Uses of Interface
org.openscience.cdk.interfaces.IChemObject

Packages that use IChemObject

Package	Description
org.openscience.cdk
org.openscience.cdk.debug
org.openscience.cdk.depict
org.openscience.cdk.dict
org.openscience.cdk.interfaces
org.openscience.cdk.io
org.openscience.cdk.io.iterator
org.openscience.cdk.io.iterator.event
org.openscience.cdk.io.program
org.openscience.cdk.io.random
org.openscience.cdk.io.rdf
org.openscience.cdk.isomorphism
org.openscience.cdk.isomorphism.matchers
org.openscience.cdk.isomorphism.matchers.smarts
org.openscience.cdk.layout
org.openscience.cdk.libio.md
org.openscience.cdk.pharmacophore
org.openscience.cdk.protein.data
org.openscience.cdk.reaction
org.openscience.cdk.renderer
org.openscience.cdk.renderer.generators
org.openscience.cdk.renderer.selection
org.openscience.cdk.silent
org.openscience.cdk.tools
org.openscience.cdk.tools.diff
org.openscience.cdk.tools.manipulator
org.openscience.cdk.validate

Uses of IChemObject in org.openscience.cdk

Classes in org.openscience.cdk that implement IChemObject

Modifier and Type	Class and 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	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	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 the ISubstance interface.

Methods in org.openscience.cdk that return IChemObject

Modifier and Type	Method and 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 and Description
Iterable<IChemObject>	Mapping.relatedChemObjects() Returns an Iterable to the two IChemObjects.

Constructors in org.openscience.cdk with parameters of type IChemObject

Constructor and 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 and 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 and 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 and Description
Iterable<IChemObject>	DebugMapping.relatedChemObjects() Returns an Iterable to the two IChemObjects.

Constructors in org.openscience.cdk.debug with parameters of type IChemObject

Constructor and Description
DebugChemObject(IChemObject object)
DebugMapping(IChemObject objectOne, IChemObject objectTwo)

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 and 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 and Description
static void	CDKDictionaryReferences.makeReferencesExplicit(IChemObject object)

Uses of IChemObject in org.openscience.cdk.interfaces

Subinterfaces of IChemObject in org.openscience.cdk.interfaces

Modifier and Type	Interface and 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 An IChemObject 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 and 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 and Description
Iterable<IChemObject>	IMapping.relatedChemObjects() Returns an Iterable to the two IChemObjects.

Uses of IChemObject in org.openscience.cdk.io

Methods in org.openscience.cdk.io with type parameters of type IChemObject

Modifier and Type	Method and Description
<T extends IChemObject> T	XYZReader.read(T object) reads the content from a XYZ input.
<T extends IChemObject> T	ShelXReader.read(T object) Read a ChemFile from input.
<T extends IChemObject> T	RGroupQueryReader.read(T object) Check input IChemObject and proceed to parse.
<T extends IChemObject> T	PMPReader.read(T object) reads the content from a PMP input.
<T extends IChemObject> T	PCSubstanceXMLReader.read(T object)
<T extends IChemObject> T	PCCompoundXMLReader.read(T object)
<T extends IChemObject> T	PCCompoundASNReader.read(T object)
<T extends IChemObject> T	Mopac7Reader.read(T object)
<T extends IChemObject> T	Mol2Reader.read(T object)
<T extends IChemObject> T	MDLV3000Reader.read(T object)
<T extends IChemObject> T	MDLV2000Reader.read(T object) Takes an object which subclasses IChemObject, e.g.
<T extends IChemObject> T	MDLReader.read(T object) Deprecated. Takes an object which subclasses IChemObject, e.g.
<T extends IChemObject> T	MDLRXNV3000Reader.read(T object)
<T extends IChemObject> T	MDLRXNV2000Reader.read(T object) Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file, database, internet etc).
<T extends IChemObject> T	MDLRXNReader.read(T object) Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file, database, internet etc).
<T extends IChemObject> T	ISimpleChemObjectReader.read(T object) Reads an IChemObject of type "object" from input.
<T extends IChemObject> T	HINReader.read(T object) Reads the content from a HIN input.
<T extends IChemObject> T	GhemicalMMReader.read(T object)
<T extends IChemObject> T	Gaussian98Reader.read(T object)
<T extends IChemObject> T	Gaussian03Reader.read(T object)
<T extends IChemObject> T	CTXReader.read(T object)
<T extends IChemObject> T	CMLReader.read(T object) Read a IChemObject from input.
<T extends IChemObject> T	CIFReader.read(T object) Read a ChemFile from input.
<T extends IChemObject> T	ZMatrixReader.read(T object) Returns a IChemObject of type object bye reading from the input.
<T extends IChemObject> T	VASPReader.read(T object)
<T extends IChemObject> T	INChIReader.read(T object) Reads a IChemObject of type object from input.
<T extends IChemObject> T	INChIPlainTextReader.read(T object) Reads a IChemObject of type object from input.
<T extends IChemObject> T	GamessReader.read(T object)
<T extends IChemObject> T	CrystClustReader.read(T object)
<T extends IChemObject> T	SMILESReader.read(T object) Reads the content from a XYZ input.
<T extends IChemObject> T	MoSSOutputReader.read(T object) Read a IAtomContainerSet from the input source.
<T extends IChemObject> T	PDBReader.read(T oObj) Takes an object which subclasses IChemObject, e.g.

