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

Packages that use IChemObjectBuilder

Package	Description
org.openscience.cdk
org.openscience.cdk.atomtype
org.openscience.cdk.config
org.openscience.cdk.config.atomtypes
org.openscience.cdk.config.isotopes
org.openscience.cdk.debug
org.openscience.cdk.fingerprint
org.openscience.cdk.formula
org.openscience.cdk.inchi
org.openscience.cdk.interfaces
org.openscience.cdk.io
org.openscience.cdk.io.iterator
org.openscience.cdk.io.iterator.event
org.openscience.cdk.io.pubchemxml
org.openscience.cdk.io.random
org.openscience.cdk.isomorphism.matchers
org.openscience.cdk.isomorphism.matchers.smarts
org.openscience.cdk.iupac.parser
org.openscience.cdk.layout
org.openscience.cdk.libio.jena
org.openscience.cdk.modeling.builder3d
org.openscience.cdk.qsar
org.openscience.cdk.qsar.descriptors.molecular
org.openscience.cdk.qsar.descriptors.substance
org.openscience.cdk.signature
org.openscience.cdk.silent
org.openscience.cdk.smiles
org.openscience.cdk.smiles.smarts
org.openscience.cdk.smiles.smarts.parser
org.openscience.cdk.stereo
org.openscience.cdk.templates.saturatedhydrocarbons
org.openscience.cdk.tools
org.openscience.cdk.tools.manipulator

Uses of IChemObjectBuilder in org.openscience.cdk

Classes in org.openscience.cdk that implement IChemObjectBuilder

Modifier and Type	Class and Description
class	DefaultChemObjectBuilder A factory class to provide implementation independent ICDKObjects.

Methods in org.openscience.cdk that return IChemObjectBuilder

Modifier and Type	Method and Description
IChemObjectBuilder	ChemObject.getBuilder()
static IChemObjectBuilder	DefaultChemObjectBuilder.getInstance() Access the singleton instance of this DefaultChemObjectBuilder.

Uses of IChemObjectBuilder in org.openscience.cdk.atomtype

Methods in org.openscience.cdk.atomtype with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
static SybylAtomTypeMatcher	SybylAtomTypeMatcher.getInstance(IChemObjectBuilder builder) Returns an instance of this atom typer.
static CDKAtomTypeMatcher	CDKAtomTypeMatcher.getInstance(IChemObjectBuilder builder)
static CDKAtomTypeMatcher	CDKAtomTypeMatcher.getInstance(IChemObjectBuilder builder, int mode)

Uses of IChemObjectBuilder in org.openscience.cdk.config

Methods in org.openscience.cdk.config with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
static XMLIsotopeFactory	XMLIsotopeFactory.getInstance(IChemObjectBuilder builder) Returns an IsotopeFactory instance.
static AtomTypeFactory	AtomTypeFactory.getInstance(IChemObjectBuilder builder) Method to create a default AtomTypeFactory, using the structgen atom type list.
static AtomTypeFactory	AtomTypeFactory.getInstance(InputStream ins, String format, IChemObjectBuilder builder) Method to create a default AtomTypeFactory, using the given InputStream.
static AtomTypeFactory	AtomTypeFactory.getInstance(String configFile, IChemObjectBuilder builder) Method to create a specialized AtomTypeFactory.
List<IAtomType>	TXTBasedAtomTypeConfigurator.readAtomTypes(IChemObjectBuilder builder) Reads a text based configuration file.
List<IAtomType>	OWLBasedAtomTypeConfigurator.readAtomTypes(IChemObjectBuilder builder) Reads the atom types from the OWL based atom type list.
List<IAtomType>	IAtomTypeConfigurator.readAtomTypes(IChemObjectBuilder builder) Reads a set of configured AtomType's into a List.
List<IAtomType>	CDKBasedAtomTypeConfigurator.readAtomTypes(IChemObjectBuilder builder) Reads the atom types from the CDK based atom type list.

Uses of IChemObjectBuilder in org.openscience.cdk.config.atomtypes

Methods in org.openscience.cdk.config.atomtypes with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
List<IAtomType>	OWLAtomTypeReader.readAtomTypes(IChemObjectBuilder builder) Reads the atom types from the data file.
List<IAtomType>	AtomTypeReader.readAtomTypes(IChemObjectBuilder builder) Reads the atom types from the data file.

