_SIZE
Used as property key for indicating the ring size of a certain atom type.- See Also:
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CHEMICAL_GROUP_CONSTANT
Used as property key for indicating the chemical group of a certain atom type.- See Also:
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SPHERICAL_MATCHER
Used as property key for indicating the HOSE code for a certain atom type.- See Also:
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PI_BOND_COUNT
Used as property key for indicating the HOSE code for a certain atom type.- See Also:
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LONE_PAIR_COUNT
Used as property key for indicating the HOSE code for a certain atom type.- See Also:
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SINGLE_ELECTRON_COUNT
Used as property key for indicating the number of single electrons on the atom type.- See Also:
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Constructor Details
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CDKConstants
public CDKConstants()
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IBond.Order
DOUBLE directly.