Uses of Interface
org.openscience.cdk.interfaces.IChemObjectBuilder
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Uses of IChemObjectBuilder in org.openscience.cdk
Classes in org.openscience.cdk that implement IChemObjectBuilder Modifier and Type Class Description class
DefaultChemObjectBuilder
A factory class to provide implementation independentICDKObject
s.Methods in org.openscience.cdk that return IChemObjectBuilder Modifier and Type Method 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 Description static CDKAtomTypeMatcher
CDKAtomTypeMatcher. getInstance(IChemObjectBuilder builder)
static CDKAtomTypeMatcher
CDKAtomTypeMatcher. getInstance(IChemObjectBuilder builder, int mode)
static SybylAtomTypeMatcher
SybylAtomTypeMatcher. getInstance(IChemObjectBuilder builder)
Returns an instance of this atom typer. -
Uses of IChemObjectBuilder in org.openscience.cdk.config
Methods in org.openscience.cdk.config with parameters of type IChemObjectBuilder Modifier and Type Method Description 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.static AtomTypeFactory
AtomTypeFactory. getInstance(IChemObjectBuilder builder)
Method to create a default AtomTypeFactory, using the structgen atom type list.static XMLIsotopeFactory
XMLIsotopeFactory. getInstance(IChemObjectBuilder builder)
Returns an IsotopeFactory instance.List<IAtomType>
CDKBasedAtomTypeConfigurator. readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the CDK based atom type list.List<IAtomType>
IAtomTypeConfigurator. readAtomTypes(IChemObjectBuilder builder)
Reads a set of configured AtomType's into a List.List<IAtomType>
OWLBasedAtomTypeConfigurator. readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the OWL based atom type list.List<IAtomType>
TXTBasedAtomTypeConfigurator. readAtomTypes(IChemObjectBuilder builder)
Reads a text based configuration file. -
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 Description List<IAtomType>
AtomTypeReader. readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the data file.List<IAtomType>
OWLAtomTypeReader. readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the data file.Constructors in org.openscience.cdk.config.atomtypes with parameters of type IChemObjectBuilder Constructor 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 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 giveninput
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Uses of IChemObjectBuilder in org.openscience.cdk.debug
Classes in org.openscience.cdk.debug that implement IChemObjectBuilder Modifier and Type Class Description class
DebugChemObjectBuilder
A helper class to instantiate aIChemObject
for the original CDK implementation.Methods in org.openscience.cdk.debug that return IChemObjectBuilder Modifier and Type Method Description IChemObjectBuilder
DebugAdductFormula. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugAminoAcid. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugAtom. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugAtomContainer. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugAtomContainerSet. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugAtomType. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugBioPolymer. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugBond. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugChemFile. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugChemModel. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugChemObject. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugChemSequence. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugCrystal. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugElectronContainer. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugElement. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugFragmentAtom. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugIsotope. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugLonePair. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugMapping. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugMolecularFormula. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugMolecularFormulaSet. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugMonomer. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugPolymer. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugPseudoAtom. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugReaction. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugReactionScheme. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugReactionSet. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugRing. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugSingleElectron. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugStrand. getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.IChemObjectBuilder
