Uses of Interface
org.openscience.cdk.interfaces.IChemObject
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Uses of IChemObject in org.openscience.cdk
Classes in org.openscience.cdk that implement IChemObject Modifier and Type Class Description class
AminoAcid
A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.class
Association
Base class for storing interactions like hydrogen bonds and ionic interactions.class
Atom
Represents the idea of an chemical atom.class
AtomContainer
Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.class
AtomContainerSet
A set of AtomContainers.class
AtomRef
An atom ref, references a CDKIAtom
indirectly.class
AtomType
The base class for atom types.class
BioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.class
Bond
Implements the concept of a covalent bond between two or more atoms.class
BondRef
A bond ref, references a CDKIBond
indirectly.class
ChemFile
A Object containing a number of ChemSequences.class
ChemModel
An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.class
ChemObject
The base class for all chemical objects in this cdk.class
ChemSequence
A sequence of ChemModels, which can, for example, be used to store the course of a reaction.class
Crystal
Class representing a molecular crystal.class
ElectronContainer
Base class for entities containing electrons, like bonds, orbitals, lone-pairs.class
Element
Implements the idea of an element in the periodic table.class
EnzymeResidueLocator
Atom that represents part of an residue in an enzyme, like Arg255.class
FragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.class
Isotope
Used to store and retrieve data of a particular isotope.class
LonePair
A LonePair is an orbital primarily located with one Atom, containing two electrons.class
Mapping
A Mapping is an relation between two ChemObjects in a non-chemical entity.class
Monomer
A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.class
Polymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.class
PseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.class
Reaction
Represents the idea of a chemical reaction.class
ReactionScheme
Classes that extends the definition of reaction to a scheme.class
ReactionSet
A set of reactions, for example those taking part in a reaction.class
Ring
Class representing a ring structure in a molecule.class
RingSet
Maintains a set of Ring objects.class
SingleElectron
A Single Electron is an orbital which is occupied by only one electron.class
Strand
A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.class
Substance
An implementation of theISubstance
interface.Methods in org.openscience.cdk that return IChemObject Modifier and Type Method Description IChemObject
Mapping. getChemObject(int pos)
Retrieves the first or second of the related IChemObjects.Methods in org.openscience.cdk that return types with arguments of type IChemObject Modifier and Type Method Description Iterable<IChemObject>
Mapping. relatedChemObjects()
Returns an Iterable to the two IChemObjects.Constructors in org.openscience.cdk with parameters of type IChemObject Constructor Description ChemObject(IChemObject chemObject)
Constructs a new IChemObject by copying the flags, and the identifier.Mapping(IChemObject objectOne, IChemObject objectTwo)
Constructs an unconnected lone pair. -
Uses of IChemObject in org.openscience.cdk.debug
Classes in org.openscience.cdk.debug that implement IChemObject Modifier and Type Class Description class
DebugAminoAcid
Debugging data class.class
DebugAtom
Debugging data class.class
DebugAtomContainer
Debugging data class.class
DebugAtomContainerSet
Debugging data class.class
DebugAtomType
Debugging data class.class
DebugBioPolymer
Debugging data class.class
DebugBond
Debugging data class.class
DebugChemFile
Debugging data class.class
DebugChemModel
Debugging data class.class
DebugChemObject
Debugging data class.class
DebugChemSequence
Debugging data class.class
DebugCrystal
Debugging data class.class
DebugElectronContainer
Debugging data class.class
DebugElement
Debugging data class.class
DebugFragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.class
DebugIsotope
Debugging data class.class
DebugLonePair
Debugging data class.class
DebugMapping
Debugging data class.class
DebugMonomer
Debugging data class.class
DebugPDBAtom
Debugging data class.class
DebugPDBMonomer
Debugging data class.class
DebugPDBPolymer
Debugging data class.class
DebugPDBStructure
Debugging data class.class
DebugPolymer
Debugging data class.class
DebugPseudoAtom
Debugging data class.class
DebugReaction
Debugging data class.class
DebugReactionScheme
Debugging data class.class
DebugReactionSet
Debugging data class.class
DebugRing
Debugging data class.class
DebugRingSet
Debugging data class.class
DebugSingleElectron
Debugging data class.class