Constructors in org.openscience.cdk.config.atomtypes with parameters of type IChemObjectBuilder

Constructor and Description
AtomTypeHandler(IChemObjectBuilder build) Constructs a new AtomTypeHandler and will create IAtomType implementations using the given IChemObjectBuilder.
OWLAtomTypeHandler(IChemObjectBuilder build) Constructs a new AtomTypeHandler and will create IAtomType implementations using the given IChemObjectBuilder.

Uses of IChemObjectBuilder in org.openscience.cdk.config.isotopes

Constructors in org.openscience.cdk.config.isotopes with parameters of type IChemObjectBuilder

Constructor and Description
IsotopeHandler(IChemObjectBuilder builder) Constructs an IsotopeHandler used by the IsotopeReader.
IsotopeReader(InputStream input, IChemObjectBuilder builder) Instantiates a new reader that parses the XML from the given input.

Uses of IChemObjectBuilder in org.openscience.cdk.debug

Classes in org.openscience.cdk.debug that implement IChemObjectBuilder

Modifier and Type	Class and Description
class	DebugChemObjectBuilder A helper class to instantiate a IChemObject for the original CDK implementation.

Methods in org.openscience.cdk.debug that return IChemObjectBuilder

Modifier and Type	Method and Description
IChemObjectBuilder	DebugSubstance.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugStrand.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugSingleElectron.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugRing.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugReactionSet.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugReactionScheme.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugReaction.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugPseudoAtom.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugPolymer.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugMonomer.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugMolecularFormulaSet.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugMolecularFormula.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugMapping.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugLonePair.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugIsotope.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugFragmentAtom.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugElement.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugElectronContainer.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugCrystal.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugChemSequence.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugChemObject.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugChemModel.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugChemFile.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugBond.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugBioPolymer.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugAtomType.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugAtomContainerSet.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugAtomContainer.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugAtom.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugAminoAcid.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DebugAdductFormula.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
static IChemObjectBuilder	DebugChemObjectBuilder.getInstance() Access the singleton instance of this DebugChemObjectBuilder.

Uses of IChemObjectBuilder in org.openscience.cdk.fingerprint

Constructors in org.openscience.cdk.fingerprint with parameters of type IChemObjectBuilder

Constructor and Description
MACCSFingerprinter(IChemObjectBuilder builder)
PubchemFingerprinter(IChemObjectBuilder builder)

Uses of IChemObjectBuilder in org.openscience.cdk.formula

Methods in org.openscience.cdk.formula that return IChemObjectBuilder

Modifier and Type	Method and Description
IChemObjectBuilder	MolecularFormulaSet.getBuilder()
IChemObjectBuilder	MolecularFormula.getBuilder()
IChemObjectBuilder	AdductFormula.getBuilder()

Methods in org.openscience.cdk.formula with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
protected void	MolecularFormulaGenerator.checkInputParameters(IChemObjectBuilder builder, double minMass, double maxMass, MolecularFormulaRange mfRange) Checks if input parameters are valid and throws an IllegalArgumentException otherwise.

Constructors in org.openscience.cdk.formula with parameters of type IChemObjectBuilder

Constructor and Description
MassToFormulaTool(IChemObjectBuilder builder) Deprecated. Construct an instance of MassToFormulaTool.
MolecularFormulaGenerator(IChemObjectBuilder builder, double minMass, double maxMass, MolecularFormulaRange mfRange) Initiate the MolecularFormulaGenerator.

Uses of IChemObjectBuilder in org.openscience.cdk.inchi

Methods in org.openscience.cdk.inchi with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
protected void	InChIToStructure.generateAtomContainerFromInchi(IChemObjectBuilder builder) Gets structure from InChI, and converts InChI library data structure into an IAtomContainer.
InChIToStructure	InChIGeneratorFactory.getInChIToStructure(String inchi, IChemObjectBuilder builder) Gets structure generator for an InChI string.
InChIToStructure	InChIGeneratorFactory.getInChIToStructure(String inchi, IChemObjectBuilder builder, List<String> options) Gets structure generator for an InChI string.
InChIToStructure	InChIGeneratorFactory.getInChIToStructure(String inchi, IChemObjectBuilder builder, String options) Gets structure generator for an InChI string.

