Uses of Class
org.openscience.cdk.exception.CDKException
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Uses of CDKException in org.openscience.cdk.aromaticity
Methods in org.openscience.cdk.aromaticity that throw CDKException Modifier and Type Method Description boolean
Aromaticity. apply(IAtomContainer molecule)
Apply this aromaticity model to a molecule.static boolean
CDKHueckelAromaticityDetector. detectAromaticity(IAtomContainer atomContainer)
Deprecated.static boolean
DoubleBondAcceptingAromaticityDetector. detectAromaticity(IAtomContainer atomContainer)
Deprecated.Set<IBond>
Aromaticity. findBonds(IAtomContainer molecule)
Find the bonds of amolecule
which this model determined were aromatic.static void
Kekulization. kekulize(IAtomContainer ac)
Assign a Kekulé representation to the aromatic systems of a compound. -
Uses of CDKException in org.openscience.cdk.atomtype
Methods in org.openscience.cdk.atomtype that throw CDKException Modifier and Type Method Description IAtomType
CDKAtomTypeMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
Method that assigns an atom type to a given atom belonging to an atom container.IAtomType
IAtomTypeMatcher. findMatchingAtomType(IAtomContainer container, IAtom atom)
Method that assigns an atom type to a given atom belonging to an atom container.IAtomType
MM2AtomTypeMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atomInterface)
Deprecated.Assign the mm2 atom type to a given atom.IAtomType
MMFF94AtomTypeMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atomInterface)
Deprecated.Assign the mmff94 atom type to a given atom.IAtomType
StructGenMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state.IAtomType
SybylAtomTypeMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
Sybyl atom type perception for a single atom.IAtomType[]
CDKAtomTypeMatcher. findMatchingAtomTypes(IAtomContainer atomContainer)
Method that assigns atom types to atoms in the given atom container.IAtomType[]
EStateAtomTypeMatcher. findMatchingAtomTypes(IAtomContainer atomContainer)
IAtomType[]
IAtomTypeMatcher. findMatchingAtomTypes(IAtomContainer container)
Method that assigns atom types to atoms in the given atom container.IAtomType[]
MM2AtomTypeMatcher. findMatchingAtomTypes(IAtomContainer atomContainer)
Deprecated.IAtomType[]
MMFF94AtomTypeMatcher. findMatchingAtomTypes(IAtomContainer atomContainer)
Deprecated.IAtomType[]
StructGenMatcher. findMatchingAtomTypes(IAtomContainer atomContainer)
IAtomType[]
SybylAtomTypeMatcher. findMatchingAtomTypes(IAtomContainer atomContainer)
Method that assigns atom types to atoms in the given atom container.List<IAtomType>
IAtomTypeGuesser. possibleAtomTypes(IAtomContainer container, IAtom atom)
Method that returns an iterator with a suitable list of atom types given the provided atom.List<IAtomType>
StructGenAtomTypeGuesser. possibleAtomTypes(IAtomContainer atomContainer, IAtom atom)
Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state. -
Uses of CDKException in org.openscience.cdk.charges
Methods in org.openscience.cdk.charges that throw CDKException Modifier and Type Method Description double[]
GasteigerMarsiliPartialCharges. assignGasteigerSigmaMarsiliFactors(IAtomContainer ac)
Method which stores and assigns the factors a,b,c and CHI+.IAtomContainer
MMFF94PartialCharges. assignMMFF94PartialCharges(IAtomContainer ac)
Main method which assigns MMFF94 partial chargesvoid
AtomTypeCharges. calculateCharges(IAtomContainer container)
void
GasteigerMarsiliPartialCharges. calculateCharges(IAtomContainer container)
void
GasteigerPEPEPartialCharges. calculateCharges(IAtomContainer container)
void
IElectronicPropertyCalculator. calculateCharges(IAtomContainer container)
void
InductivePartialCharges. calculateCharges(IAtomContainer container)
void
MMFF94PartialCharges. calculateCharges(IAtomContainer container)
double
InductivePartialCharges. getAtomicSoftnessCore(IAtomContainer ac, int atomPosition)
Gets the atomicSoftnessCore attribute of the InductivePartialCharges object.double[]
InductivePartialCharges. getPaulingElectronegativities(IAtomContainer ac, boolean modified)
Gets the paulingElectronegativities attribute of the InductivePartialCharges object. -
Uses of CDKException in org.openscience.cdk.config
Methods in org.openscience.cdk.config that throw CDKException Modifier and Type Method Description IAtom
AtomTypeFactory. configure(IAtom atom)
Configures an atom. -
Uses of CDKException in org.openscience.cdk.depict
Methods in org.openscience.cdk.depict that throw CDKException Modifier and Type Method Description Depiction
DepictionGenerator. depict(Iterable<IAtomContainer> mols)
Depict a set of molecules, they will be depicted in a grid.Depiction
DepictionGenerator. depict(Iterable<IAtomContainer> mols, int nrow, int ncol)
Depict a set of molecules, they will be depicted in a grid with the specified number of rows and columns.Depiction
DepictionGenerator. depict(IAtomContainer mol)
Depict a single molecule.Depiction
DepictionGenerator. depict(IReaction rxn)
Depict a reaction.Depiction
DepictionGenerator. depict(IReactionSet rxns)
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Uses of CDKException in org.openscience.cdk.exception
Subclasses of CDKException in org.openscience.cdk.exception Modifier and Type Class Description class
Intractable
Indicates a computation did not complete within some predefined bound.class
InvalidSmilesException
Exception thrown when an error is occurred during SMILES parsing.class
NoSuchAtomTypeException
Exception that may be thrown when an atom type is looked up or perceived but no such atom type was found.class
UnsupportedChemObjectException
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Uses of CDKException in org.openscience.cdk.fingerprint
Methods in org.openscience.cdk.fingerprint that throw CDKException Modifier and Type Method Description void
CircularFingerprinter. calculate(IAtomContainer mol)
Calculates the fingerprints for the givenIAtomContainer
, and stores them for subsequent retrieval.protected void
Fingerprinter. encodePaths(IAtomContainer mol, int depth, BitSet fp, int size)
protected int[]
Fingerprinter. findPathes(IAtomContainer container, int searchDepth)
Deprecated.IBitFingerprint
AtomPairs2DFingerprinter. getBitFingerprint(IAtomContainer container)
IBitFingerprint
CircularFingerprinter. getBitFingerprint(IAtomContainer mol)
Calculates the circular fingerprint for the givenIAtomContainer
, and folds the result into a single bitset (see getSize()).IBitFingerprint
EStateFingerprinter. getBitFingerprint(IAtomContainer atomContainer)
Returns the bit fingerprint for the givenIAtomContainer
.IBitFingerprint
ExtendedFingerprinter. getBitFingerprint(IAtomContainer container)
Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics.IBitFingerprint
ExtendedFingerprinter. getBitFingerprint(IAtomContainer atomContainer, IRingSet ringSet, List<IRingSet> rslist)
Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics.IBitFingerprint
Fingerprinter. getBitFingerprint(IAtomContainer container)
Generates a fingerprint of the default size for the given AtomContainer.IBitFingerprint
Fingerprinter. getBitFingerprint(IAtomContainer container, AllRingsFinder ringFinder)
Generates a fingerprint of the default size for the given AtomContainer.IBitFingerprint
IFingerprinter. getBitFingerprint(IAtomContainer container)
Returns the bit fingerprint for the givenIAtomContainer
.IBitFingerprint
LingoFingerprinter. getBitFingerprint(IAtomContainer iAtomContainer)
IBitFingerprint
MACCSFingerprinter. getBitFingerprint(IAtomContainer container)
Returns the bit fingerprint for the givenIAtomContainer
.IBitFingerprint
PubchemFingerprinter. getBitFingerprint(IAtomContainer atomContainer)
Calculate 881 bit Pubchem fingerprint for a molecule.IBitFingerprint
ShortestPathFingerprinter. getBitFingerprint(IAtomContainer ac)
Generates a shortest path based BitSet fingerprint for the given AtomContainer.IBitFingerprint
SignatureFingerprinter. getBitFingerprint(IAtomContainer atomContainer)
IBitFingerprint
SubstructureFingerprinter. getBitFingerprint(IAtomContainer atomContainer)
Returns the bit fingerprint for the givenIAtomContainer
.ICountFingerprint
AtomPairs2DFingerprinter. getCountFingerprint(IAtomContainer mol)
ICountFingerprint
CircularFingerprinter. getCountFingerprint(IAtomContainer mol)
Calculates the circular fingerprint for the givenIAtomContainer
, and returns a datastructure that enumerates all of the fingerprints, and their counts (i.e.ICountFingerprint
EStateFingerprinter. getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the givenIAtomContainer
.ICountFingerprint
ExtendedFingerprinter. getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the givenIAtomContainer
.ICountFingerprint
Fingerprinter. getCountFingerprint(IAtomContainer container)