DebugSubstance. getBuilder()
Returns aIChemObjectBuilder
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 Description MACCSFingerprinter(IChemObjectBuilder builder)
PubchemFingerprinter(IChemObjectBuilder builder)
PubchemFingerprinter(IChemObjectBuilder builder, boolean esssr)
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Uses of IChemObjectBuilder in org.openscience.cdk.formula
Methods in org.openscience.cdk.formula that return IChemObjectBuilder Modifier and Type Method Description IChemObjectBuilder
AdductFormula. getBuilder()
IChemObjectBuilder
MolecularFormula. getBuilder()
IChemObjectBuilder
MolecularFormulaSet. getBuilder()
Methods in org.openscience.cdk.formula with parameters of type IChemObjectBuilder Modifier and Type Method 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 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 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, String options)
Gets structure generator for an InChI string.InChIToStructure
InChIGeneratorFactory. getInChIToStructure(String inchi, IChemObjectBuilder builder, List<String> options)
Gets structure generator for an InChI string.Constructors in org.openscience.cdk.inchi with parameters of type IChemObjectBuilder Constructor Description InChIToStructure(String inchi, IChemObjectBuilder builder)
Constructor.InChIToStructure(String inchi, IChemObjectBuilder builder, io.github.dan2097.jnainchi.InchiOptions options)
Constructor.InChIToStructure(String inchi, IChemObjectBuilder builder, String options)
Constructor.InChIToStructure(String inchi, IChemObjectBuilder builder, List<String> options)
Constructor. -
Uses of IChemObjectBuilder in org.openscience.cdk.interfaces
Methods in org.openscience.cdk.interfaces that return IChemObjectBuilder Modifier and Type Method Description IChemObjectBuilder
ICDKObject. getBuilder()
Returns aIChemObjectBuilder
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 Description IAtomContainer
MDLV3000Reader. readConnectionTable(IChemObjectBuilder builder)
IAtomContainer
MDLV3000Reader. readMolecule(IChemObjectBuilder builder)
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Uses of IChemObjectBuilder in org.openscience.cdk.io.iterator
Constructors in org.openscience.cdk.io.iterator with parameters of type IChemObjectBuilder Constructor 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 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 Description IAtomContainer
PubChemXMLHelper. parseMolecule(XMLStreamReader parser, IChemObjectBuilder builder)
Constructors in org.openscience.cdk.io.pubchemxml with parameters of type IChemObjectBuilder Constructor Description PubChemXMLHelper(IChemObjectBuilder builder)
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Uses of IChemObjectBuilder in org.openscience.cdk.io.random
Fields in org.openscience.cdk.io.random declared as IChemObjectBuilder Modifier and Type Field Description protected IChemObjectBuilder
RandomAccessReader. builder
Constructors in org.openscience.cdk.io.random with parameters of type IChemObjectBuilder Constructor 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)
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Uses of IChemObjectBuilder in org.openscience.cdk.isomorphism.matchers
Methods in org.openscience.cdk.isomorphism.matchers that return IChemObjectBuilder Modifier and Type Method Description IChemObjectBuilder
QueryChemObject. getBuilder()
Constructors in org.openscience.cdk.isomorphism.matchers with parameters of type IChemObjectBuilder Constructor Description CTFileQueryBond(IChemObjectBuilder builder)
Deprecated.InverseSymbolSetQueryAtom(IChemObjectBuilder builder)
Deprecated.Constructor for the InverseSymbolSetQueryAtom objectOrderQueryBond(IChemObjectBuilder builder)
Deprecated.OrderQueryBond(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order, IChemObjectBuilder builder)
Deprecated.OrderQueryBondOrderOnly(IChemObjectBuilder builder)
Deprecated.OrderQueryBondOrderOnly(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order, IChemObjectBuilder builder)
Deprecated.QueryAtom(String symbol, IChemObjectBuilder builder)
QueryAtom(IChemObjectBuilder builder)
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.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.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)
Deprecated.SymbolChargeIDQueryAtom(IChemObjectBuilder builder)
SymbolQueryAtom(IChemObjectBuilder builder)
Deprecated.SymbolSetQueryAtom(IChemObjectBuilder builder)
Deprecated.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 Description AliphaticAtom(IChemObjectBuilder builder)
Deprecated.Creates a new instanceAliphaticSymbolAtom(String symbol, IChemObjectBuilder builder)
Deprecated.Creates a new instance.AnyAtom(IChemObjectBuilder builder)
Deprecated.Creates a new instanceAnyOrderQueryBond(IChemObjectBuilder builder)