DebugStrand
Debugging data class.class
DebugSubstance
Debugging data class.Methods in org.openscience.cdk.debug that return IChemObject Modifier and Type Method Description IChemObject
DebugMapping. getChemObject(int pos)
Retrieves the first or second of the related IChemObjects.Methods in org.openscience.cdk.debug that return types with arguments of type IChemObject Modifier and Type Method Description Iterable<IChemObject>
DebugMapping. relatedChemObjects()
Returns an Iterable to the two IChemObjects.Constructors in org.openscience.cdk.debug with parameters of type IChemObject Constructor Description DebugChemObject(IChemObject object)
DebugMapping(IChemObject objectOne, IChemObject objectTwo)
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Uses of IChemObject in org.openscience.cdk.depict
Method parameters in org.openscience.cdk.depict with type arguments of type IChemObject Modifier and Type Method Description DepictionGenerator
DepictionGenerator. withHighlight(Iterable<? extends IChemObject> chemObjs, Color color)
Highlight the provided set of atoms and bonds in the depiction in the specified color. -
Uses of IChemObject in org.openscience.cdk.dict
Methods in org.openscience.cdk.dict with parameters of type IChemObject Modifier and Type Method Description static void
CDKDictionaryReferences. makeReferencesExplicit(IChemObject object)
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Uses of IChemObject in org.openscience.cdk.interfaces
Classes in org.openscience.cdk.interfaces with type parameters of type IChemObject Modifier and Type Interface Description interface
IStereoElement<F extends IChemObject,C extends IChemObject>
Representation of stereochemical configuration.interface
IStereoElement<F extends IChemObject,C extends IChemObject>
Representation of stereochemical configuration.Subinterfaces of IChemObject in org.openscience.cdk.interfaces Modifier and Type Interface Description interface
IAminoAcid
A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.interface
IAtom
Represents the idea of an chemical atom.interface
IAtomContainer
Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.interface
IAtomContainerSet
A set of AtomContainers.interface
IAtomType
The base class for atom types.interface
IBioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.interface
IBond
Implements the concept of a covalent bond between two or more atoms.interface
IChemFile
AnIChemObject
containing a number of ChemSequences.interface
IChemModel
An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.interface
IChemSequence
A sequence of ChemModels, which can, for example, be used to store the course of a reaction.interface
ICrystal
Class representing a molecular crystal.interface
IElectronContainer
Base class for entities containing electrons, like bonds, orbitals, lone-pairs.interface
IElement
Implements the idea of an element in the periodic table.interface
IFragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.interface
IIsotope
Used to store and retrieve data of a particular isotope.interface
ILonePair
A LonePair is an orbital primarily located with one Atom, containing two electrons.interface
IMapping
Represents a mapping of two atoms.interface
IMonomer
A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.interface
IPDBAtom
A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.interface
IPDBMonomer
Represents the idea of an protein monomer as found in PDB files.interface
IPDBPolymer
A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.interface
IPolymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.interface
IPseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.interface
IReaction
Represents the idea of a chemical reaction.interface
IReactionScheme
Classes that implement this interface of a scheme.interface
IReactionSet
A set of reactions, for example those taking part in a reaction.interface
IRing
Class representing a ring structure in a molecule.interface
IRingSet
Maintains a set of Ring objects.interface
ISingleElectron
A Single Electron is an orbital which is occupied by only one electron.interface
IStrand
A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.interface
ISubstance
A chemical substance that consists of one or more chemical structures.Methods in org.openscience.cdk.interfaces that return IChemObject Modifier and Type Method Description IChemObject
IMapping. getChemObject(int pos)
Retrieve the first or second of the related IChemObjects.Methods in org.openscience.cdk.interfaces that return types with arguments of type IChemObject Modifier and Type Method Description Iterable<IChemObject>
IMapping. relatedChemObjects()
Returns anIterable
to the two IChemObjects.Method parameters in org.openscience.cdk.interfaces with type arguments of type IChemObject Modifier and Type Method Description IStereoElement<F,C>