ICountFingerprint
IFingerprinter. getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the givenIAtomContainer
.ICountFingerprint
LingoFingerprinter. getCountFingerprint(IAtomContainer container)
ICountFingerprint
MACCSFingerprinter. getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the givenIAtomContainer
.ICountFingerprint
PubchemFingerprinter. getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the givenIAtomContainer
.ICountFingerprint
ShortestPathFingerprinter. getCountFingerprint(IAtomContainer iac)
ICountFingerprint
SignatureFingerprinter. getCountFingerprint(IAtomContainer container)
ICountFingerprint
SubstructureFingerprinter. getCountFingerprint(IAtomContainer atomContainer)
Returns the count fingerprint for the givenIAtomContainer
.BitSet
AbstractFingerprinter. getFingerprint(IAtomContainer mol)
Generate a binary fingerprint as a bit.BitSet
ExtendedFingerprinter. getFingerprint(IAtomContainer mol)
BitSet
IFingerprinter. getFingerprint(IAtomContainer mol)
Generate a binary fingerprint as a bit.Map<String,Integer>
AtomPairs2DFingerprinter. getRawFingerprint(IAtomContainer mol)
Map<String,Integer>
CircularFingerprinter. getRawFingerprint(IAtomContainer mol)
Invalid: it is not appropriate to convert the integer hash codes into strings.Map<String,Integer>
EStateFingerprinter. getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.Map<String,Integer>
ExtendedFingerprinter. getRawFingerprint(IAtomContainer container)
Returns the raw representation of the fingerprint for the given IAtomContainer.Map<String,Integer>
Fingerprinter. getRawFingerprint(IAtomContainer container)
Returns the raw representation of the fingerprint for the given IAtomContainer.Map<String,Integer>
IFingerprinter. getRawFingerprint(IAtomContainer container)
Returns the raw representation of the fingerprint for the given IAtomContainer.Map<String,Integer>
LingoFingerprinter. getRawFingerprint(IAtomContainer atomContainer)
Map<String,Integer>
MACCSFingerprinter. getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.Map<String,Integer>
PubchemFingerprinter. getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.Map<String,Integer>
ShortestPathFingerprinter. getRawFingerprint(IAtomContainer ac)
Returns the raw representation of the fingerprint for the given IAtomContainer.Map<String,Integer>
SignatureFingerprinter. getRawFingerprint(IAtomContainer atomContainer)
Map<String,Integer>
SubstructureFingerprinter. getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer. -
Uses of CDKException in org.openscience.cdk.fingerprint.model
Methods in org.openscience.cdk.fingerprint.model that throw CDKException Modifier and Type Method Description void
Bayesian. addMolecule(IAtomContainer mol, boolean active)
Appends a new row to the model source data, which consists of a molecule and whether or not it is considered active.void
Bayesian. build()
Performs that Bayesian model generation, using the {molecule:activity} pairs that have been submitted up to this point.double
Bayesian. predict(IAtomContainer mol)
For a given molecule, determines its fingerprints and uses them to calculate a Bayesian prediction. -
Uses of CDKException in org.openscience.cdk.formula
Methods in org.openscience.cdk.formula that throw CDKException Modifier and Type Method Description void
MassToFormulaTool. setRestrictions(List<IRule> rulesNew)
Deprecated.Set the restrictions that must be presents in the molecular formula. -
Uses of CDKException in org.openscience.cdk.formula.rules
Methods in org.openscience.cdk.formula.rules that throw CDKException Modifier and Type Method Description void
ChargeRule. setParameters(Object[] params)
Sets the parameters attribute of the ChargeRule object.void
ElementRule. setParameters(Object[] params)
Sets the parameters attribute of the ElementRule object.void
IRule. setParameters(Object[] params)
Sets the parameters for this rule.void
IsotopePatternRule. setParameters(Object[] params)
Sets the parameters attribute of the IsotopePatternRule object.void
MMElementRule. setParameters(Object[] params)
Sets the parameters attribute of the MMElementRule object.void
NitrogenRule. setParameters(Object[] params)
Sets the parameters attribute of the NitrogenRule object.void
RDBERule. setParameters(Object[] params)
Sets the parameters attribute of the RDBE object.void
ToleranceRangeRule. setParameters(Object[] params)
Sets the parameters attribute of the ToleranceRangeRule object.double
ChargeRule. validate(IMolecularFormula formula)
Validate the charge of this IMolecularFormula.double
ElementRule. validate(IMolecularFormula formula)
Validate the occurrence of this IMolecularFormula.double
IRule. validate(IMolecularFormula formula)
Analyze the validity for the given IMolecularFormula.double
IsotopePatternRule. validate(IMolecularFormula formula)
Validate the isotope pattern of this IMolecularFormula.double
MMElementRule. validate(IMolecularFormula formula)
Validate the occurrence of this IMolecularFormula.double
NitrogenRule. validate(IMolecularFormula formula)
Validate the nitrogen rule of this IMolecularFormula.double
RDBERule. validate(IMolecularFormula formula)
Validate the RDBRule of this IMolecularFormula.boolean
RDBERule. validate(IMolecularFormula formula, double value)
Validate the ion state.double
ToleranceRangeRule. validate(IMolecularFormula formula)
Validate the Tolerance Range of this IMolecularFormula. -
Uses of CDKException in org.openscience.cdk.fragment
Methods in org.openscience.cdk.fragment that throw CDKException Modifier and Type Method Description void
ExhaustiveFragmenter. generateFragments(IAtomContainer atomContainer)
Generate fragments for the input molecule.void
IFragmenter. generateFragments(IAtomContainer atomContainer)
Generate fragments for the input molecule.void
MurckoFragmenter. generateFragments(IAtomContainer atomContainer)
Perform the fragmentation procedure. -
Uses of CDKException in org.openscience.cdk.geometry
Methods in org.openscience.cdk.geometry that throw CDKException Modifier and Type Method Description static List<IAtom>
GeometryTools. findClosestInSpace(IAtomContainer container, IAtom startAtom, int max)
Deprecated.Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.static List<IAtom>
GeometryUtil. findClosestInSpace(IAtomContainer container, IAtom startAtom, int max)
Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.static double
GeometryTools. getAllAtomRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, Map<Integer,Integer> mappedAtoms, boolean Coords3d)
Deprecated.Return the RMSD between the 2 aligned molecules.static double
GeometryUtil. getAllAtomRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, Map<Integer,Integer> mappedAtoms, boolean Coords3d)
Return the RMSD between the 2 aligned molecules.static boolean
BondTools. isCisTrans(IAtom firstOuterAtom, IAtom firstInnerAtom, IAtom secondInnerAtom, IAtom secondOuterAtom, IAtomContainer ac)
Says if two atoms are in cis or trans position around a double bond.static Map<Integer,Integer>
GeometryTools. mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, double searchRadius, Map<Integer,Integer> mappedAtoms)
Deprecated.Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomcontainer.static Map<Integer,Integer>
GeometryUtil. mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, double searchRadius, Map<Integer,Integer> mappedAtoms)
Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomcontainer. -
Uses of CDKException in org.openscience.cdk.geometry.alignment
Constructors in org.openscience.cdk.geometry.alignment that throw CDKException Constructor Description KabschAlignment(IAtom[] al1, IAtom[] al2)
Sets up variables for the alignment algorithm.KabschAlignment(IAtom[] al1, IAtom[] al2, double[] wts)
Sets up variables for the alignment algorithm.KabschAlignment(IAtomContainer ac1, IAtomContainer ac2)
Sets up variables for the alignment algorithm.KabschAlignment(IAtomContainer ac1, IAtomContainer ac2, double[] wts)
Sets up variables for the alignment algorithm. -
Uses of CDKException in org.openscience.cdk.geometry.surface
Methods in org.openscience.cdk.geometry.surface that throw CDKException Modifier and Type Method Description double
NumericalSurface. getSurfaceArea(int atomIdx)
Get the surface area for the specified atom.javax.vecmath.Point3d[]
NumericalSurface. getSurfacePoints(int atomIdx)
Get an array of the points on the accessible surface of a specific atom. -
Uses of CDKException in org.openscience.cdk.geometry.volume
Methods in org.openscience.cdk.geometry.volume that throw CDKException Modifier and Type Method Description static double
VABCVolume. calculate(IAtomContainer molecule)
Calculates the volume for the givenIAtomContainer
. -
Uses of CDKException in org.openscience.cdk.graph
Methods in org.openscience.cdk.graph that throw CDKException Modifier and Type Method Description static List<List<IAtom>>