Methods in org.openscience.cdk.io with parameters of type IChemObject

Modifier and Type	Method and Description
boolean	Mol2Reader.accepts(IChemObject object)
boolean	MDLRXNV3000Reader.accepts(IChemObject object)
boolean	MDLRXNV2000Reader.accepts(IChemObject object)
boolean	MDLRXNReader.accepts(IChemObject object)
void	XYZWriter.write(IChemObject object)
void	SDFWriter.write(IChemObject object) Writes a IChemObject to the MDL SD file formated output.
void	RGroupQueryWriter.write(IChemObject object) The actual writing of the output.
void	Mol2Writer.write(IChemObject object)
void	MDLV3000Writer.write(IChemObject object) Writes a molecule to the V3000 format.
void	MDLV2000Writer.write(IChemObject object) Writes a IChemObject to the MDL molfile formated output.
void	MDLRXNWriter.write(IChemObject object) Writes a IChemObject to the MDL RXN file formated output.
void	IChemObjectWriter.write(IChemObject object) Writes the content of "object" to output.
void	HINWriter.write(IChemObject object)
void	CDKSourceCodeWriter.write(IChemObject object)
void	ShelXWriter.write(IChemObject object) Serializes the IChemObject to ShelX 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	RssWriter.write(IChemObject object) Writes a IChemObject to the MDL molfile formated output.
void	CMLWriter.write(IChemObject object) Serializes the IChemObject to CML and redirects it to the output Writer.
void	SMILESWriter.write(IChemObject object) Writes the content from object to output.
void	PDBWriter.write(IChemObject object)

Method parameters in org.openscience.cdk.io with type arguments of type IChemObject