Constructors in org.openscience.cdk.inchi with parameters of type IChemObjectBuilder

Constructor and Description
InChIToStructure(String inchi, IChemObjectBuilder builder) Constructor.
InChIToStructure(String inchi, IChemObjectBuilder builder, List<String> options) Constructor.
InChIToStructure(String inchi, IChemObjectBuilder builder, String options) Constructor.

Uses of IChemObjectBuilder in org.openscience.cdk.interfaces

Methods in org.openscience.cdk.interfaces that return IChemObjectBuilder

Modifier and Type	Method and Description
IChemObjectBuilder	ICDKObject.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.

Uses of IChemObjectBuilder in org.openscience.cdk.io

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

Modifier and Type	Method and Description
IAtomContainer	MDLV3000Reader.readConnectionTable(IChemObjectBuilder builder)
IAtomContainer	MDLV3000Reader.readMolecule(IChemObjectBuilder builder)

Uses of IChemObjectBuilder in org.openscience.cdk.io.iterator

Constructors in org.openscience.cdk.io.iterator with parameters of type IChemObjectBuilder

Constructor and Description
IteratingMDLConformerReader(InputStream in, IChemObjectBuilder builder)
IteratingMDLConformerReader(Reader in, IChemObjectBuilder builder)
IteratingPCCompoundASNReader(InputStream in, IChemObjectBuilder builder) Constructs a new IteratingPCCompoundASNReader that can read Molecule from a given InputStream and IChemObjectBuilder.
IteratingPCCompoundASNReader(Reader in, IChemObjectBuilder builder) Constructs a new IteratingPCCompoundASNReader that can read Molecule from a given Reader.
IteratingPCCompoundXMLReader(InputStream in, IChemObjectBuilder builder) Constructs a new IteratingPCCompoundXLReader that can read Molecule from a given InputStream and IChemObjectBuilder.
IteratingPCCompoundXMLReader(Reader in, IChemObjectBuilder builder) Constructs a new IteratingPCCompoundXMLReader that can read Molecule from a given Reader and IChemObjectBuilder.
IteratingPCSubstancesXMLReader(InputStream in, IChemObjectBuilder builder) Constructs a new IteratingPCSubstancesXMLReader that can read Molecule from a given InputStream and IChemObjectBuilder.
IteratingPCSubstancesXMLReader(Reader in, IChemObjectBuilder builder) Constructs a new IteratingPCSubstancesXMLReader that can read Molecule from a given Reader and IChemObjectBuilder.
IteratingSDFReader(InputStream in, IChemObjectBuilder builder) Constructs a new IteratingMDLReader that can read Molecule from a given InputStream.
IteratingSDFReader(InputStream in, IChemObjectBuilder builder, boolean skip) Constructs a new IteratingMDLReader that can read Molecule from a given a InputStream.
IteratingSDFReader(Reader in, IChemObjectBuilder builder) Constructs a new IteratingMDLReader that can read Molecule from a given Reader.
IteratingSDFReader(Reader in, IChemObjectBuilder builder, boolean skip) Constructs a new IteratingMDLReader that can read Molecule from a given a Reader.
IteratingSMILESReader(InputStream in, IChemObjectBuilder builder) Constructs a new IteratingSMILESReader that can read Molecule from a given InputStream and IChemObjectBuilder.
IteratingSMILESReader(Reader in, IChemObjectBuilder builder) Constructs a new IteratingSMILESReader that can read Molecule from a given Reader.

Uses of IChemObjectBuilder in org.openscience.cdk.io.iterator.event

Constructors in org.openscience.cdk.io.iterator.event with parameters of type IChemObjectBuilder

Constructor and Description
EventCMLHandler(DefaultEventChemObjectReader eventReader, IChemObjectBuilder builder) Constructs an iterating-abled CDO.
EventCMLReader(Reader input, IReaderListener listener, IChemObjectBuilder builder) Define this CMLReader to take the input from a java.io.Reader class.