Deprecated.AnyOrderQueryBond(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order, IChemObjectBuilder builder)
Deprecated.Creates a new instance.AromaticAtom(IChemObjectBuilder builder)
Deprecated.Creates a new instanceAromaticOrSingleQueryBond(IChemObjectBuilder builder)
Deprecated.Creates a new instance.AromaticOrSingleQueryBond(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order, IChemObjectBuilder builder)
Deprecated.Creates a new instanceAromaticQueryBond(IChemObjectBuilder builder)
Deprecated.Creates a new instance.AromaticQueryBond(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order, IChemObjectBuilder builder)
Deprecated.Creates a new instanceAromaticSymbolAtom(String symbol, IChemObjectBuilder builder)
Deprecated.AtomicNumberAtom(int atomicNumber, IChemObjectBuilder builder)
Deprecated.Creates a new instance.ChiralityAtom(IChemObjectBuilder builder)
Deprecated.Creates a new instanceExplicitConnectionAtom(int degree, IChemObjectBuilder builder)
Deprecated.Create a query atom for matching the degree of an atom.FormalChargeAtom(int charge, IChemObjectBuilder builder)
Deprecated.Creates a new instanceHybridizationNumberAtom(int hybridizationNumber, IChemObjectBuilder builder)
Deprecated.Creates a new instanceHydrogenAtom(IChemObjectBuilder builder)
Deprecated.Creates a new instance.ImplicitHCountAtom(int hcount, IChemObjectBuilder builder)
Deprecated.Creates a new instanceLogicalOperatorAtom(IChemObjectBuilder builder)
Deprecated.LogicalOperatorBond(IChemObjectBuilder builder)
Deprecated.MassAtom(int mass, IChemObjectBuilder builder)
Deprecated.Creates a new instanceNonCHHeavyAtom(IChemObjectBuilder builder)
Deprecated.Creates a new instanceOrderQueryBond(IBond.Order order, IChemObjectBuilder builder)
Deprecated.Creates a new instancePeriodicGroupNumberAtom(int groupNumber, IChemObjectBuilder builder)
Deprecated.Creates a new instanceReactionRoleQueryAtom(IChemObjectBuilder builder, int role)
Deprecated.RingBond(IChemObjectBuilder builder)
Deprecated.Creates a new instanceRingIdentifierAtom(IChemObjectBuilder builder)
Deprecated.RingMembershipAtom(int num, IChemObjectBuilder builder)
Deprecated.Ring membership query atom.SmallestRingAtom(int ringSize, IChemObjectBuilder builder)
Deprecated.Creates a matcher for specified ring size.SMARTSAtom(IChemObjectBuilder builder)
Deprecated.SMARTSBond(IChemObjectBuilder builder)
Deprecated.SMARTSBond(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order, IChemObjectBuilder builder)
Deprecated.StereoBond(IChemObjectBuilder builder, StereoBond.Direction direction, boolean unspecified)
Deprecated.TotalConnectionAtom(int connectivity, IChemObjectBuilder builder)
Deprecated.Creates a new instance.TotalHCountAtom(int totalHCount, IChemObjectBuilder builder)
Deprecated.TotalRingConnectionAtom(int ringConnectivity, IChemObjectBuilder builder)
Deprecated.Create a matcher for the number of rings an atom belongs to.TotalValencyAtom(int valence, IChemObjectBuilder builder)
Deprecated.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 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 Description MoleculeBuilder(IChemObjectBuilder builder)
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Uses of IChemObjectBuilder in org.openscience.cdk.layout
Methods in org.openscience.cdk.layout with parameters of type IChemObjectBuilder Modifier and Type Method Description void
TemplateHandler. loadTemplates(IChemObjectBuilder builder)
Loads all existing templates into memory.Constructors in org.openscience.cdk.layout with parameters of type IChemObjectBuilder Constructor 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 Description static IAtomContainer
Convertor. model2Molecule(org.apache.jena.rdf.model.Model model, IChemObjectBuilder builder)
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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 Description static ModelBuilder3D
ModelBuilder3D. getInstance(IChemObjectBuilder builder)
static ModelBuilder3D
ModelBuilder3D. getInstance(TemplateHandler3D templateHandler, String ffname, IChemObjectBuilder chemObjectBuilder)
void
MM2BasedParameterSetReader. readParameterSets(IChemObjectBuilder builder)
The main method which parses through the force field configuration filevoid
MMFF94BasedParameterSetReader. readParameterSets(IChemObjectBuilder builder)
The main method which parses through the force field configuration filevoid
ForceFieldConfigurator. setForceFieldConfigurator(String ffname, IChemObjectBuilder builder)
Constructor for the ForceFieldConfigurator objectvoid
ForceFieldConfigurator. setMM2Parameters(IChemObjectBuilder builder)
Sets the parameters attribute of the ForceFieldConfigurator object, default is mm2 force fieldvoid
ForceFieldConfigurator. setMMFF94Parameters(IChemObjectBuilder builder)