Modifier and Type	Method and Description
boolean	XYZWriter.accepts(Class<? extends IChemObject> classObject)
boolean	XYZReader.accepts(Class<? extends IChemObject> classObject)
boolean	ShelXReader.accepts(Class<? extends IChemObject> classObject)
boolean	SDFWriter.accepts(Class<? extends IChemObject> classObject)
boolean	RGroupQueryWriter.accepts(Class<? extends IChemObject> classObject) Returns true for accepted input types.
boolean	RGroupQueryReader.accepts(Class<? extends IChemObject> classObject)
boolean	PMPReader.accepts(Class<? extends IChemObject> classObject)
boolean	PCSubstanceXMLReader.accepts(Class<? extends IChemObject> classObject)
boolean	PCCompoundXMLReader.accepts(Class<? extends IChemObject> classObject)
boolean	PCCompoundASNReader.accepts(Class<? extends IChemObject> classObject)
boolean	Mopac7Reader.accepts(Class<? extends IChemObject> classObject)
boolean	Mol2Writer.accepts(Class<? extends IChemObject> classObject)
boolean	Mol2Reader.accepts(Class<? extends IChemObject> classObject)
boolean	MDLV3000Writer.accepts(Class<? extends IChemObject> c) Returns whether the given IChemObject can be read or written.
boolean	MDLV3000Reader.accepts(Class<? extends IChemObject> classObject)
boolean	MDLV2000Writer.accepts(Class<? extends IChemObject> classObject)
boolean	MDLV2000Reader.accepts(Class<? extends IChemObject> classObject)
boolean	MDLReader.accepts(Class<? extends IChemObject> classObject) Deprecated.
boolean	MDLRXNWriter.accepts(Class<? extends IChemObject> classObject)
boolean	MDLRXNV3000Reader.accepts(Class<? extends IChemObject> classObject)
boolean	MDLRXNV2000Reader.accepts(Class<? extends IChemObject> classObject)
boolean	MDLRXNReader.accepts(Class<? extends IChemObject> classObject)
boolean	IChemObjectIO.accepts(Class<? extends IChemObject> classObject) Returns whether the given IChemObject can be read or written.
boolean	HINWriter.accepts(Class<? extends IChemObject> classObject)
boolean	HINReader.accepts(Class<? extends IChemObject> classObject)
boolean	GhemicalMMReader.accepts(Class<? extends IChemObject> classObject)
boolean	Gaussian98Reader.accepts(Class<? extends IChemObject> classObject)
boolean	Gaussian03Reader.accepts(Class<? extends IChemObject> classObject)
boolean	CTXReader.accepts(Class<? extends IChemObject> classObject)
boolean	CMLReader.accepts(Class<? extends IChemObject> classObject)
boolean	CIFReader.accepts(Class<? extends IChemObject> testClass)
boolean	CDKSourceCodeWriter.accepts(Class<? extends IChemObject> classObject)
boolean	ZMatrixReader.accepts(Class<? extends IChemObject> classObject)
boolean	ShelXWriter.accepts(Class<? extends IChemObject> classObject)
boolean	INChIReader.accepts(Class<? extends IChemObject> classObject)
boolean	INChIPlainTextReader.accepts(Class<? extends IChemObject> classObject)
boolean	GamessReader.accepts(Class<? extends IChemObject> classObject)
boolean	CrystClustWriter.accepts(Class<? extends IChemObject> classObject)
boolean	CrystClustReader.accepts(Class<? extends IChemObject> classObject)
boolean	RssWriter.accepts(Class<? extends IChemObject> classObject)
boolean	CMLWriter.accepts(Class<? extends IChemObject> classObject)
boolean	SMILESWriter.accepts(Class<? extends IChemObject> classObject)
boolean	SMILESReader.accepts(Class<? extends IChemObject> classObject)
boolean	MoSSOutputReader.accepts(Class<? extends IChemObject> testClass) Returns whether the given IChemObject can be read or written.
boolean	PDBWriter.accepts(Class<? extends IChemObject> classObject)
boolean	PDBReader.accepts(Class<? extends IChemObject> classObject)

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 and 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 and Description
boolean	DefaultIteratingChemObjectReader.accepts(Class<? extends IChemObject> objectClass)

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 and 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 and Description
boolean	DefaultEventChemObjectReader.accepts(Class<? extends IChemObject> objectClass)

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 and Description
void	Mopac7Writer.write(IChemObject arg0) Writes the content of "object" to output.
void	GaussianInputWriter.write(IChemObject object)

Method parameters in org.openscience.cdk.io.program with type arguments of type IChemObject

Modifier and Type	Method and Description
boolean	Mopac7Writer.accepts(Class<? extends IChemObject> classObject)
boolean	GaussianInputWriter.accepts(Class<? extends IChemObject> classObject)