PathTools. getLimitedPathsOfLengthUpto(IAtomContainer atomContainer, IAtom start, int length, int limit)
Get all the paths starting from an atom of length 0 up to the specified length. -
Uses of CDKException in org.openscience.cdk.graph.invariant
Methods in org.openscience.cdk.graph.invariant that throw CDKException Modifier and Type Method Description static long[]
InChINumbersTools. getNumbers(IAtomContainer atomContainer)
Makes an array containing the InChI atom numbers of the non-hydrogen atoms in the atomContainer.static long[]
InChINumbersTools. getUSmilesNumbers(IAtomContainer container)
Obtain the InChI numbers for the input container to be used to order atoms in Universal SMILES [O'Boyle, Noel. Journal of Cheminformatics. 2012. 4]. -
Uses of CDKException in org.openscience.cdk.graph.rebond
Methods in org.openscience.cdk.graph.rebond that throw CDKException Modifier and Type Method Description void
RebondTool. rebond(IAtomContainer container)
Rebonding using a Binary Space Partition Tree. -
Uses of CDKException in org.openscience.cdk.inchi
Methods in org.openscience.cdk.inchi that throw CDKException Modifier and Type Method Description protected void
InChIToStructure. generateAtomContainerFromInchi(IChemObjectBuilder builder)
Gets structure from InChI, and converts InChI library data structure into an IAtomContainer.InChIGenerator
InChIGeneratorFactory. getInChIGenerator(IAtomContainer container)
Gets an Standard InChI generator for aIAtomContainer
.InChIGenerator
InChIGeneratorFactory. getInChIGenerator(IAtomContainer container, io.github.dan2097.jnainchi.InchiFlag... flags)
Get an InChI generator providing flags to customise the generation.InChIGenerator
InChIGeneratorFactory. getInChIGenerator(IAtomContainer container, io.github.dan2097.jnainchi.InchiOptions options)
Get an InChI generator providing flags to customise the generation.InChIGenerator
InChIGeneratorFactory. getInChIGenerator(IAtomContainer container, String options)
Gets InChI generator for CDK IAtomContainer.InChIGenerator
InChIGeneratorFactory. getInChIGenerator(IAtomContainer container, List<INCHI_OPTION> options)
String
InChIGenerator. getInchiKey()
Gets generated InChIKey string.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.static InChIGeneratorFactory
InChIGeneratorFactory. getInstance()
Gives the oneInChIGeneratorFactory
instance, if needed also creates it.Constructors in org.openscience.cdk.inchi that throw CDKException Constructor Description InChIGenerator(IAtomContainer atomContainer, boolean ignoreAromaticBonds)
Constructor.InChIGenerator(IAtomContainer atomContainer, io.github.dan2097.jnainchi.InchiOptions options, boolean ignoreAromaticBonds)
InChIGenerator(IAtomContainer atomContainer, String optStr, boolean ignoreAromaticBonds)
Constructor.InChIGenerator(IAtomContainer atomContainer, List<INCHI_OPTION> opts, boolean ignoreAromaticBonds)
Deprecated.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 CDKException in org.openscience.cdk.io
Methods in org.openscience.cdk.io that throw CDKException Modifier and Type Method Description void
DefaultChemObjectReader. handleError(String message)
Redirects an error message to theIChemObjectReaderErrorHandler
.void
DefaultChemObjectReader. handleError(String message, int row, int colStart, int colEnd)
Redirects an error message to theIChemObjectReaderErrorHandler
.void
DefaultChemObjectReader. handleError(String message, int row, int colStart, int colEnd, Exception exception)
Redirects an error message to theIChemObjectReaderErrorHandler
.void
DefaultChemObjectReader. handleError(String message, Exception exception)
Redirects an error message to theIChemObjectReaderErrorHandler
.void
IChemObjectReader. handleError(String message)
Redirects an error message to theIChemObjectReaderErrorHandler
.void
IChemObjectReader. handleError(String message, int row, int colStart, int colEnd)
Redirects an error message to theIChemObjectReaderErrorHandler
.void
IChemObjectReader. handleError(String message, int row, int colStart, int colEnd, Exception exception)
Redirects an error message to theIChemObjectReaderErrorHandler
.void
IChemObjectReader. handleError(String message, Exception exception)
Redirects an error message to theIChemObjectReaderErrorHandler
.boolean
MDLV3000Reader. isReady()
static MDLV2000Writer.SPIN_MULTIPLICITY
MDLV2000Writer.SPIN_MULTIPLICITY. ofValue(int value)
Create a SPIN_MULTIPLICITY instance for the specified value.<T extends IChemObject>
TCIFReader. read(T object)
Read a ChemFile from input.<T extends IChemObject>
TCMLReader. read(T object)
Read a IChemObject from input.<T extends IChemObject>
TCrystClustReader. read(T object)
<T extends IChemObject>
TCTXReader. read(T object)
<T extends IChemObject>
TGamessReader. read(T object)
<T extends IChemObject>
TGaussian03Reader. read(T object)
<T extends IChemObject>
TGaussian98Reader. read(T object)
<T extends IChemObject>
TGhemicalMMReader. read(T object)
<T extends IChemObject>
THINReader. read(T object)
Reads the content from a HIN input.<T extends IChemObject>
TINChIPlainTextReader. read(T object)
Reads a IChemObject of type object from input.<T extends IChemObject>
TINChIReader. read(T object)
Reads a IChemObject of type object from input.<T extends IChemObject>
TISimpleChemObjectReader. read(T object)
Reads an IChemObject of type "object" from input.<T extends IChemObject>
TMDLReader. read(T object)
Deprecated.Takes an object which subclasses IChemObject, e.g.<T extends IChemObject>
TMDLRXNReader. read(T object)
Deprecated.Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file, database, internet etc).<T extends IChemObject>
TMDLRXNV2000Reader. read(T object)
Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file, database, internet etc).<T extends IChemObject>
TMDLRXNV3000Reader. read(T object)
<T extends IChemObject>
TMDLV2000Reader. read(T object)
Takes an object which subclasses IChemObject, e.g.<T extends IChemObject>
TMDLV3000Reader. read(T object)
<T extends IChemObject>
TMol2Reader. read(T object)
<T extends IChemObject>
TMopac7Reader. read(T object)
<T extends IChemObject>
TMoSSOutputReader. read(T object)
Read aIAtomContainerSet
from the input source.<T extends IChemObject>
TPCCompoundASNReader. read(T object)
<T extends IChemObject>
TPCCompoundXMLReader. read(T object)
<T extends IChemObject>
TPCSubstanceXMLReader. read(T object)
<T extends IChemObject>
TPDBReader. read(T oObj)
Takes an object which subclasses IChemObject, e.g.<T extends IChemObject>
TPMPReader. read(T object)
reads the content from a PMP input.<T extends IChemObject>
TRGroupQueryReader. read(T object)
Check input IChemObject and proceed to parse.<T extends IChemObject>
TShelXReader. read(T object)
Read a ChemFile from input.<T extends IChemObject>
TSMILESReader. read(T object)
Reads the content from a XYZ input.<T extends IChemObject>
TVASPReader. read(T object)
<T extends IChemObject>
TXYZReader. read(T object)
reads the content from a XYZ input.<T extends IChemObject>
TZMatrixReader. read(T object)
Returns a IChemObject of type object bye reading from the input.void
MDLV3000Reader. readAtomBlock(org.openscience.cdk.io.MDLV3000Reader.ReadState state)
Reads the atoms, coordinates and charges.void
MDLV3000Reader. readBondBlock(org.openscience.cdk.io.MDLV3000Reader.ReadState state)
Reads the bond atoms, order and stereo configuration.IAtomContainer
MDLV3000Reader. readConnectionTable(IChemObjectBuilder builder)
String
MDLV3000Reader. readHeader(org.openscience.cdk.io.MDLV3000Reader.ReadState state)
String
MDLV3000Reader. readLine()
IAtomContainer
MDLV3000Reader. readMolecule(IChemObjectBuilder builder)
void
MDLV3000Reader. readSGroup(org.openscience.cdk.io.MDLV3000Reader.ReadState state)
Reads labels.void
CIFReader. setReader(InputStream input)
void
CIFReader. setReader(Reader reader)
void
CMLReader. setReader(InputStream input)
void
CMLReader. setReader(Reader reader)
This method must not be used; XML reading requires the use of an InputStream.void
CrystClustReader. setReader(InputStream input)
void
CrystClustReader. setReader(Reader reader)
void
CTXReader. setReader(InputStream input)
void
CTXReader. setReader(Reader reader)
void
GamessReader. setReader(InputStream input)
void
GamessReader. setReader(Reader reader)
void
Gaussian03Reader. setReader(InputStream input)
void
Gaussian03Reader. setReader(Reader reader)
void
Gaussian98Reader. setReader(InputStream input)
void
Gaussian98Reader. setReader(Reader input)
Sets the reader attribute of the Gaussian98Reader object.void
GhemicalMMReader. setReader(InputStream input)
void
GhemicalMMReader. setReader(Reader input)
void
HINReader. setReader(InputStream input)
void
HINReader. setReader(Reader input)
void
IChemObjectReader. setReader(InputStream reader)