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Uses of IChemObjectBuilder in org.openscience.cdk.qsar
Methods in org.openscience.cdk.qsar with parameters of type IChemObjectBuilder Modifier and Type Method 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 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 Description void
AcidicGroupCountDescriptor. initialise(IChemObjectBuilder builder)
void
BasicGroupCountDescriptor. initialise(IChemObjectBuilder builder)
void
FractionalPSADescriptor. initialise(IChemObjectBuilder builder)
void
SmallRingDescriptor. initialise(IChemObjectBuilder builder)
void
SpiroAtomCountDescriptor. initialise(IChemObjectBuilder builder)
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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 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 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 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 Description class
SilentChemObjectBuilder
A factory class to provide implementation independentICDKObject
s.Methods in org.openscience.cdk.silent that return IChemObjectBuilder Modifier and Type Method Description IChemObjectBuilder
AdductFormula. getBuilder()
IChemObjectBuilder
ChemObject. getBuilder()
IChemObjectBuilder
MolecularFormula. getBuilder()
IChemObjectBuilder
MolecularFormulaSet. getBuilder()
static IChemObjectBuilder
SilentChemObjectBuilder. getInstance()
Access the singleton instance of this SilentChemObjectBuilder. -
Uses of IChemObjectBuilder in org.openscience.cdk.smarts
Methods in org.openscience.cdk.smarts with parameters of type IChemObjectBuilder Modifier and Type Method Description static SmartsPattern
SmartsPattern. create(String smarts, IChemObjectBuilder builder)
Create aPattern
that will match the givensmarts
query. -
Uses of IChemObjectBuilder in org.openscience.cdk.smiles
Constructors in org.openscience.cdk.smiles with parameters of type IChemObjectBuilder Constructor Description SmilesParser(IChemObjectBuilder builder)
Create a new SMILES parser which will createIAtomContainer
s 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 Description static SmartsPattern
SmartsPattern. create(String smarts, IChemObjectBuilder builder)
Deprecated.Create aPattern
that will match the givensmarts
query.Constructors in org.openscience.cdk.smiles.smarts with parameters of type IChemObjectBuilder Constructor Description SMARTSQueryTool(String smarts, IChemObjectBuilder builder)
Deprecated.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 Description static QueryAtomContainer
SMARTSParser. parse(String smarts, IChemObjectBuilder builder)
This method parses a Smarts String and returns an instance ofQueryAtomContainer
Constructors in org.openscience.cdk.smiles.smarts.parser with parameters of type IChemObjectBuilder Constructor Description SmartsQueryVisitor(IChemObjectBuilder builder)
Deprecated. -
Uses of IChemObjectBuilder in org.openscience.cdk.stereo
Methods in org.openscience.cdk.stereo with parameters of type IChemObjectBuilder Modifier and Type Method Description void
DoubleBondStereochemistry. setBuilder(IChemObjectBuilder builder)
void
TetrahedralChirality. setBuilder(IChemObjectBuilder builder)
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Uses of IChemObjectBuilder in org.openscience.cdk.structgen.maygen
Methods in org.openscience.cdk.structgen.maygen that return IChemObjectBuilder Modifier and Type Method Description IChemObjectBuilder
Maygen. getBuilder()
Constructors in org.openscience.cdk.structgen.maygen with parameters of type IChemObjectBuilder Constructor Description Maygen(IChemObjectBuilder builder)
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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 Description static IAtomContainer
IsoAlkanes. getIsobutane(IChemObjectBuilder builder)
static IAtomContainer
IsoAlkanes. getIsohexane(IChemObjectBuilder builder)
static IAtomContainer
IsoAlkanes. getIsopentane(IChemObjectBuilder builder)
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Uses of IChemObjectBuilder in org.openscience.cdk.tools
Methods in org.openscience.cdk.tools with parameters of type IChemObjectBuilder Modifier and Type Method 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
SaturationChecker. getAtomTypeFactory(IChemObjectBuilder builder)
protected AtomTypeFactory
SmilesValencyChecker. getAtomTypeFactory(IChemObjectBuilder builder)
static CDKHydrogenAdder
CDKHydrogenAdder. getInstance(IChemObjectBuilder builder)
static CDKValencyChecker
CDKValencyChecker. getInstance(IChemObjectBuilder builder)
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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 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.
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