Uses of IChemObjectBuilder in org.openscience.cdk.io.pubchemxml

Methods in org.openscience.cdk.io.pubchemxml with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
IAtomContainer	PubChemXMLHelper.parseMolecule(XMLStreamReader parser, IChemObjectBuilder builder)

Constructors in org.openscience.cdk.io.pubchemxml with parameters of type IChemObjectBuilder

Constructor and Description
PubChemXMLHelper(IChemObjectBuilder builder)

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

Fields in org.openscience.cdk.io.random declared as IChemObjectBuilder

Modifier and Type	Field and Description
protected IChemObjectBuilder	RandomAccessReader.builder

Constructors in org.openscience.cdk.io.random with parameters of type IChemObjectBuilder

Constructor and Description
RandomAccessReader(File file, IChemObjectBuilder builder) Reads the file and builds an index file, if the index file doesn't already exist.
RandomAccessReader(File file, IChemObjectBuilder builder, IReaderListener listener) Reads the file and builds an index file, if the index file doesn't already exist.
RandomAccessSDFReader(File file, IChemObjectBuilder builder)
RandomAccessSDFReader(File file, IChemObjectBuilder builder, IReaderListener listener)

Uses of IChemObjectBuilder in org.openscience.cdk.isomorphism.matchers

Methods in org.openscience.cdk.isomorphism.matchers that return IChemObjectBuilder

Modifier and Type	Method and Description
IChemObjectBuilder	QueryChemObject.getBuilder()

Constructors in org.openscience.cdk.isomorphism.matchers with parameters of type IChemObjectBuilder

Constructor and Description
CTFileQueryBond(IChemObjectBuilder builder)
InverseSymbolSetQueryAtom(IChemObjectBuilder builder) Constructor for the InverseSymbolSetQueryAtom object
OrderQueryBond(IChemObjectBuilder builder)
OrderQueryBond(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order, IChemObjectBuilder builder)
OrderQueryBondOrderOnly(IChemObjectBuilder builder)
OrderQueryBondOrderOnly(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order, IChemObjectBuilder builder)
QueryAtom(IChemObjectBuilder builder)
QueryAtom(String symbol, IChemObjectBuilder builder)
QueryAtomContainer(IAtomContainer container, IChemObjectBuilder builder) Constructs an AtomContainer with a copy of the atoms and electronContainers of another AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).
QueryAtomContainer(IChemObjectBuilder builder) Constructs an empty AtomContainer.
QueryAtomContainer(int atomCount, int bondCount, int lpCount, int seCount, IChemObjectBuilder builder) Constructs an empty AtomContainer that will contain a certain number of atoms and electronContainers.
QueryBond(IAtom[] atoms, IBond.Order order, IChemObjectBuilder builder) Constructs a multi-center query bond, with a specified order and no stereo information.
QueryBond(IAtom[] atoms, IChemObjectBuilder builder) Constructs a multi-center query bond, with undefined order and no stereo information.
QueryBond(IAtom atom1, IAtom atom2, IBond.Order order, IBond.Stereo stereo, IChemObjectBuilder builder) Constructs a query bond with a given order and stereo orientation from an array of atoms.
QueryBond(IAtom atom1, IAtom atom2, IBond.Order order, IChemObjectBuilder builder) Constructs a query bond with a given order.
QueryBond(IAtom atom1, IAtom atom2, IChemObjectBuilder builder) Constructs a query bond with a single query bond order..
QueryBond(IChemObjectBuilder builder) Constructs an empty query bond.
QueryChemObject(IChemObjectBuilder builder)
RGroupQuery(IChemObjectBuilder builder)
SymbolAndChargeQueryAtom(IChemObjectBuilder builder)
SymbolChargeIDQueryAtom(IChemObjectBuilder builder)
SymbolQueryAtom(IChemObjectBuilder builder)
SymbolSetQueryAtom(IChemObjectBuilder builder) Constructor for the SymbolSetQueryAtom object

Uses of IChemObjectBuilder in org.openscience.cdk.isomorphism.matchers.smarts

Constructors in org.openscience.cdk.isomorphism.matchers.smarts with parameters of type IChemObjectBuilder