IStereoElement. map(Map<IChemObject,IChemObject> chemobjs)
Update the stereo using the remapping of atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.IStereoElement<F,C>
IStereoElement. map(Map<IChemObject,IChemObject> chemobjs)
Update the stereo using the remapping of atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.IStereoElement<F,C>
IStereoElement. mapStrict(Map<IChemObject,IChemObject> chemobjs)
Update the stereo using the remapping of atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.IStereoElement<F,C>
IStereoElement. mapStrict(Map<IChemObject,IChemObject> chemobjs)
Update the stereo using the remapping of atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping. -
Uses of IChemObject in org.openscience.cdk.io
Methods in org.openscience.cdk.io with type parameters of type IChemObject Modifier and Type Method Description <T extends IChemObject>
TCIFReader. read(T object)
Read a ChemFile from input.<T extends IChemObject>
TCMLReader. read(T object)
Read a IChemObject from input.<T extends IChemObject>
TCrystClustReader. read(T object)
<T extends IChemObject>
TCTXReader. read(T object)
<T extends IChemObject>
TGamessReader. read(T object)
<T extends IChemObject>
TGaussian03Reader. read(T object)
<T extends IChemObject>
TGaussian98Reader. read(T object)
<T extends IChemObject>
TGhemicalMMReader. read(T object)
<T extends IChemObject>
THINReader. read(T object)
Reads the content from a HIN input.<T extends IChemObject>
TINChIPlainTextReader. read(T object)
Reads a IChemObject of type object from input.<T extends IChemObject>
TINChIReader. read(T object)
Reads a IChemObject of type object from input.<T extends IChemObject>
TISimpleChemObjectReader. read(T object)
Reads an IChemObject of type "object" from input.<T extends IChemObject>
TMDLReader. read(T object)
Deprecated.Takes an object which subclasses IChemObject, e.g.<T extends IChemObject>
TMDLRXNReader. read(T object)
Deprecated.Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file, database, internet etc).<T extends IChemObject>
TMDLRXNV2000Reader. read(T object)
Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file, database, internet etc).<T extends IChemObject>
TMDLRXNV3000Reader. read(T object)
<T extends IChemObject>
TMDLV2000Reader. read(T object)
Takes an object which subclasses IChemObject, e.g.<T extends IChemObject>
TMDLV3000Reader. read(T object)
<T extends IChemObject>
TMol2Reader. read(T object)
<T extends IChemObject>
TMopac7Reader. read(T object)
<T extends IChemObject>
TMoSSOutputReader. read(T object)
Read aIAtomContainerSet
from the input source.<T extends IChemObject>
TPCCompoundASNReader. read(T object)
<T extends IChemObject>
TPCCompoundXMLReader. read(T object)
<T extends IChemObject>
TPCSubstanceXMLReader. read(T object)
<T extends IChemObject>
TPDBReader. read(T oObj)
Takes an object which subclasses IChemObject, e.g.<T extends IChemObject>
TPMPReader. read(T object)
reads the content from a PMP input.<T extends IChemObject>
TRGroupQueryReader. read(T object)
Check input IChemObject and proceed to parse.<T extends IChemObject>
TShelXReader. read(T object)
Read a ChemFile from input.<T extends IChemObject>
TSMILESReader. read(T object)
Reads the content from a XYZ input.<T extends IChemObject>
TVASPReader. read(T object)
<T extends IChemObject>
TXYZReader. read(T object)
reads the content from a XYZ input.<T extends IChemObject>
TZMatrixReader. read(T object)
Returns a IChemObject of type object bye reading from the input.Methods in org.openscience.cdk.io with parameters of type IChemObject Modifier and Type Method Description boolean
MDLRXNReader. accepts(IChemObject object)
Deprecated.boolean
MDLRXNV2000Reader. accepts(IChemObject object)
boolean
MDLRXNV3000Reader. accepts(IChemObject object)
boolean
Mol2Reader. accepts(IChemObject object)
void
CDKSourceCodeWriter. write(IChemObject object)
void
CMLWriter. write(IChemObject object)
Serializes the IChemObject to CML and redirects it to the output Writer.void
CrystClustWriter. write(IChemObject object)
Serializes the IChemObject to CrystClust format and redirects it to the output Writer.void
HINWriter. write(IChemObject object)
void
IChemObjectWriter. write(IChemObject object)
Writes the content of "object" to output.void
MDLRXNWriter. write(IChemObject object)
Writes a IChemObject to the MDL RXN file formated output.void
MDLV2000Writer. write(IChemObject object)
Writes aIChemObject
to the MDL molfile formated output.void
MDLV3000Writer. write(IChemObject object)
Writes a molecule to the V3000 format.void
Mol2Writer. write(IChemObject object)
void
PDBWriter. write(IChemObject object)
void
RGroupQueryWriter. write(IChemObject object)
The actual writing of the output.void
RssWriter. write(IChemObject object)