Uses of IChemObject in org.openscience.cdk.io.random

Methods in org.openscience.cdk.io.random that return IChemObject

Modifier and Type	Method and Description
IChemObject	RandomAccessReader.first()
IChemObject	RandomAccessReader.last()
IChemObject	RandomAccessReader.next()
IChemObject	RandomAccessReader.previous()
protected IChemObject	RandomAccessSDFReader.processContent()
protected IChemObject	RandomAccessReader.processContent() The reader is already set to read the record buffer.
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 and 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 and Description
boolean	RandomAccessSDFReader.accepts(Class<? extends IChemObject> classObject)

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 and Description
<T extends IChemObject> T	CDKOWLReader.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 and 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 and Description
boolean	CDKOWLWriter.accepts(Class<? extends IChemObject> classObject) Returns whether the given IChemObject can be read or written.
boolean	CDKOWLReader.accepts(Class<? extends IChemObject> classObject) Returns whether the given IChemObject 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 and 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 and Description
interface	IQueryAtom Defines the ability to be matched against IAtom'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 and Description
class	CTFileQueryBond Captures query bond types defined in the CTFile.
class	InverseSymbolSetQueryAtom A QueryAtom that matches all symbols but those in this container.
class	OrderQueryBond
class	OrderQueryBondOrderOnly IQueryBond that matches IBond object only based on bond order, and disregarding any aromaticity flag.
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
class	SymbolChargeIDQueryAtom
class	SymbolQueryAtom
class	SymbolSetQueryAtom A QueryAtom that matches all symbols in this container.

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 and Description
class	AliphaticAtom This matcher any non-aromatic atom.
class	AliphaticSymbolAtom This smarts atom matches aliphatic atom with element symbol specified.
class	AnyAtom This matcher any Atom including explicit hydrogens.
class	AnyOrderQueryBond This matches a bond of any order.
class	AromaticAtom This matcher any aromatic atom.
class	AromaticOrSingleQueryBond This matches an aromatic or a single bond, used when no bond is specified between an atom.
class	AromaticQueryBond This matches an aromatic bond.
class	AromaticSymbolAtom This class matches aromatic atom with element symbol specified.
class	AtomicNumberAtom This matches an atom using the atomic number.
class	ChiralityAtom This matches an atom with chirality property.
class	ExplicitConnectionAtom Match an atom with the defined degree.
class	FormalChargeAtom This matcher checks the formal charge of the Atom.
class	HybridizationNumberAtom This matcher checks the hybridization state of an atom.
class	HydrogenAtom This matches Hydrogen atoms.
class	ImplicitHCountAtom This matcher checks the number of implicit hydrogens of the Atom.
class	LogicalOperatorAtom This class matches a logical operator that connects two query atoms.
class	LogicalOperatorBond This class matches a logical operator that connects two query bonds.
class	MassAtom This class matches an atom based on the atomic mass.
class	NonCHHeavyAtom This matcher any heavy atom that is not C or H.
class	PeriodicGroupNumberAtom This matcher checks the periodic group number of an atom.
class	ReactionRoleQueryAtom Matches atoms with a particular role in a reaction.
class	RecursiveSmartsAtom This matches recursive smarts atoms.
class	RingBond This smarts bond matches any bond that is in a ring.
class	RingIdentifierAtom This encapsulates an atom with a ring identifier, with an optional ring bond specified.
class	RingMembershipAtom This query is found in a specified number of ring.
class	SmallestRingAtom Match an atom in a specific size ring.
class	SMARTSAtom Abstract smarts atom.
class	SMARTSBond Abstract smarts bond.
class	StereoBond This query bond indicates a particular geometric stereo configuration.
class	TotalConnectionAtom This matches an atom using total number of connections - referred to in SMARTS as the connectivity.
class	TotalHCountAtom SMARTS query atom for matching the total hydrogen count.
class	TotalRingConnectionAtom This matcher checks the number of ring connections of the checked Atom with other Atom's.
class	TotalValencyAtom This matcher checks the valence of the Atom.

Uses of IChemObject in org.openscience.cdk.layout

Constructors in org.openscience.cdk.layout with parameters of type IChemObject

Constructor and Description
OverlapResolver.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 and 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 and 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 and 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 and 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 and 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 and 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 and Description
void	RendererModel.registerParameters(IGenerator<? extends IChemObject> generator) Registers rendering parameters from IGenerators 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 and Description
interface	IGenerator<T extends IChemObject> An IGenerator converts chemical entities into parts of the chemical drawing expressed as IRenderingElements.