Sets the InputStream from which this ChemObjectReader should read the contents.void
IChemObjectReader. setReader(Reader reader)
Sets the Reader from which this ChemObjectReader should read the contents.void
INChIPlainTextReader. setReader(InputStream input)
void
INChIReader. setReader(InputStream input)
void
INChIReader. setReader(Reader reader)
This method must not be used; XML reading requires the use of an InputStream.void
MDLReader. setReader(InputStream input)
Deprecated.void
MDLReader. setReader(Reader input)
Deprecated.void
MDLRXNReader. setReader(InputStream input)
Deprecated.void
MDLRXNReader. setReader(Reader input)
Deprecated.void
MDLRXNV2000Reader. setReader(InputStream input)
void
MDLRXNV2000Reader. setReader(Reader input)
void
MDLRXNV3000Reader. setReader(InputStream input)
void
MDLRXNV3000Reader. setReader(Reader input)
void
MDLV2000Reader. setReader(InputStream input)
void
MDLV2000Reader. setReader(Reader input)
void
MDLV3000Reader. setReader(InputStream input)
void
MDLV3000Reader. setReader(Reader input)
void
Mol2Reader. setReader(InputStream input)
void
Mol2Reader. setReader(Reader input)
void
Mopac7Reader. setReader(InputStream input)
void
Mopac7Reader. setReader(Reader input)
void
MoSSOutputReader. setReader(InputStream input)
Sets the InputStream from which this ChemObjectReader should read the contents.void
MoSSOutputReader. setReader(Reader reader)
Sets the Reader from which this ChemObjectReader should read the contents.void
PCCompoundASNReader. setReader(InputStream input)
void
PCCompoundASNReader. setReader(Reader input)
void
PCCompoundXMLReader. setReader(InputStream input)
void
PCCompoundXMLReader. setReader(Reader input)
void
PCSubstanceXMLReader. setReader(InputStream input)
void
PCSubstanceXMLReader. setReader(Reader input)
void
PDBReader. setReader(InputStream input)
void
PDBReader. setReader(Reader input)
void
PMPReader. setReader(InputStream input)
void
PMPReader. setReader(Reader input)
void
RGroupQueryReader. setReader(InputStream input)
void
RGroupQueryReader. setReader(Reader input)
Sets the input Reader.void
ShelXReader. setReader(InputStream input)
void
ShelXReader. setReader(Reader input)
void
SMILESReader. setReader(InputStream input)
void
SMILESReader. setReader(Reader input)
void
VASPReader. setReader(InputStream input)
void
VASPReader. setReader(Reader input)
void
XYZReader. setReader(InputStream input)
void
XYZReader. setReader(Reader input)
void
ZMatrixReader. setReader(InputStream input)
void
ZMatrixReader. setReader(Reader input)
void
CDKSourceCodeWriter. setWriter(OutputStream output)
void
CDKSourceCodeWriter. setWriter(Writer out)
void
CMLWriter. setWriter(OutputStream output)
void
CMLWriter. setWriter(Writer writer)
void
CrystClustWriter. setWriter(OutputStream output)
void
CrystClustWriter. setWriter(Writer out)
void
HINWriter. setWriter(OutputStream output)
void
HINWriter. setWriter(Writer out)
void
IChemObjectWriter. setWriter(OutputStream writer)
Sets the OutputStream from which this ChemObjectWriter should write the contents.void
IChemObjectWriter. setWriter(Writer writer)
Sets the Writer from which this ChemObjectWriter should write the contents.void
MDLRXNWriter. setWriter(OutputStream output)
void
MDLRXNWriter. setWriter(Writer out)
void
MDLV2000Writer. setWriter(OutputStream output)
void
MDLV2000Writer. setWriter(Writer out)
void
MDLV3000Writer. setWriter(OutputStream writer)
Sets the OutputStream from which this ChemObjectWriter should write the contents.void
MDLV3000Writer. setWriter(Writer writer)
Sets the Writer from which this ChemObjectWriter should write the contents.void
Mol2Writer. setWriter(OutputStream output)
void
Mol2Writer. setWriter(Writer out)
void
PDBWriter. setWriter(OutputStream output)
void
PDBWriter. setWriter(Writer out)
void
RGroupQueryWriter. setWriter(OutputStream output)
Sets the writer to given output stream.void
RGroupQueryWriter. setWriter(Writer out)
Sets the writer.void
RssWriter. setWriter(OutputStream output)
void
RssWriter. setWriter(Writer out)
void
SDFWriter. setWriter(OutputStream output)
void
SDFWriter. setWriter(Writer out)
void
ShelXWriter. setWriter(OutputStream output)
void
ShelXWriter. setWriter(Writer out)
void
SMILESWriter. setWriter(OutputStream output)
void
SMILESWriter. setWriter(Writer out)
void
XYZWriter. setWriter(OutputStream output)
void
XYZWriter. setWriter(Writer out)
void
CDKSourceCodeWriter. write(IChemObject object)
void
CMLWriter. write(IChemObject object)
Serializes the IChemObject to CML and redirects it to the output Writer.void
HINWriter. write(IChemObject object)
void
IChemObjectWriter. write(IChemObject object)
Writes the content of "object" to output.void
MDLRXNWriter. write(IChemObject object)
Writes a IChemObject to the MDL RXN file formated output.void
MDLV2000Writer. write(IChemObject object)
Writes aIChemObject
to the MDL molfile formated output.void
MDLV3000Writer. write(IChemObject object)
Writes a molecule to the V3000 format.void
Mol2Writer. write(IChemObject object)
void
PDBWriter. write(IChemObject object)
void
RGroupQueryWriter. write(IChemObject object)
The actual writing of the output.void
RssWriter. write(IChemObject object)
Writes a IChemObject to the MDL molfile formated output.void
SDFWriter. write(IChemObject object)
Writes a IChemObject to the MDL SD file formated output.void
ShelXWriter. write(IChemObject object)
Serializes the IChemObject to ShelX and redirects it to the output Writer.void
SMILESWriter. write(IChemObject object)
Writes the content from object to output.void
XYZWriter. write(IChemObject object)
void
PDBWriter. writeCrystal(ICrystal crystal)
void
PDBWriter. writeMolecule(IAtomContainer molecule)
Writes a single frame in PDB format to the Writer.Constructors in org.openscience.cdk.io that throw CDKException Constructor Description MDLV3000Writer(OutputStream out)
Create a new V3000 writer, output to the provided JDK output stream. -
Uses of CDKException in org.openscience.cdk.io.iterator
Methods in org.openscience.cdk.io.iterator that throw CDKException Modifier and Type Method Description void
DefaultIteratingChemObjectReader. handleError(String message)
Redirects an error message to theIChemObjectReaderErrorHandler
.void
DefaultIteratingChemObjectReader. handleError(String message, int row, int colStart, int colEnd)
Redirects an error message to theIChemObjectReaderErrorHandler
.void
DefaultIteratingChemObjectReader. handleError(String message, int row, int colStart, int colEnd, Exception exception)
Redirects an error message to theIChemObjectReaderErrorHandler
.void
DefaultIteratingChemObjectReader. handleError(String message, Exception exception)
Redirects an error message to theIChemObjectReaderErrorHandler
.void
IteratingPCCompoundXMLReader. setReader(InputStream reader)
void
IteratingPCCompoundXMLReader. setReader(Reader reader)
void
IteratingPCSubstancesXMLReader. setReader(InputStream reader)
void
IteratingPCSubstancesXMLReader. setReader(Reader reader)
-
Uses of CDKException in org.openscience.cdk.io.iterator.event
Methods in org.openscience.cdk.io.iterator.event that throw CDKException Modifier and Type Method Description void
EventCMLReader. process()
Starts the reading of the CML file.void
EventCMLReader. setReader(Reader reader)
-
Uses of CDKException in org.openscience.cdk.io.program
Methods in org.openscience.cdk.io.program that throw CDKException Modifier and Type Method Description void
GaussianInputWriter. setWriter(OutputStream output)
void
GaussianInputWriter. setWriter(Writer out)
void
Mopac7Writer. setWriter(OutputStream writer)
void
Mopac7Writer. setWriter(Writer writer)
void
GaussianInputWriter. write(IChemObject object)
void
Mopac7Writer. write(IChemObject arg0)
Writes the content of "object" to output. -
Uses of CDKException in org.openscience.cdk.io.random
Methods in org.openscience.cdk.io.random that throw CDKException Modifier and Type Method Description protected IChemObject
RandomAccessReader. processContent()
The reader is already set to read the record buffer.protected IChemObject
RandomAccessSDFReader. processContent()
protected String
RandomAccessReader. readContent(int record)
Reads the record text content into a String.void
RandomAccessSDFReader. setReader(InputStream reader)
void
RandomAccessSDFReader. setReader(Reader reader)
-
Uses of CDKException in org.openscience.cdk.io.rdf
Methods in org.openscience.cdk.io.rdf that throw CDKException Modifier and Type Method Description <T extends IChemObject>
TCDKOWLReader. read(T object)
Reads an IChemObject of type "object" from input.void
CDKOWLReader. setReader(InputStream input)
Sets the InputStream from which this ChemObjectReader should read the contents.void
CDKOWLReader. setReader(Reader reader)
Deprecated.void
CDKOWLWriter. setWriter(OutputStream output)
Sets the OutputStream from which this ChemObjectWriter should write the contents.void