Constructor and Description
AliphaticAtom(IChemObjectBuilder builder) Creates a new instance
AliphaticSymbolAtom(String symbol, IChemObjectBuilder builder) Creates a new instance.
AnyAtom(IChemObjectBuilder builder) Creates a new instance
AnyOrderQueryBond(IChemObjectBuilder builder)
AnyOrderQueryBond(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order, IChemObjectBuilder builder) Creates a new instance.
AromaticAtom(IChemObjectBuilder builder) Creates a new instance
AromaticOrSingleQueryBond(IChemObjectBuilder builder) Creates a new instance.
AromaticOrSingleQueryBond(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order, IChemObjectBuilder builder) Creates a new instance
AromaticQueryBond(IChemObjectBuilder builder) Creates a new instance.
AromaticQueryBond(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order, IChemObjectBuilder builder) Creates a new instance
AromaticSymbolAtom(String symbol, IChemObjectBuilder builder)
AtomicNumberAtom(int atomicNumber, IChemObjectBuilder builder) Creates a new instance.
ChiralityAtom(IChemObjectBuilder builder) Creates a new instance
ExplicitConnectionAtom(int degree, IChemObjectBuilder builder) Create a query atom for matching the degree of an atom.
FormalChargeAtom(int charge, IChemObjectBuilder builder) Creates a new instance
HybridizationNumberAtom(int hybridizationNumber, IChemObjectBuilder builder) Creates a new instance
HydrogenAtom(IChemObjectBuilder builder) Creates a new instance.
ImplicitHCountAtom(int hcount, IChemObjectBuilder builder) Creates a new instance
LogicalOperatorAtom(IChemObjectBuilder builder)
LogicalOperatorBond(IChemObjectBuilder builder)
MassAtom(int mass, IChemObjectBuilder builder) Creates a new instance
NonCHHeavyAtom(IChemObjectBuilder builder) Creates a new instance
OrderQueryBond(IBond.Order order, IChemObjectBuilder builder) Creates a new instance
PeriodicGroupNumberAtom(int groupNumber, IChemObjectBuilder builder) Creates a new instance
ReactionRoleQueryAtom(IChemObjectBuilder builder, int role)
RingBond(IChemObjectBuilder builder) Creates a new instance
RingIdentifierAtom(IChemObjectBuilder builder)
RingMembershipAtom(int num, IChemObjectBuilder builder) Ring membership query atom.
SmallestRingAtom(int ringSize, IChemObjectBuilder builder) Creates a matcher for specified ring size.
SMARTSAtom(IChemObjectBuilder builder)
SMARTSBond(IChemObjectBuilder builder)
SMARTSBond(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order, IChemObjectBuilder builder)
StereoBond(IChemObjectBuilder builder, StereoBond.Direction direction, boolean unspecified)
TotalConnectionAtom(int connectivity, IChemObjectBuilder builder) Creates a new instance.
TotalHCountAtom(int totalHCount, IChemObjectBuilder builder)
TotalRingConnectionAtom(int ringConnectivity, IChemObjectBuilder builder) Create a matcher for the number of rings an atom belongs to.
TotalValencyAtom(int valence, IChemObjectBuilder builder) Match the valence of atom.

Uses of IChemObjectBuilder in org.openscience.cdk.iupac.parser

Methods in org.openscience.cdk.iupac.parser with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
static IAtomContainer	NomParser.generate(String stringToParse, IChemObjectBuilder builder) Deprecated. Parses the chemical name and returns the built molecule.

Constructors in org.openscience.cdk.iupac.parser with parameters of type IChemObjectBuilder

Constructor and Description
MoleculeBuilder(IChemObjectBuilder builder)

Uses of IChemObjectBuilder in org.openscience.cdk.layout

Methods in org.openscience.cdk.layout with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
void	TemplateHandler.loadTemplates(IChemObjectBuilder builder) Loads all existing templates into memory.

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

Constructor and Description
TemplateHandler(IChemObjectBuilder builder) Creates a new TemplateHandler with default templates loaded.

Uses of IChemObjectBuilder in org.openscience.cdk.libio.jena

Methods in org.openscience.cdk.libio.jena with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
static IAtomContainer	Convertor.model2Molecule(com.hp.hpl.jena.rdf.model.Model model, IChemObjectBuilder builder) Converts a Model into an IAtomContainer using the given IChemObjectBuilder.