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 and Description
<E extends IChemObject> Collection<E>	IChemObjectSelection.elements(Class<E> clazz) Returns a Collection of all selected IChemObjects of the given type.

Methods in org.openscience.cdk.renderer.selection with parameters of type IChemObject

Modifier and Type	Method and Description
protected void	AbstractSelection.addToAtomContainer(IAtomContainer ac, IChemObject item) Utility method to add an IChemObject to an IAtomContainer.
boolean	IChemObjectSelection.contains(IChemObject obj) Determines if the IChemObject is part of the current selection.

Uses of IChemObject in org.openscience.cdk.silent

Methods in org.openscience.cdk.silent that return IChemObject

Modifier and Type	Method and 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 and Description
Iterable<IChemObject>	Mapping.relatedChemObjects() Returns an Iterable to the two IChemObjects.

Constructors in org.openscience.cdk.silent with parameters of type IChemObject

Constructor and 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.tools

Methods in org.openscience.cdk.tools with parameters of type IChemObject

Modifier and Type	Method and 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 and Description
static String	SingleElectronDiff.diff(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as a String.
static String	LonePairDiff.diff(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as a String.
static String	IsotopeDiff.diff(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as a String.
static String	ElementDiff.diff(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as a String.
static String	ElectronContainerDiff.diff(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as a String.
static String	ChemObjectDiff.diff(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as a String.
static String	BondDiff.diff(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as a String.
static String	AtomTypeDiff.diff(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as a String.
static String	AtomDiff.diff(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as a String.
static String	AtomContainerDiff.diff(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as a String.
static IDifference	SingleElectronDiff.difference(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as an IDifference.
static IDifference	LonePairDiff.difference(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as an IDifference.
static IDifference	IsotopeDiff.difference(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as an IDifference.
static IDifference	ElementDiff.difference(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as an IDifference.
static IDifference	ElectronContainerDiff.difference(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as an IDifference.
static IDifference	ChemObjectDiff.difference(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as an IDifference.
static IDifference	BondDiff.difference(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as an IDifference.
static IDifference	AtomTypeDiff.difference(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as an IDifference.
static IDifference	AtomDiff.difference(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as an IDifference.
static IDifference	AtomContainerDiff.difference(IChemObject first, IChemObject second) Compare two IChemObject classes and return the difference as an IDifference.

Uses of IChemObject in org.openscience.cdk.tools.manipulator

Methods in org.openscience.cdk.tools.manipulator that return IChemObject

Modifier and Type	Method and Description
static IChemObject	ReactionManipulator.getMappedChemObject(IReaction reaction, IChemObject chemObject) get the IAtom which is mapped

Methods in org.openscience.cdk.tools.manipulator that return types with arguments of type IChemObject

Modifier and Type	Method and Description
static List<IChemObject>	MoleculeSetManipulator.getAllChemObjects(IAtomContainerSet set)
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>	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 and Description
static IChemObject	ReactionManipulator.getMappedChemObject(IReaction reaction, IChemObject chemObject) get the IAtom which is mapped

Uses of IChemObject in org.openscience.cdk.validate

Methods in org.openscience.cdk.validate that return IChemObject

Modifier and Type	Method and Description
IChemObject	ValidationTest.getChemObject()

Methods in org.openscience.cdk.validate with parameters of type IChemObject

Modifier and Type	Method and 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	ValidatorEngine.validateChemObject(IChemObject subject)
ValidationReport	IValidator.validateChemObject(IChemObject object)
ValidationReport	DictionaryValidator.validateChemObject(IChemObject subject)
ValidationReport	AbstractValidator.validateChemObject(IChemObject subject)

Constructors in org.openscience.cdk.validate with parameters of type IChemObject

Constructor and Description
ValidationTest(IChemObject object, String error)
ValidationTest(IChemObject object, String error, String details)