CDKOWLWriter. setWriter(Writer out)
Sets the Writer from which this ChemObjectWriter should write the contents.void
CDKOWLWriter. write(IChemObject object)
Writes the content of "object" to output. -
Uses of CDKException in org.openscience.cdk.io.setting
Methods in org.openscience.cdk.io.setting that throw CDKException Modifier and Type Method Description void
BooleanIOSetting. setSetting(String setting)
Sets the setting for a certain question.void
IntegerIOSetting. setSetting(String setting)
Sets the setting for a certain question.void
IOSetting. setSetting(String setting)
Sets the setting for a certain question.void
OptionIOSetting. setSetting(int setting)
Sets the setting for a certain question.void
OptionIOSetting. setSetting(String setting)
Sets the setting for a certain question.void
StringIOSetting. setSetting(String setting)
Sets the setting for a certain question. -
Uses of CDKException in org.openscience.cdk.isomorphism
Methods in org.openscience.cdk.isomorphism that throw CDKException Modifier and Type Method Description static RGraph
UniversalIsomorphismTester. buildRGraph(IAtomContainer g1, IAtomContainer g2)
Builds theRGraph
( resolution graph ), from two atomContainer (description of the two molecules to compare) This is the interface point between the CDK model and the generic MCSS algorithm based on the RGRaph.static List<RMap>
UniversalIsomorphismTester. checkSingleAtomCases(IAtomContainer g1, IAtomContainer g2)
Checks for single atom cases before doing subgraph/isomorphism search.List<RMap>
UniversalIsomorphismTester. getIsomorphAtomsMap(IAtomContainer g1, IAtomContainer g2)
Returns the first isomorph 'atom mapping' found for g2 in g1.List<RMap>
UniversalIsomorphismTester. getIsomorphMap(IAtomContainer g1, IAtomContainer g2)
Returns the first isomorph mapping found or null.List<List<RMap>>
UniversalIsomorphismTester. getIsomorphMaps(IAtomContainer g1, IAtomContainer g2)
Returns all the isomorph 'mappings' found between two atom containers.List<IAtomContainer>
UniversalIsomorphismTester. getOverlaps(IAtomContainer g1, IAtomContainer g2)
Returns all the maximal common substructure between two atom containers.List<RMap>
UniversalIsomorphismTester. getSubgraphAtomsMap(IAtomContainer g1, IAtomContainer g2)
Returns the first subgraph 'atom mapping' found for g2 in g1, where g2 must be a substructure of g1.List<List<RMap>>
UniversalIsomorphismTester. getSubgraphAtomsMaps(IAtomContainer g1, IAtomContainer g2)
Returns all subgraph 'atom mappings' found for g2 in g1, where g2 must be a substructure of g1.List<RMap>
UniversalIsomorphismTester. getSubgraphMap(IAtomContainer g1, IAtomContainer g2)
Returns the first subgraph 'bond mapping' found for g2 in g1.List<List<RMap>>
UniversalIsomorphismTester. getSubgraphMaps(IAtomContainer g1, IAtomContainer g2)
Returns all the subgraph 'bond mappings' found for g2 in g1.boolean
UniversalIsomorphismTester. isIsomorph(IAtomContainer g1, IAtomContainer g2)
Tests if g1 and g2 are isomorph.boolean
UniversalIsomorphismTester. isSubgraph(IAtomContainer g1, IAtomContainer g2)
Deprecated.Use the Pattern APIs from the cdk-isomorphism modulestatic Map<Integer,Integer>
AtomMappingTools. mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, Map<Integer,Integer> mappedAtoms)
Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomContainer.List<List<RMap>>
UniversalIsomorphismTester. search(IAtomContainer g1, IAtomContainer g2, BitSet c1, BitSet c2, boolean findAllStructure, boolean findAllMap)
GeneralRGraph
parsing method (usually not used directly) This method is the entry point for the recursive search adapted to the atom container input. -
Uses of CDKException in org.openscience.cdk.isomorphism.matchers
Methods in org.openscience.cdk.isomorphism.matchers that throw CDKException Modifier and Type Method Description List<IAtomContainer>
RGroupQuery. getAllConfigurations()
void
RGroupList. setOccurrence(String occurrence)
Picky setter for occurrence fields.Constructors in org.openscience.cdk.isomorphism.matchers that throw CDKException Constructor Description RGroupList(int rGroupNumber, boolean restH, String occurrence, int requiredRGroupNumber)
Constructor with attributes given. -
Uses of CDKException in org.openscience.cdk.iupac.parser
Methods in org.openscience.cdk.iupac.parser that throw CDKException Modifier and Type Method Description protected IAtomContainer
MoleculeBuilder. buildMolecule(int mainChain, List<AttachedGroup> attachedSubstituents, List<AttachedGroup> attachedGroups, boolean isMainCyclic, String name)
Start of the process of building a molecule from the parsed data.static IAtomContainer
NomParser. generate(String stringToParse)
Deprecated.Parses the chemical name and returns the built molecule.static IAtomContainer
NomParser. generate(String stringToParse, IChemObjectBuilder builder)
Deprecated.Parses the chemical name and returns the built molecule. -
Uses of CDKException in org.openscience.cdk.layout
Methods in org.openscience.cdk.layout that throw CDKException Modifier and Type Method Description static void
AtomPlacer. breadthFirstSearch(IAtomContainer ac, List<IAtom> sphere, IAtomContainer[] pathes)
Performs a breadthFirstSearch in an AtomContainer starting with a particular sphere, which usually consists of one start atom, and searches for the longest aliphatic chain which is yet unplaced.void
StructureDiagramGenerator. generateCoordinates()
The main method of this StructurDiagramGenerator.void
StructureDiagramGenerator. generateCoordinates(javax.vecmath.Vector2d firstBondVector)
The main method of this StructurDiagramGenerator.void
StructureDiagramGenerator. generateCoordinates(IAtomContainer mol)
Convenience method for generating 2D coordinates.void
StructureDiagramGenerator. generateCoordinates(IReaction reaction)
Convenience method to generate 2D coordinates for a reaction.void
StructureDiagramGenerator. generateExperimentalCoordinates()
Deprecated.void
StructureDiagramGenerator. generateExperimentalCoordinates(javax.vecmath.Vector2d firstBondVector)
Deprecated.static IAtomContainer
AtomPlacer. getInitialLongestChain(IAtomContainer molecule)
Search an aliphatic molecule for the longest chain.static IAtomContainer
AtomPlacer. getLongestUnplacedChain(IAtomContainer molecule, IAtom startAtom)
Search a molecule for the longest unplaced, aliphatic chain in it.IAtomContainerSet
TemplateHandler. getMappedSubstructures(IAtomContainer molecule)
Checks if one of the loaded templates is a substructure in the given Molecule and returns all matched substructures in a IAtomContainerSet.static String
AtomPlacer. listNumbers(IAtomContainer mol, IAtomContainer ac)
Returns a string with the numbers of all atoms in an AtomContainer relative to a given molecule.boolean
TemplateHandler. mapTemplateExact(IAtomContainer molecule)
Checks if one of the loaded templates is isomorph to the given Molecule.boolean
TemplateHandler. mapTemplates(IAtomContainer molecule)
Checks if one of the loaded templates is a substructure in the given Molecule.IAtomContainer
TemplateHandler. removeMolecule(IAtomContainer molecule)
-
Uses of CDKException in org.openscience.cdk.modeling.builder3d
Methods in org.openscience.cdk.modeling.builder3d that throw CDKException Modifier and Type Method Description void
AtomTetrahedralLigandPlacer3D. add3DCoordinatesForSinglyBondedLigands(IAtomContainer atomContainer)
Generate coordinates for all atoms which are singly bonded and have no coordinates.IRingSet
ForceFieldConfigurator. assignAtomTyps(IAtomContainer molecule)
Method assigns atom types to atoms (calculates sssr and aromaticity)IAtom
ForceFieldConfigurator. configureAtom(IAtom atom, String hoseCode, boolean _boolean)
IAtomContainer
ModelBuilder3D. generate3DCoordinates(IAtomContainer molecule, boolean clone)
Generate 3D coordinates with force field information.javax.vecmath.Point3d[]
AtomTetrahedralLigandPlacer3D. get3DCoordinatesForLigands(IAtom refAtom, IAtomContainer noCoords, IAtomContainer withCoords, IAtom atomC, int nwanted, double length, double angle)
Adds 3D coordinates for singly-bonded ligands of a reference atom (A).static ModelBuilder3D
ModelBuilder3D. getInstance(IChemObjectBuilder builder)
static ModelBuilder3D
ModelBuilder3D. getInstance(TemplateHandler3D templateHandler, String ffname, IChemObjectBuilder chemObjectBuilder)
static TemplateHandler3D
TemplateHandler3D. getInstance()
void
TemplateHandler3D. mapTemplates(IAtomContainer ringSystems, double numberOfRingAtoms)
void
TemplateHandler3D. mapTemplates(IAtomContainer mol, int numberOfRingAtoms)
Checks if one of the loaded templates is a substructure in the given Molecule.void
AtomPlacer3D. placeAliphaticHeavyChain(IAtomContainer molecule, IAtomContainer chain)
Method assigns 3D coordinates to the heavy atoms in an aliphatic chain.void