Uses of IChemObjectBuilder in org.openscience.cdk.modeling.builder3d

Methods in org.openscience.cdk.modeling.builder3d with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
static ModelBuilder3D	ModelBuilder3D.getInstance(IChemObjectBuilder builder)
static ModelBuilder3D	ModelBuilder3D.getInstance(TemplateHandler3D templateHandler, String ffname, IChemObjectBuilder chemObjectBuilder)
void	MMFF94BasedParameterSetReader.readParameterSets(IChemObjectBuilder builder) The main method which parses through the force field configuration file
void	MM2BasedParameterSetReader.readParameterSets(IChemObjectBuilder builder) The main method which parses through the force field configuration file
void	ForceFieldConfigurator.setForceFieldConfigurator(String ffname, IChemObjectBuilder builder) Constructor for the ForceFieldConfigurator object
void	ForceFieldConfigurator.setMM2Parameters(IChemObjectBuilder builder) Sets the parameters attribute of the ForceFieldConfigurator object, default is mm2 force field
void	ForceFieldConfigurator.setMMFF94Parameters(IChemObjectBuilder builder)

Uses of IChemObjectBuilder in org.openscience.cdk.qsar

Methods in org.openscience.cdk.qsar with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
void	IDescriptor.initialise(IChemObjectBuilder builder) Initialise the descriptor with the specified chem object builder.

Constructors in org.openscience.cdk.qsar with parameters of type IChemObjectBuilder

Constructor and Description
DescriptorEngine(Class<? extends IDescriptor> c, IChemObjectBuilder builder) Create a descriptor engine for all descriptor types.
DescriptorEngine(List<String> classNames, IChemObjectBuilder builder) Instantiates the DescriptorEngine.

Uses of IChemObjectBuilder in org.openscience.cdk.qsar.descriptors.molecular

Methods in org.openscience.cdk.qsar.descriptors.molecular with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
void	SmallRingDescriptor.initialise(IChemObjectBuilder builder)
void	FractionalPSADescriptor.initialise(IChemObjectBuilder builder)
void	BasicGroupCountDescriptor.initialise(IChemObjectBuilder builder)
void	AcidicGroupCountDescriptor.initialise(IChemObjectBuilder builder)

Uses of IChemObjectBuilder in org.openscience.cdk.qsar.descriptors.substance

Methods in org.openscience.cdk.qsar.descriptors.substance with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
void	OxygenAtomCountDescriptor.initialise(IChemObjectBuilder builder) Initialise the descriptor with the specified chem object builder.

Uses of IChemObjectBuilder in org.openscience.cdk.signature

Methods in org.openscience.cdk.signature with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
static IAtomContainer	MoleculeSignature.fromSignatureString(String signatureString, IChemObjectBuilder coBuilder) Builder for molecules (rather, for atom containers) from signature strings.

Constructors in org.openscience.cdk.signature with parameters of type IChemObjectBuilder

Constructor and Description
MoleculeFromSignatureBuilder(IChemObjectBuilder builder) Uses the chem object builder for making molecules.

Uses of IChemObjectBuilder in org.openscience.cdk.silent

Classes in org.openscience.cdk.silent that implement IChemObjectBuilder

Modifier and Type	Class and Description
class	SilentChemObjectBuilder A factory class to provide implementation independent ICDKObjects.

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

Modifier and Type	Method and Description
IChemObjectBuilder	MolecularFormulaSet.getBuilder()
IChemObjectBuilder	MolecularFormula.getBuilder()
IChemObjectBuilder	ChemObject.getBuilder()
IChemObjectBuilder	AdductFormula.getBuilder()
static IChemObjectBuilder	SilentChemObjectBuilder.getInstance() Access the singleton instance of this SilentChemObjectBuilder.

Uses of IChemObjectBuilder in org.openscience.cdk.smiles

Constructors in org.openscience.cdk.smiles with parameters of type IChemObjectBuilder

Constructor and Description
SmilesParser(IChemObjectBuilder builder) Create a new SMILES parser which will create IAtomContainers with the specified builder.

