Modifier and Type | Class and Description |
---|---|
class |
DefaultChemObjectBuilder
A factory class to provide implementation independent
ICDKObject s. |
Modifier and Type | Method and Description |
---|---|
IChemObjectBuilder |
ChemObject.getBuilder() |
static IChemObjectBuilder |
DefaultChemObjectBuilder.getInstance()
Access the singleton instance of this DefaultChemObjectBuilder.
|
Modifier and Type | Method and Description |
---|---|
static CDKAtomTypeMatcher |
CDKAtomTypeMatcher.getInstance(IChemObjectBuilder builder) |
static SybylAtomTypeMatcher |
SybylAtomTypeMatcher.getInstance(IChemObjectBuilder builder)
Returns an instance of this atom typer.
|
static CDKAtomTypeMatcher |
CDKAtomTypeMatcher.getInstance(IChemObjectBuilder builder,
int mode) |
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> |
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> |
CDKBasedAtomTypeConfigurator.readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the CDK based atom type list.
|
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.
|
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.
|
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 . |
Modifier and Type | Class and Description |
---|---|
class |
DebugChemObjectBuilder
A helper class to instantiate a
IChemObject for the original CDK
implementation. |
Modifier and Type | Method and Description |
---|---|
IChemObjectBuilder |
DebugAtom.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 |
DebugRing.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 |
DebugChemObject.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 |
DebugPseudoAtom.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 |
DebugAtomContainerSet.getBuilder()
Returns a
IChemObjectBuilder for the data classes that extend
this class. |
IChemObjectBuilder |
DebugSubstance.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 |
DebugLonePair.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 |
DebugFragmentAtom.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 |
DebugReaction.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 |
DebugMonomer.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 |
DebugMolecularFormulaSet.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 |
DebugMapping.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 |
DebugIsotope.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 |
DebugAdductFormula.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 |
DebugAtomContainer.getBuilder()
Returns a
IChemObjectBuilder for the data classes that extend
this class. |
static IChemObjectBuilder |
DebugChemObjectBuilder.getInstance()
Access the singleton instance of this DebugChemObjectBuilder.
|
Constructor and Description |
---|
MACCSFingerprinter(IChemObjectBuilder builder) |
PubchemFingerprinter(IChemObjectBuilder builder) |
Modifier and Type | Method and Description |
---|---|
IChemObjectBuilder |
MolecularFormulaSet.getBuilder() |
IChemObjectBuilder |
MolecularFormula.getBuilder() |
IChemObjectBuilder |
AdductFormula.getBuilder() |
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.
|
Constructor and Description |
---|
MassToFormulaTool(IChemObjectBuilder builder)
Deprecated.
Construct an instance of MassToFormulaTool.
|
MolecularFormulaGenerator(IChemObjectBuilder builder,
double minMass,
double maxMass,
MolecularFormulaRange mfRange)
Initiate the MolecularFormulaGenerator.
|
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.
|
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.
|
Modifier and Type | Method and Description |
---|---|
IChemObjectBuilder |
ICDKObject.getBuilder()
Returns a
IChemObjectBuilder for the data classes that extend
this class. |
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
MDLV3000Reader.readConnectionTable(IChemObjectBuilder builder) |
IAtomContainer |
MDLV3000Reader.readMolecule(IChemObjectBuilder builder) |
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.
|
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.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
PubChemXMLHelper.parseMolecule(XMLStreamReader parser,
IChemObjectBuilder builder) |
Constructor and Description |
---|
PubChemXMLHelper(IChemObjectBuilder builder) |
Modifier and Type | Field and Description |
---|---|
protected IChemObjectBuilder |
RandomAccessReader.builder |
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) |
Modifier and Type | Method and Description |
---|---|
IChemObjectBuilder |
QueryChemObject.getBuilder() |
Constructor and Description |
---|
CTFileQueryBond(IChemObjectBuilder builder)
Deprecated.
|
InverseSymbolSetQueryAtom(IChemObjectBuilder builder)
Deprecated.
Constructor for the InverseSymbolSetQueryAtom object
|
OrderQueryBond(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(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)
Deprecated.
|
SymbolChargeIDQueryAtom(IChemObjectBuilder builder) |
SymbolQueryAtom(IChemObjectBuilder builder)
Deprecated.
|
SymbolSetQueryAtom(IChemObjectBuilder builder)
Deprecated.
Constructor for the SymbolSetQueryAtom object
|
Constructor and Description |
---|
AliphaticAtom(IChemObjectBuilder builder)
Deprecated.
Creates a new instance
|
AliphaticSymbolAtom(String symbol,
IChemObjectBuilder builder)
Deprecated.
Creates a new instance.
|
AnyAtom(IChemObjectBuilder builder)
Deprecated.
Creates a new instance
|
AnyOrderQueryBond(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 instance
|
AromaticOrSingleQueryBond(IChemObjectBuilder builder)
Deprecated.
Creates a new instance.
|
AromaticOrSingleQueryBond(IQueryAtom atom1,
IQueryAtom atom2,
IBond.Order order,
IChemObjectBuilder builder)
Deprecated.
Creates a new instance
|
AromaticQueryBond(IChemObjectBuilder builder)
Deprecated.
Creates a new instance.
|
AromaticQueryBond(IQueryAtom atom1,
IQueryAtom atom2,
IBond.Order order,
IChemObjectBuilder builder)
Deprecated.
Creates a new instance
|
AromaticSymbolAtom(String symbol,
IChemObjectBuilder builder)
Deprecated.
|
AtomicNumberAtom(int atomicNumber,
IChemObjectBuilder builder)
Deprecated.
Creates a new instance.
|
ChiralityAtom(IChemObjectBuilder builder)
Deprecated.