Writes a IChemObject to the MDL molfile formated output.void
SDFWriter. write(IChemObject object)
Writes a IChemObject to the MDL SD file formated output.void
ShelXWriter. write(IChemObject object)
Serializes the IChemObject to ShelX and redirects it to the output Writer.void
SMILESWriter. write(IChemObject object)
Writes the content from object to output.void
XYZWriter. write(IChemObject object)
Method parameters in org.openscience.cdk.io with type arguments of type IChemObject Modifier and Type Method Description boolean
CDKSourceCodeWriter. accepts(Class<? extends IChemObject> classObject)
boolean
CIFReader. accepts(Class<? extends IChemObject> testClass)
boolean
CMLReader. accepts(Class<? extends IChemObject> classObject)
boolean
CMLWriter. accepts(Class<? extends IChemObject> classObject)
boolean
CrystClustReader. accepts(Class<? extends IChemObject> classObject)
boolean
CrystClustWriter. accepts(Class<? extends IChemObject> classObject)
boolean
CTXReader. accepts(Class<? extends IChemObject> classObject)
boolean
GamessReader. accepts(Class<? extends IChemObject> classObject)
boolean
Gaussian03Reader. accepts(Class<? extends IChemObject> classObject)
boolean
Gaussian98Reader. accepts(Class<? extends IChemObject> classObject)
boolean
GhemicalMMReader. accepts(Class<? extends IChemObject> classObject)
boolean
HINReader. accepts(Class<? extends IChemObject> classObject)
boolean
HINWriter. accepts(Class<? extends IChemObject> classObject)
boolean
IChemObjectIO. accepts(Class<? extends IChemObject> classObject)
Returns whether the givenIChemObject
can be read or written.boolean
INChIPlainTextReader. accepts(Class<? extends IChemObject> classObject)
boolean
INChIReader. accepts(Class<? extends IChemObject> classObject)
boolean
MDLReader. accepts(Class<? extends IChemObject> classObject)
Deprecated.boolean
MDLRXNReader. accepts(Class<? extends IChemObject> classObject)
Deprecated.boolean
MDLRXNV2000Reader. accepts(Class<? extends IChemObject> classObject)
boolean
MDLRXNV3000Reader. accepts(Class<? extends IChemObject> classObject)
boolean
MDLRXNWriter. accepts(Class<? extends IChemObject> classObject)
boolean
MDLV2000Reader. accepts(Class<? extends IChemObject> classObject)
boolean
MDLV2000Writer. accepts(Class<? extends IChemObject> classObject)
boolean
MDLV3000Reader. accepts(Class<? extends IChemObject> classObject)
boolean
MDLV3000Writer. accepts(Class<? extends IChemObject> c)
Returns whether the givenIChemObject
can be read or written.boolean
Mol2Reader. accepts(Class<? extends IChemObject> classObject)
boolean
Mol2Writer. accepts(Class<? extends IChemObject> classObject)
boolean
Mopac7Reader. accepts(Class<? extends IChemObject> classObject)
boolean
MoSSOutputReader. accepts(Class<? extends IChemObject> testClass)
Returns whether the givenIChemObject
can be read or written.boolean
PCCompoundASNReader. accepts(Class<? extends IChemObject> classObject)
boolean
PCCompoundXMLReader. accepts(Class<? extends IChemObject> classObject)
boolean
PCSubstanceXMLReader. accepts(Class<? extends IChemObject> classObject)
boolean
PDBReader. accepts(Class<? extends IChemObject> classObject)
boolean
PDBWriter. accepts(Class<? extends IChemObject> classObject)
boolean
PMPReader. accepts(Class<? extends IChemObject> classObject)
boolean
RGroupQueryReader. accepts(Class<? extends IChemObject> classObject)
boolean
RGroupQueryWriter. accepts(Class<? extends IChemObject> classObject)
Returns true for accepted input types.boolean
RssWriter. accepts(Class<? extends IChemObject> classObject)
boolean
SDFWriter. accepts(Class<? extends IChemObject> classObject)
boolean
ShelXReader. accepts(Class<? extends IChemObject> classObject)
boolean
ShelXWriter. accepts(Class<? extends IChemObject> classObject)
boolean
SMILESReader. accepts(Class<? extends IChemObject> classObject)
boolean
SMILESWriter. accepts(Class<? extends IChemObject> classObject)
boolean
XYZReader. accepts(Class<? extends IChemObject> classObject)
boolean
XYZWriter. accepts(Class<? extends IChemObject> classObject)
boolean
ZMatrixReader. accepts(Class<? extends IChemObject> classObject)
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Uses of IChemObject in org.openscience.cdk.io.iterator
Classes in org.openscience.cdk.io.iterator with type parameters of type IChemObject Modifier and Type Class Description class
DefaultIteratingChemObjectReader<T extends IChemObject>
Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.interface
IIteratingChemObjectReader<T extends IChemObject>
Interface for an iterating molecule reader.Method parameters in org.openscience.cdk.io.iterator with type arguments of type IChemObject Modifier and Type Method Description boolean
DefaultIteratingChemObjectReader. accepts(Class<? extends IChemObject> objectClass)