Uses of IChemObjectBuilder in org.openscience.cdk.smiles.smarts

Methods in org.openscience.cdk.smiles.smarts with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
static SmartsPattern	SmartsPattern.create(String smarts, IChemObjectBuilder builder) Create a Pattern that will match the given smarts query.

Constructors in org.openscience.cdk.smiles.smarts with parameters of type IChemObjectBuilder

Constructor and Description
SMARTSQueryTool(String smarts, IChemObjectBuilder builder) Create a new SMARTS query tool for the specified SMARTS string.

Uses of IChemObjectBuilder in org.openscience.cdk.smiles.smarts.parser

Methods in org.openscience.cdk.smiles.smarts.parser with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
static QueryAtomContainer	SMARTSParser.parse(String smarts, IChemObjectBuilder builder) This method parses a Smarts String and returns an instance of QueryAtomContainer

Constructors in org.openscience.cdk.smiles.smarts.parser with parameters of type IChemObjectBuilder

Constructor and Description
SmartsQueryVisitor(IChemObjectBuilder builder)

Uses of IChemObjectBuilder in org.openscience.cdk.stereo

Methods in org.openscience.cdk.stereo that return IChemObjectBuilder

Modifier and Type	Method and Description
IChemObjectBuilder	TetrahedralChirality.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	ExtendedTetrahedral.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
IChemObjectBuilder	DoubleBondStereochemistry.getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.

Methods in org.openscience.cdk.stereo with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
void	TetrahedralChirality.setBuilder(IChemObjectBuilder builder) Sets a new IChemObjectBuilder.
void	DoubleBondStereochemistry.setBuilder(IChemObjectBuilder builder) Sets a new IChemObjectBuilder.

Uses of IChemObjectBuilder in org.openscience.cdk.templates.saturatedhydrocarbons

Methods in org.openscience.cdk.templates.saturatedhydrocarbons with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
static IAtomContainer	IsoAlkanes.getIsobutane(IChemObjectBuilder builder)
static IAtomContainer	IsoAlkanes.getIsohexane(IChemObjectBuilder builder)
static IAtomContainer	IsoAlkanes.getIsopentane(IChemObjectBuilder builder)

Uses of IChemObjectBuilder in org.openscience.cdk.tools

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

Modifier and Type	Method and Description
static IBioPolymer	ProteinBuilderTool.createProtein(String sequence, IChemObjectBuilder builder) Creates a BioPolymer from a sequence of amino acid as identified by a the sequence of their one letter codes.
protected AtomTypeFactory	SmilesValencyChecker.getAtomTypeFactory(IChemObjectBuilder builder)
protected AtomTypeFactory	SaturationChecker.getAtomTypeFactory(IChemObjectBuilder builder)
static CDKValencyChecker	CDKValencyChecker.getInstance(IChemObjectBuilder builder)
static CDKHydrogenAdder	CDKHydrogenAdder.getInstance(IChemObjectBuilder builder)

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

Methods in org.openscience.cdk.tools.manipulator with parameters of type IChemObjectBuilder

Modifier and Type	Method and Description
static IAtomContainer	MolecularFormulaManipulator.getAtomContainer(String formulaString, IChemObjectBuilder builder) Converts a formula string (like "C2H4") into an atom container with atoms but no bonds.
static IMolecularFormula	MolecularFormulaManipulator.getMajorIsotopeMolecularFormula(String stringMF, IChemObjectBuilder builder) Construct an instance of IMolecularFormula, initialized with a molecular formula string.
static IMolecularFormula	MolecularFormulaRangeManipulator.getMaximalFormula(MolecularFormulaRange mfRange, IChemObjectBuilder builder) Returns the maximal occurrence of the IIsotope into IMolecularFormula from this MolelecularFormulaRange.
static IMolecularFormula	MolecularFormulaRangeManipulator.getMinimalFormula(MolecularFormulaRange mfRange, IChemObjectBuilder builder) Returns the minimal occurrence of the IIsotope into IMolecularFormula from this MolelecularFormulaRange.
static IMolecularFormula	MolecularFormulaManipulator.getMolecularFormula(String stringMF, IChemObjectBuilder builder) Construct an instance of IMolecularFormula, initialized with a molecular formula string.