Creates a new instance
|
ExplicitConnectionAtom(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 instance
|
HybridizationNumberAtom(int hybridizationNumber,
IChemObjectBuilder builder)
Deprecated.
Creates a new instance
|
HydrogenAtom(IChemObjectBuilder builder)
Deprecated.
Creates a new instance.
|
ImplicitHCountAtom(int hcount,
IChemObjectBuilder builder)
Deprecated.
Creates a new instance
|
LogicalOperatorAtom(IChemObjectBuilder builder)
Deprecated.
|
LogicalOperatorBond(IChemObjectBuilder builder)
Deprecated.
|
MassAtom(int mass,
IChemObjectBuilder builder)
Deprecated.
Creates a new instance
|
NonCHHeavyAtom(IChemObjectBuilder builder)
Deprecated.
Creates a new instance
|
OrderQueryBond(IBond.Order order,
IChemObjectBuilder builder)
Deprecated.
Creates a new instance
|
PeriodicGroupNumberAtom(int groupNumber,
IChemObjectBuilder builder)
Deprecated.
Creates a new instance
|
ReactionRoleQueryAtom(IChemObjectBuilder builder,
int role)
Deprecated.
|
RingBond(IChemObjectBuilder builder)
Deprecated.
Creates a new instance
|
RingIdentifierAtom(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.
|
Modifier and Type | Method and Description |
---|---|
static IAtomContainer |
NomParser.generate(String stringToParse,
IChemObjectBuilder builder)
Deprecated.
Parses the chemical name and returns the built molecule.
|
Constructor and Description |
---|
MoleculeBuilder(IChemObjectBuilder builder) |
Modifier and Type | Method and Description |
---|---|
void |
TemplateHandler.loadTemplates(IChemObjectBuilder builder)
Loads all existing templates into memory.
|
Constructor and Description |
---|
TemplateHandler(IChemObjectBuilder builder)
Creates a new TemplateHandler with default templates loaded.
|
Modifier and Type | Method and Description |
---|---|
static IAtomContainer |
Convertor.model2Molecule(com.hp.hpl.jena.rdf.model.Model model,
IChemObjectBuilder builder)
|
Modifier and Type | Method and 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 file
|
void |
MMFF94BasedParameterSetReader.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) |
Modifier and Type | Method and Description |
---|---|
void |
IDescriptor.initialise(IChemObjectBuilder builder)
Initialise the descriptor with the specified chem object builder.
|
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.
|
Modifier and Type | Method and Description |
---|---|
void |
FractionalPSADescriptor.initialise(IChemObjectBuilder builder) |
void |
AcidicGroupCountDescriptor.initialise(IChemObjectBuilder builder) |
void |
SpiroAtomCountDescriptor.initialise(IChemObjectBuilder builder) |
void |
BasicGroupCountDescriptor.initialise(IChemObjectBuilder builder) |
void |
SmallRingDescriptor.initialise(IChemObjectBuilder builder) |
Modifier and Type | Method and Description |
---|---|
void |
OxygenAtomCountDescriptor.initialise(IChemObjectBuilder builder)
Initialise the descriptor with the specified chem object builder.
|
Modifier and Type | Method and Description |
---|---|
static IAtomContainer |
MoleculeSignature.fromSignatureString(String signatureString,
IChemObjectBuilder coBuilder)
Builder for molecules (rather, for atom containers) from signature
strings.
|
Constructor and Description |
---|
MoleculeFromSignatureBuilder(IChemObjectBuilder builder)
Uses the chem object builder for making molecules.
|
Modifier and Type | Class and Description |
---|---|
class |
SilentChemObjectBuilder
A factory class to provide implementation independent
ICDKObject s. |
Modifier and Type | Method and Description |
---|---|
IChemObjectBuilder |
MolecularFormulaSet.getBuilder() |
IChemObjectBuilder |
ChemObject.getBuilder() |
IChemObjectBuilder |
MolecularFormula.getBuilder() |
IChemObjectBuilder |
AdductFormula.getBuilder() |
static IChemObjectBuilder |
SilentChemObjectBuilder.getInstance()
Access the singleton instance of this SilentChemObjectBuilder.
|
Modifier and Type | Method and Description |
---|---|
static SmartsPattern |
SmartsPattern.create(String smarts,
IChemObjectBuilder builder)
Create a
Pattern that will match the given smarts query. |
Constructor and Description |
---|
SmilesParser(IChemObjectBuilder builder)
Create a new SMILES parser which will create
IAtomContainer s with
the specified builder. |
Modifier and Type | Method and Description |
---|---|
static SmartsPattern |
SmartsPattern.create(String smarts,
IChemObjectBuilder builder)
Deprecated.
Create a
Pattern that will match the given smarts query. |
Constructor and Description |
---|
SMARTSQueryTool(String smarts,
IChemObjectBuilder builder)
Deprecated.
Create a new SMARTS query tool for the specified SMARTS string.
|
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 |
Constructor and Description |
---|
SmartsQueryVisitor(IChemObjectBuilder builder)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
void |
DoubleBondStereochemistry.setBuilder(IChemObjectBuilder builder) |
void |
TetrahedralChirality.setBuilder(IChemObjectBuilder builder) |
Modifier and Type | Method and Description |
---|---|
static IAtomContainer |
IsoAlkanes.getIsobutane(IChemObjectBuilder builder) |
static IAtomContainer |
IsoAlkanes.getIsohexane(IChemObjectBuilder builder) |
static IAtomContainer |
IsoAlkanes.getIsopentane(IChemObjectBuilder builder) |
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 CDKHydrogenAdder |
CDKHydrogenAdder.getInstance(IChemObjectBuilder builder) |
static CDKValencyChecker |
CDKValencyChecker.getInstance(IChemObjectBuilder builder) |
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.
|
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