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Uses of IChemObject in org.openscience.cdk.io.iterator.event
Methods in org.openscience.cdk.io.iterator.event with parameters of type IChemObject Modifier and Type Method Description boolean
DefaultEventChemObjectReader. accepts(IChemObject object)
Method parameters in org.openscience.cdk.io.iterator.event with type arguments of type IChemObject Modifier and Type Method Description boolean
DefaultEventChemObjectReader. accepts(Class<? extends IChemObject> objectClass)
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Uses of IChemObject in org.openscience.cdk.io.program
Methods in org.openscience.cdk.io.program with parameters of type IChemObject Modifier and Type Method Description void
GaussianInputWriter. write(IChemObject object)
void
Mopac7Writer. write(IChemObject arg0)
Writes the content of "object" to output.Method parameters in org.openscience.cdk.io.program with type arguments of type IChemObject Modifier and Type Method Description boolean
GaussianInputWriter. accepts(Class<? extends IChemObject> classObject)
boolean
Mopac7Writer. accepts(Class<? extends IChemObject> classObject)
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Uses of IChemObject in org.openscience.cdk.io.random
Methods in org.openscience.cdk.io.random that return IChemObject Modifier and Type Method Description IChemObject
RandomAccessReader. first()
IChemObject
RandomAccessReader. last()
IChemObject
RandomAccessReader. next()
IChemObject
RandomAccessReader. previous()
protected IChemObject
RandomAccessReader. processContent()
The reader is already set to read the record buffer.protected IChemObject
RandomAccessSDFReader. processContent()
IChemObject
RandomAccessReader. readRecord(int record)
Returns the object at given record No.Methods in org.openscience.cdk.io.random with parameters of type IChemObject Modifier and Type Method Description void
RandomAccessReader. add(IChemObject arg0)
void
RandomAccessReader. set(IChemObject arg0)
Method parameters in org.openscience.cdk.io.random with type arguments of type IChemObject Modifier and Type Method Description boolean
RandomAccessSDFReader. accepts(Class<? extends IChemObject> classObject)
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Uses of IChemObject in org.openscience.cdk.io.rdf
Methods in org.openscience.cdk.io.rdf with type parameters of type IChemObject Modifier and Type Method Description <T extends IChemObject>
TCDKOWLReader. read(T object)
Reads an IChemObject of type "object" from input.Methods in org.openscience.cdk.io.rdf with parameters of type IChemObject Modifier and Type Method Description void
CDKOWLWriter. write(IChemObject object)
Writes the content of "object" to output.Method parameters in org.openscience.cdk.io.rdf with type arguments of type IChemObject Modifier and Type Method Description boolean
CDKOWLReader. accepts(Class<? extends IChemObject> classObject)
Returns whether the givenIChemObject
can be read or written.boolean
CDKOWLWriter. accepts(Class<? extends IChemObject> classObject)
Returns whether the givenIChemObject
can be read or written. -
Uses of IChemObject in org.openscience.cdk.isomorphism
Methods in org.openscience.cdk.isomorphism that return types with arguments of type IChemObject Modifier and Type Method Description Iterable<Map<IChemObject,IChemObject>>
Mappings. toAtomBondMap()
Convert the permutations to an atom-atom bond-bond map.Iterable<Map<IChemObject,IChemObject>>
Mappings. toAtomBondMap()
Convert the permutations to an atom-atom bond-bond map.Iterable<IChemObject>
Mappings. toChemObjects()
Obtain the chem objects (atoms and bonds) that have 'hit' in the target molecule. -
Uses of IChemObject in org.openscience.cdk.isomorphism.matchers
Subinterfaces of IChemObject in org.openscience.cdk.isomorphism.matchers Modifier and Type Interface Description interface
IQueryAtom
Defines the ability to be matched againstIAtom
's.interface
IQueryAtomContainer
General concept of a IAtomContainer aimed at doing molecular subgraph queries using the UniversalIsomorphismTester.interface
IQueryBond
Defines the abililty to be matched against IBond's.interface
IRGroupQuery
Interface definition for Rgroup query classes.Classes in org.openscience.cdk.isomorphism.matchers that implement IChemObject Modifier and Type Class Description class
CTFileQueryBond
Deprecated.UseExpr.Type.SINGLE_OR_AROMATIC
etc.class
InverseSymbolSetQueryAtom
Deprecated.class
OrderQueryBond
Deprecated.class
OrderQueryBondOrderOnly
Deprecated.Usenew QueryBond(beg, end, ORDER, bord)
class
QueryAtom
class
QueryAtomContainer
class
QueryBond
Implements the concept of a "query bond" between two or more atoms.class
QueryChemObject
class
RGroupQuery
Represents information contained in a Symyx RGfile (R-group query file).
It contains a root structure (the scaffold if you like), a map with R-group definitions (each of which can contain multiple substitutes) and a map with attachment points.class
SymbolAndChargeQueryAtom
Deprecated.class
SymbolChargeIDQueryAtom
class
SymbolQueryAtom
Deprecated.class
SymbolSetQueryAtom
Deprecated.Usenew Expr(Element, 6).and(new Expr(Element, 8))
etc -
Uses of IChemObject in org.openscience.cdk.isomorphism.matchers.smarts
Classes in org.openscience.cdk.isomorphism.matchers.smarts that implement IChemObject Modifier and Type Class Description class
AliphaticAtom
Deprecated.class
AliphaticSymbolAtom
Deprecated.class
AnyAtom
Deprecated.class
AnyOrderQueryBond
Deprecated.class
AromaticAtom
Deprecated.class
AromaticOrSingleQueryBond
Deprecated.class
AromaticQueryBond
Deprecated.class
AromaticSymbolAtom
Deprecated.class
AtomicNumberAtom
Deprecated.class
ChiralityAtom
Deprecated.class
ExplicitConnectionAtom
Deprecated.class
FormalChargeAtom
Deprecated.class
HybridizationNumberAtom
Deprecated.class
HydrogenAtom
Deprecated.class
ImplicitHCountAtom
Deprecated.class
LogicalOperatorAtom
Deprecated.class
LogicalOperatorBond
Deprecated.class
MassAtom
Deprecated.class
NonCHHeavyAtom
Deprecated.class
OrderQueryBond
Deprecated.class
PeriodicGroupNumberAtom
Deprecated.class
ReactionRoleQueryAtom
Deprecated.class
RecursiveSmartsAtom
Deprecated.class
RingBond
Deprecated.class
RingIdentifierAtom
Deprecated.class
RingMembershipAtom
Deprecated.class
SmallestRingAtom
Deprecated.class
SMARTSAtom
Deprecated.class
SMARTSBond
Deprecated.class
StereoBond
Deprecated.class
TotalConnectionAtom
Deprecated.class
TotalHCountAtom
Deprecated.class
TotalRingConnectionAtom
Deprecated.class
TotalValencyAtom
Deprecated. -
Uses of IChemObject in org.openscience.cdk.layout
Constructors in org.openscience.cdk.layout with parameters of type IChemObject Constructor Description OverlapPair(IChemObject co1, IChemObject co2)
Constructor for the OverlapPair object. -
Uses of IChemObject in org.openscience.cdk.libio.md
Classes in org.openscience.cdk.libio.md that implement IChemObject Modifier and Type Class Description class
ChargeGroup
A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule.class
MDMolecule
class
Residue
A residue is a named, numbered collection of atoms in an MDMolecule. -
Uses of IChemObject in org.openscience.cdk.pharmacophore
Classes in org.openscience.cdk.pharmacophore that implement IChemObject Modifier and Type Class Description class
PharmacophoreAngleBond
Represents an angle relationship between three pharmacophore groups.class
PharmacophoreAtom
A representation of a pharmacophore group.class
PharmacophoreBond
Represents a distance relationship between two pharmacophore groups.class
PharmacophoreQuery
Represents a colleciton of pharmacophore groups and constraints.class
PharmacophoreQueryAngleBond
Represents a pharmacophore query angle constraint.class
PharmacophoreQueryAtom
Represents a query pharmacophore group.class
PharmacophoreQueryBond
Represents a pharmacophore query distance constraint. -
Uses of IChemObject in org.openscience.cdk.protein.data
Classes in org.openscience.cdk.protein.data that implement IChemObject Modifier and Type Class Description class
PDBAtom
Represents the idea of an atom as used in PDB files.class
PDBMonomer
Represents the idea of an monomer as used in PDB files.class
PDBPolymer
An entry in the PDB database.class
PDBStrand
An entry in the PDB database.class
PDBStructure
Holder for secundary protein structure elements. -
Uses of IChemObject in org.openscience.cdk.reaction
Classes in org.openscience.cdk.reaction that implement IChemObject Modifier and Type Class Description class
ReactionChain
Classes that extends the definition of reaction to a chain reaction. -
Uses of IChemObject in org.openscience.cdk.renderer
Classes in org.openscience.cdk.renderer with type parameters of type IChemObject Modifier and Type Class Description class
AbstractRenderer<T extends IChemObject>
The base class for all renderers, handling the core aspects of rendering such as the location of the model in 'model space' and the location on the screen to draw the model.interface
IRenderer<T extends IChemObject>
Interface that all 2D renderers implement.Methods in org.openscience.cdk.renderer that return types with arguments of type IChemObject Modifier and Type Method Description Map<IChemObject,Color>
RendererModel.ColorHash. getDefault()
Gets the default value for this parameter.Method parameters in org.openscience.cdk.renderer with type arguments of type IChemObject Modifier and Type Method Description void
RendererModel. registerParameters(IGenerator<? extends IChemObject> generator)
Registers rendering parameters fromIGenerator
s with this model. -
Uses of IChemObject in org.openscience.cdk.renderer.generators
Classes in org.openscience.cdk.renderer.generators with type parameters of type IChemObject Modifier and Type Interface Description interface
IGenerator<T extends IChemObject>
AnIGenerator
converts chemical entities into parts of the chemical drawing expressed asIRenderingElement
s. -
Uses of IChemObject in org.openscience.cdk.renderer.selection
Methods in org.openscience.cdk.renderer.selection with type parameters of type IChemObject Modifier and Type Method Description <E extends IChemObject>
Collection<E>IChemObjectSelection. elements(Class<E> clazz)
Returns aCollection
of all selectedIChemObject
s of the given type.Methods in org.openscience.cdk.renderer.selection with parameters of type IChemObject Modifier and Type Method Description protected void
AbstractSelection. addToAtomContainer(IAtomContainer ac, IChemObject item)
Utility method to add anIChemObject
to anIAtomContainer
.boolean
IChemObjectSelection. contains(IChemObject obj)
Determines if theIChemObject
is part of the current selection. -
Uses of IChemObject in org.openscience.cdk.silent
Classes in org.openscience.cdk.silent that implement IChemObject Modifier and Type Class Description class
AminoAcid
A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.class
Atom
Represents the idea of an chemical atom.class
AtomContainer
Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.class
AtomContainerSet
A set of AtomContainers.class
AtomType
The base class for atom types.class
BioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.class
Bond
Implements the concept of a covalent bond between two or more atoms.class
ChemFile
A Object containing a number of ChemSequences.class
ChemModel
An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.class
ChemObject
The base class for all chemical objects in this cdk.class
ChemSequence
A sequence of ChemModels, which can, for example, be used to store the course of a reaction.class
Crystal
Class representing a molecular crystal.class
ElectronContainer
Base class for entities containing electrons, like bonds, orbitals, lone-pairs.class
Element
Implements the idea of an element in the periodic table.class
FragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.class
Isotope
Used to store and retrieve data of a particular isotope.class
LonePair
A LonePair is an orbital primarily located with one Atom, containing two electrons.class
Mapping
A Mapping is an relation between two ChemObjects in a non-chemical entity.class
Monomer
A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.class
PDBAtom
Represents the idea of an atom as used in PDB files.class
PDBMonomer
Represents the idea of an monomer as used in PDB files.class
PDBPolymer
An entry in the PDB database.class
PDBStructure
Holder for secundary protein structure elements.class
Polymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.class
PseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.class
Reaction
Represents the idea of a chemical reaction.class
ReactionScheme
Classes that extends the definition of reaction to a scheme.class
ReactionSet
A set of reactions, for example those taking part in a reaction.class
Ring
Class representing a ring structure in a molecule.class
RingSet
Maintains a set of Ring objects.class
SingleElectron
A Single Electron is an orbital which is occupied by only one electron.class
Strand
A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.class
Substance
An implementation of theISubstance
interface.Methods in org.openscience.cdk.silent that return IChemObject Modifier and Type Method Description IChemObject
Mapping. getChemObject(int pos)
Retrieves the first or second of the related IChemObjects.Methods in org.openscience.cdk.silent that return types with arguments of type IChemObject Modifier and Type Method Description Iterable<IChemObject>
Mapping. relatedChemObjects()
Returns an Iterable to the two IChemObjects.Constructors in org.openscience.cdk.silent with parameters of type IChemObject Constructor Description ChemObject(IChemObject chemObject)
Constructs a new IChemObject by copying the flags, and the identifier.Mapping(IChemObject objectOne, IChemObject objectTwo)
Constructs an unconnected lone pair. -
Uses of IChemObject in org.openscience.cdk.stereo
Method parameters in org.openscience.cdk.stereo with type arguments of type IChemObject Modifier and Type Method Description ITetrahedralChirality
TetrahedralChirality. map(Map<IChemObject,IChemObject> chemobjs)
ITetrahedralChirality
TetrahedralChirality. map(Map<IChemObject,IChemObject> chemobjs)
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Uses of IChemObject in org.openscience.cdk.tools
Methods in org.openscience.cdk.tools with parameters of type IChemObject Modifier and Type Method Description static void
IDCreator. createIDs(IChemObject chemObject)
Labels the Atom's and Bond's in the AtomContainer using the a1, a2, b1, b2 scheme often used in CML. -
Uses of IChemObject in org.openscience.cdk.tools.diff
Methods in org.openscience.cdk.tools.diff with parameters of type IChemObject Modifier and Type Method Description static String
AtomContainerDiff. diff(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as aString
.static String
AtomDiff. diff(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as aString
.static String
AtomTypeDiff. diff(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as aString
.static String
BondDiff. diff(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as aString
.static String
ChemObjectDiff. diff(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as aString
.static String
ElectronContainerDiff. diff(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as aString
.static String
ElementDiff. diff(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as aString
.static String
IsotopeDiff. diff(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as aString
.static String
LonePairDiff. diff(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as aString
.static String
SingleElectronDiff. diff(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as aString
.static IDifference
AtomContainerDiff. difference(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as anIDifference
.static IDifference
AtomDiff. difference(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as anIDifference
.static IDifference
AtomTypeDiff. difference(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as anIDifference
.static IDifference
BondDiff. difference(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as anIDifference
.static IDifference
ChemObjectDiff. difference(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as anIDifference
.static IDifference
ElectronContainerDiff. difference(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as anIDifference
.static IDifference
ElementDiff. difference(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as anIDifference
.static IDifference
IsotopeDiff. difference(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as anIDifference
.static IDifference
LonePairDiff. difference(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as anIDifference
.static IDifference
SingleElectronDiff. difference(IChemObject first, IChemObject second)
Compare twoIChemObject
classes and return the difference as anIDifference
. -
Uses of IChemObject in org.openscience.cdk.tools.manipulator
Methods in org.openscience.cdk.tools.manipulator that return IChemObject Modifier and Type Method Description static IChemObject
ReactionManipulator. getMappedChemObject(IReaction reaction, IChemObject chemObject)
Returns theIAtom
that is mapped.Methods in org.openscience.cdk.tools.manipulator that return types with arguments of type IChemObject Modifier and Type Method Description static List<IChemObject>
AtomContainerSetManipulator. getAllChemObjects(IAtomContainerSet set)
Does not recursively return the contents of the AtomContainer.static List<IChemObject>
ChemFileManipulator. getAllChemObjects(IChemFile file)
Returns a List of all IChemObject inside a ChemFile.static List<IChemObject>
ChemModelManipulator. getAllChemObjects(IChemModel chemModel)
Retrieve a List of all ChemObject objects within an IChemModel.static List<IChemObject>
ChemSequenceManipulator. getAllChemObjects(IChemSequence sequence)
Returns a List of all IChemObject inside a ChemSequence.static List<IChemObject>
MoleculeSetManipulator. getAllChemObjects(IAtomContainerSet set)
static List<IChemObject>
ReactionManipulator. getAllChemObjects(IReaction reaction)
static List<IChemObject>
ReactionSetManipulator. getAllChemObjects(IReactionSet set)
Methods in org.openscience.cdk.tools.manipulator with parameters of type IChemObject Modifier and Type Method Description static IChemObject
ReactionManipulator. getMappedChemObject(IReaction reaction, IChemObject chemObject)
Returns theIAtom
that is mapped.Method parameters in org.openscience.cdk.tools.manipulator with type arguments of type IChemObject Modifier and Type Method Description static List<Sgroup>
SgroupManipulator. copy(Collection<Sgroup> sgroups, Map<? extends IChemObject,? extends IChemObject> replace)
static List<Sgroup>
SgroupManipulator. copy(Collection<Sgroup> sgroups, Map<? extends IChemObject,? extends IChemObject> replace)
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Uses of IChemObject in org.openscience.cdk.validate
Methods in org.openscience.cdk.validate that return IChemObject Modifier and Type Method Description IChemObject
ValidationTest. getChemObject()
Methods in org.openscience.cdk.validate with parameters of type IChemObject Modifier and Type Method Description static void
ProblemMarker. markWithError(IChemObject object)
static void
ProblemMarker. markWithWarning(IChemObject object)
static void
ProblemMarker. unmark(IChemObject object)
static void
ProblemMarker. unmarkWithError(IChemObject object)
static void
ProblemMarker. unmarkWithWarning(IChemObject object)
ValidationReport
AbstractValidator. validateChemObject(IChemObject subject)
ValidationReport
DictionaryValidator. validateChemObject(IChemObject subject)
ValidationReport
IValidator. validateChemObject(IChemObject object)
ValidationReport
ValidatorEngine. validateChemObject(IChemObject subject)
Constructors in org.openscience.cdk.validate with parameters of type IChemObject Constructor Description ValidationTest(IChemObject object, String error)
ValidationTest(IChemObject object, String error, String details)
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