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 field -
Uses of CDKException in org.openscience.cdk.normalize
Methods in org.openscience.cdk.normalize that throw CDKException Modifier and Type Method Description static boolean
Normalizer. normalize(IAtomContainer ac, Document doc)
Deprecated.The method takes an XML files like the following:
<replace-set>
<replace>O=N=O</replace>
<replacement>[O-][N+]=O</replacement>
</replace-set>
All parts in ac which are the same as replace will be changed according to replacement.static void
SMSDNormalizer. percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Deprecated.Convenience method to perceive atom types for allIAtom
s in theIAtomContainer
, using theCDKAtomTypeMatcher
. -
Uses of CDKException in org.openscience.cdk.pharmacophore
Methods in org.openscience.cdk.pharmacophore that throw CDKException Modifier and Type Method Description boolean
PharmacophoreMatcher. matches(IAtomContainer atomContainer)
Performs the pharmacophore matching.boolean
PharmacophoreMatcher. matches(IAtomContainer atomContainer, boolean initializeTarget)
Performs the pharmacophore matching.static List<PharmacophoreQuery>
PharmacophoreUtils. readPharmacophoreDefinitions(InputStream ins)
Read in a set of pharmacophore definitions to create pharmacophore queries.static List<PharmacophoreQuery>
PharmacophoreUtils. readPharmacophoreDefinitions(String filename)
Read in a set of pharmacophore definitions to create pharmacophore queries. -
Uses of CDKException in org.openscience.cdk.qsar
Subclasses of CDKException in org.openscience.cdk.qsar Modifier and Type Class Description class
DescriptorException
Exception that is thrown by descriptor routines when a problem has occurred.Methods in org.openscience.cdk.qsar that throw CDKException Modifier and Type Method Description void
DescriptorEngine. process(IAtomContainer molecule)
Calculates all available (or only those specified) descriptors for a molecule.void
IDescriptor. setParameters(Object[] params)
Sets the parameters for this descriptor. -
Uses of CDKException in org.openscience.cdk.qsar.descriptors.atomic
Methods in org.openscience.cdk.qsar.descriptors.atomic that throw CDKException Modifier and Type Method Description void
AtomDegreeDescriptor. setParameters(Object[] params)
This descriptor does not have any parameter to be set.void
AtomHybridizationDescriptor. setParameters(Object[] params)
This descriptor does have any parameter.void
AtomHybridizationVSEPRDescriptor. setParameters(Object[] params)
This descriptor does have any parameter.void
AtomValenceDescriptor. setParameters(Object[] params)
This descriptor does have any parameter.void
BondsToAtomDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the BondsToAtomDescriptor objectvoid
CovalentRadiusDescriptor. setParameters(Object[] params)
This descriptor does have any parameter.void
DistanceToAtomDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the DistanceToAtomDescriptor objectvoid
EffectiveAtomPolarizabilityDescriptor. setParameters(Object[] params)
This descriptor does have any parameter.void
InductiveAtomicHardnessDescriptor. setParameters(Object[] params)
This descriptor does have any parameter.void
InductiveAtomicSoftnessDescriptor. setParameters(Object[] params)
This descriptor does have any parameter.void
IPAtomicHOSEDescriptor. setParameters(Object[] params)
This descriptor does have any parameter.void
IPAtomicLearningDescriptor. setParameters(Object[] params)
Deprecated.This descriptor does have any parameter.void
IsProtonInAromaticSystemDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the IsProtonInAromaticSystemDescriptor objectvoid
IsProtonInConjugatedPiSystemDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the IsProtonInConjugatedPiSystemDescriptor objectvoid
PartialPiChargeDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the PartialPiChargeDescriptor objectvoid
PartialSigmaChargeDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the PartialSigmaChargeDescriptor objectvoid
PartialTChargeMMFF94Descriptor. setParameters(Object[] params)
This descriptor does not have any parameter to be set.void
PartialTChargePEOEDescriptor. setParameters(Object[] params)
This descriptor does not have any parameter to be set.void
PeriodicTablePositionDescriptor. setParameters(Object[] params)
This descriptor does not have any parameter to be set.void
PiElectronegativityDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the PiElectronegativityDescriptor objectvoid
ProtonAffinityHOSEDescriptor. setParameters(Object[] params)
This descriptor does have any parameter.void
ProtonTotalPartialChargeDescriptor. setParameters(Object[] params)
This descriptor does not have any parameter to be set.void
RDFProtonDescriptor_G3R. setParameters(Object[] params)
Sets the parameters attribute of the RDFProtonDescriptor objectvoid
RDFProtonDescriptor_GDR. setParameters(Object[] params)
Sets the parameters attribute of the RDFProtonDescriptor objectvoid
RDFProtonDescriptor_GHR_topol. setParameters(Object[] params)
Sets the parameters attribute of the RDFProtonDescriptor objectvoid
RDFProtonDescriptor_GHR. setParameters(Object[] params)
Sets the parameters attribute of the RDFProtonDescriptor objectvoid
RDFProtonDescriptor_GSR. setParameters(Object[] params)
Sets the parameters attribute of the RDFProtonDescriptor objectvoid
SigmaElectronegativityDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the SigmaElectronegativityDescriptor objectvoid
StabilizationPlusChargeDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the StabilizationPlusChargeDescriptor objectvoid
VdWRadiusDescriptor. setParameters(Object[] params)
This descriptor does have any parameter. -
Uses of CDKException in org.openscience.cdk.qsar.descriptors.atompair
Methods in org.openscience.cdk.qsar.descriptors.atompair that throw CDKException Modifier and Type Method Description void
PiContactDetectionDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the PiContactDetectionDescriptor object. -
Uses of CDKException in org.openscience.cdk.qsar.descriptors.bond
Methods in org.openscience.cdk.qsar.descriptors.bond that throw CDKException Modifier and Type Method Description void
AtomicNumberDifferenceDescriptor. setParameters(Object[] params)
void
BondPartialPiChargeDescriptor. setParameters(Object[] params)
This descriptor does have any parameter.void
BondPartialSigmaChargeDescriptor. setParameters(Object[] params)
This descriptor does have any parameter.void
BondPartialTChargeDescriptor. setParameters(Object[] params)
This descriptor does have any parameter.void
BondSigmaElectronegativityDescriptor. setParameters(Object[] params)
This descriptor does have any parameter.void
IPBondLearningDescriptor. setParameters(Object[] params)
Deprecated.This descriptor does have any parameter. -
Uses of CDKException in org.openscience.cdk.qsar.descriptors.molecular
Methods in org.openscience.cdk.qsar.descriptors.molecular that throw CDKException Modifier and Type Method Description DescriptorValue
IPMolecularLearningDescriptor. calculatePlus(IAtomContainer container)
Deprecated.It calculates the 1,2,..void
AcidicGroupCountDescriptor. setParameters(Object[] params)
Sets the parameters for this descriptor.void
ALOGPDescriptor. setParameters(Object[] params)
void
AminoAcidCountDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the AminoAcidsCountDescriptor object.void
APolDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the APolDescriptor object.void
AromaticAtomsCountDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the AromaticAtomsCountDescriptor object.void
AromaticBondsCountDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the AromaticBondsCountDescriptor object.void
AtomCountDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the AtomCountDescriptor object.void
AutocorrelationDescriptorCharge. setParameters(Object[] params)
void
AutocorrelationDescriptorMass. setParameters(Object[] params)
void
AutocorrelationDescriptorPolarizability. setParameters(Object[] params)
void
BasicGroupCountDescriptor. setParameters(Object[] params)
Sets the parameters for this descriptor.void
BCUTDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the BCUTDescriptor object.void
BondCountDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the BondCountDescriptor objectvoid
BPolDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the BPolDescriptor objectvoid
CarbonTypesDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the GravitationalIndexDescriptor object.void
ChiChainDescriptor. setParameters(Object[] params)
void
ChiClusterDescriptor. setParameters(Object[] params)
void
ChiPathClusterDescriptor. setParameters(Object[] params)
void
ChiPathDescriptor. setParameters(Object[] params)
void
CPSADescriptor. setParameters(Object[] params)
Sets the parameters attribute of the CPSADescriptor object.void
EccentricConnectivityIndexDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the EccentricConnectivityIndexDescriptor objectvoid
FMFDescriptor. setParameters(Object[] params)
Sets the parameters for this descriptor.void
FractionalCSP3Descriptor. setParameters(Object[] params)
Sets the parameters for this descriptor.void
FractionalPSADescriptor. setParameters(Object[] params)
Sets the parameters for this descriptor.void
FragmentComplexityDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the FragmentComplexityDescriptor object.void
GravitationalIndexDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the GravitationalIndexDescriptor object.void
HBondAcceptorCountDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the HBondAcceptorCountDescriptor object.void
HBondDonorCountDescriptor. setParameters(Object[] params)
Sets the parameter of this HBondDonorCountDescriptor instance.void
HybridizationRatioDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the HybridizationRatioDescriptor object.void
IPMolecularLearningDescriptor. setParameters(Object[] params)
Deprecated.Sets the parameters attribute of the IPMolecularLearningDescriptor objectvoid
JPlogPDescriptor. setParameters(Object[] params)
void
KappaShapeIndicesDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the KappaShapeIndicesDescriptor objectvoid
KierHallSmartsDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the descriptor.void
LargestChainDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the LargestChain object.void
LargestPiSystemDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the LargestPiSystemDescriptor object.void
LengthOverBreadthDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the PetitjeanNumberDescriptor objectvoid
LongestAliphaticChainDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the LongestAliphaticChainDescriptor object.void
MannholdLogPDescriptor. setParameters(Object[] params)
ThisIDescriptor
does not have any parameters.void
MDEDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the WeightDescriptor object.void
MomentOfInertiaDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the MomentOfInertiaDescriptor object.void
PetitjeanNumberDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the PetitjeanNumberDescriptor objectvoid
PetitjeanShapeIndexDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the PetitjeanShapeIndexDescriptor object.void
RotatableBondsCountDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the RotatableBondsCountDescriptor objectvoid
RuleOfFiveDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the RuleOfFiveDescriptor object.void
SmallRingDescriptor. setParameters(Object[] params)
Set parameters: ignored, there are none.void
SpiroAtomCountDescriptor. setParameters(Object[] params)
Sets the parameters for this descriptor.void
TPSADescriptor. setParameters(Object[] params)
Sets the parameters attribute of the TPSADescriptor object.void
VABCDescriptor. setParameters(Object[] params)
Sets the parameters for this descriptor.void
VAdjMaDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the VAdjMaDescriptor objectvoid
WeightDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the WeightDescriptor object.void
WeightedPathDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the WeightedPathDescriptor object.void
WHIMDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the WHIMDescriptor object.void
WienerNumbersDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the WienerNumbersDescriptor object.void
XLogPDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the XLogPDescriptor object.void
ZagrebIndexDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the ZagrebIndexDescriptor object.Constructors in org.openscience.cdk.qsar.descriptors.molecular that throw CDKException Constructor Description ALOGPDescriptor()
-
Uses of CDKException in org.openscience.cdk.qsar.descriptors.protein
Methods in org.openscience.cdk.qsar.descriptors.protein that throw CDKException Modifier and Type Method Description void
TaeAminoAcidDescriptor. setParameters(Object[] params)
Sets the parameters attribute of the TaeAminoAcidDescriptor object. -
Uses of CDKException in org.openscience.cdk.qsar.descriptors.substance
Methods in org.openscience.cdk.qsar.descriptors.substance that throw CDKException Modifier and Type Method Description void
OxygenAtomCountDescriptor. setParameters(Object[] parameters)
Sets the parameters for this descriptor. -
Uses of CDKException in org.openscience.cdk.reaction
Methods in org.openscience.cdk.reaction that throw CDKException Modifier and Type Method Description IReaction
IReactionMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
Initiates the process for the given mechanism.IReactionSet
IReactionProcess. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiates the process for the given Reaction.void
IReactionProcess. setParameterList(List<IParameterReact> params)
Sets the parameters for this reaction.void
ReactionEngine. setParameterList(List<IParameterReact> params)
Returns the current parameter Map for this reaction. -
Uses of CDKException in org.openscience.cdk.reaction.mechanism
Methods in org.openscience.cdk.reaction.mechanism that throw CDKException Modifier and Type Method Description IReaction
AdductionLPMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
Initiates the process for the given mechanism.IReaction
AdductionPBMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
Initiates the process for the given mechanism.IReaction
HeterolyticCleavageMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
Initiates the process for the given mechanism.IReaction
HomolyticCleavageMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
Initiates the process for the given mechanism.IReaction
RadicalSiteIonizationMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
Initiates the process for the given mechanism.IReaction
RadicalSiteRearrangementMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
Initiates the process for the given mechanism.IReaction
RearrangementChargeMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
Initiates the process for the given mechanism.IReaction
RemovingSEofBMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
Initiates the process for the given mechanism.IReaction
RemovingSEofNBMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
Initiates the process for the given mechanism.IReaction
SharingElectronMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
Initiates the process for the given mechanism.IReaction
TautomerizationMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
Initiates the process for the given mechanism. -
Uses of CDKException in org.openscience.cdk.reaction.type
Methods in org.openscience.cdk.reaction.type that throw CDKException Modifier and Type Method Description IReactionSet
AdductionProtonLPReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
AdductionProtonPBReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
AdductionSodiumLPReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
CarbonylEliminationReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
ElectronImpactNBEReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
ElectronImpactPDBReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
ElectronImpactSDBReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
HeterolyticCleavagePBReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
HeterolyticCleavageSBReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
HomolyticCleavageReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
HyperconjugationReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
PiBondingMovementReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RadicalChargeSiteInitiationHReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RadicalChargeSiteInitiationReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RadicalSiteHrAlphaReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RadicalSiteHrBetaReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RadicalSiteHrDeltaReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RadicalSiteHrGammaReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RadicalSiteInitiationHReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RadicalSiteInitiationReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RadicalSiteRrAlphaReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RadicalSiteRrBetaReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RadicalSiteRrDeltaReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RadicalSiteRrGammaReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RearrangementAnionReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RearrangementCationReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RearrangementLonePairReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
RearrangementRadicalReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
SharingAnionReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
SharingChargeDBReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
SharingChargeSBReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
SharingLonePairReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.IReactionSet
TautomerizationReaction. initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process. -
Uses of CDKException in org.openscience.cdk.ringsearch
Methods in org.openscience.cdk.ringsearch that throw CDKException Modifier and Type Method Description void
AllRingsFinder. checkTimeout()
Deprecated.timeout not usedIRingSet
AllRingsFinder. findAllRings(IAtomContainer container)
Compute all rings in the givenIAtomContainer
.IRingSet
AllRingsFinder. findAllRings(IAtomContainer container, int maxRingSize)
Compute all rings up to and including the maxRingSize.IRingSet
AllRingsFinder. findAllRingsInIsolatedRingSystem(IAtomContainer container)
Compute all rings in the givenIAtomContainer
.IRingSet
AllRingsFinder. findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer, int maxRingSize)
Compute all rings up to an including the maxRingSize. -
Uses of CDKException in org.openscience.cdk.similarity
Methods in org.openscience.cdk.similarity that throw CDKException Modifier and Type Method Description static float
DistanceMoment. calculate(IAtomContainer query, IAtomContainer target)
Evaluate the 3D similarity between two molecules.static float
Tanimoto. calculate(double[] features1, double[] features2)
Evaluates the continuous Tanimoto coefficient for two real valued vectors.static float
Tanimoto. calculate(BitSet bitset1, BitSet bitset2)
Evaluates Tanimoto coefficient for two bit sets.static float[]
DistanceMoment. generateMoments(IAtomContainer atomContainer)
Evaluate the 12 descriptors used to characterize the 3D shape of a molecule. -
Uses of CDKException in org.openscience.cdk.smiles
Methods in org.openscience.cdk.smiles that throw CDKException Modifier and Type Method Description String
SmilesGenerator. create(IAtomContainer molecule)
Generate SMILES for the providedmolecule
.String
SmilesGenerator. create(IAtomContainer molecule, int[] order)
Creates a SMILES string of the flavour specified in the constructor and write the output order to the provided array.static String
SmilesGenerator. create(IAtomContainer molecule, int flavour, int[] order)
Creates a SMILES string of the flavour specified as a parameter and write the output order to the provided array.String
SmilesGenerator. create(IReaction reaction)
Create a SMILES for a reaction of the flavour specified in the constructor.String
SmilesGenerator. create(IReaction reaction, int[] ordering)
Create a SMILES for a reaction of the flavour specified in the constructor and write the output order to the provided array.String
SmilesGenerator. createReactionSMILES(IReaction reaction)
Deprecated.IAtomContainer
DeduceBondSystemTool. fixAromaticBondOrders(IAtomContainer atomContainer)
Deprecated.Added missing bond orders based on atom type information.boolean
DeduceBondSystemTool. isOK(IAtomContainer m)
Deprecated.Determines if, according to the algorithms implemented in this class, the given AtomContainer has properly distributed double bonds.IAtomContainer
FixBondOrdersTool. kekuliseAromaticRings(IAtomContainer molecule)
Deprecated.kekuliseAromaticRings - function to add double/single bond order information for molecules having rings containing all atoms marked SP2 or Planar3 hybridisation. -
Uses of CDKException in org.openscience.cdk.smiles.smarts
Methods in org.openscience.cdk.smiles.smarts that throw CDKException Modifier and Type Method Description boolean
SMARTSQueryTool. matches(IAtomContainer atomContainer)
Deprecated.Perform a SMARTS match and check whether the query is present in the target molecule.boolean
SMARTSQueryTool. matches(IAtomContainer atomContainer, boolean forceInitialization)
Deprecated.Perform a SMARTS match and check whether the query is present in the target molecule.void
SMARTSQueryTool. setSmarts(String smarts)
Deprecated.Set a new SMARTS pattern. -
Uses of CDKException in org.openscience.cdk.smsd
Methods in org.openscience.cdk.smsd that throw CDKException Modifier and Type Method Description void
Isomorphism. init(String sourceMolFileName, String targetMolFileName, boolean removeHydrogen, boolean cleanAndConfigureMolecule)
Deprecated.Initialize the query and targetAtomCount mol via mol filesvoid
Isomorphism. init(IAtomContainer reactant, IAtomContainer product, boolean removeHydrogen, boolean cleanAndConfigureMolecule)
Deprecated.initialize query and target molecules.void
Isomorphism. init(IQueryAtomContainer reactant, IAtomContainer product)
Deprecated. -
Uses of CDKException in org.openscience.cdk.smsd.algorithm.mcsplus
Methods in org.openscience.cdk.smsd.algorithm.mcsplus that throw CDKException Modifier and Type Method Description protected List<List<Integer>>
MCSPlus. getOverlaps(IAtomContainer ac1, IAtomContainer ac2, boolean shouldMatchBonds)
Deprecated. -
Uses of CDKException in org.openscience.cdk.smsd.algorithm.rgraph
Methods in org.openscience.cdk.smsd.algorithm.rgraph that throw CDKException Modifier and Type Method Description static CDKRGraph
CDKMCS. buildRGraph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
Deprecated.Builds the CDKRGraph ( resolution graph ), from two atomContainer (description of the two molecules to compare) This is the interface point between the CDK model and the generic MCSS algorithm based on the RGRaph.void
CDKRMapHandler. calculateIsomorphs(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
Deprecated.This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprintvoid
CDKRMapHandler. calculateOverlapsAndReduce(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
Deprecated.This function calculates all the possible combinations of MCSvoid
CDKRMapHandler. calculateOverlapsAndReduceExactMatch(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
Deprecated.This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprintvoid
CDKRMapHandler. calculateSubGraphs(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
Deprecated.This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprintstatic List<CDKRMap>
CDKMCS. checkSingleAtomCases(IAtomContainer sourceGraph, IAtomContainer targetGraph)
Deprecated.Checks for single atom cases before doing subgraph/isomorphism searchstatic List<CDKRMap>
CDKMCS. getIsomorphAtomsMap(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
Deprecated.Returns the first isomorph 'atom mapping' found for targetGraph in sourceGraph.static List<CDKRMap>
CDKMCS. getIsomorphMap(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
Deprecated.Returns the first isomorph mapping found or null.static List<List<CDKRMap>>
CDKMCS. getIsomorphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
Deprecated.Returns all the isomorph 'mappings' found between two atom containers.static List<IAtomContainer>
CDKMCS. getOverlaps(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
Deprecated.Returns all the maximal common substructure between 2 atom containers.static List<CDKRMap>
CDKMCS. getSubgraphAtomsMap(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
Deprecated.Returns the first subgraph 'atom mapping' found for targetGraph in sourceGraph.static List<List<CDKRMap>>
CDKMCS. getSubgraphAtomsMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
Deprecated.Returns all subgraph 'atom mappings' found for targetGraph in sourceGraph.static List<CDKRMap>
CDKMCS. getSubgraphMap(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
Deprecated.Returns the first subgraph 'bondA1 mapping' found for targetGraph in sourceGraph.static List<List<CDKRMap>>
CDKMCS. getSubgraphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
Deprecated.Returns all the subgraph 'bondA1 mappings' found for targetGraph in sourceGraph.protected IAtomContainerSet
CDKMCSHandler. getUncommon(IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds)
Deprecated.protected IAtomContainerSet
CDKSubGraphHandler. getUncommon(IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds)
Deprecated.static boolean
CDKMCS. isIsomorph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
Deprecated.Tests if sourceGraph and targetGraph are isomorph.static boolean
CDKMCS. isSubgraph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
Deprecated.Tests if targetGraph atom subgraph of sourceGraph.void
CDKRGraph. parse(BitSet sourceBitSet, BitSet targetBitSet, boolean findAllStructure, boolean findAllMap, TimeManager timeManager)
Deprecated.Parsing of the CDKRGraph.static List<List<CDKRMap>>
CDKMCS. search(IAtomContainer sourceGraph, IAtomContainer targetGraph, BitSet sourceBitSet, BitSet targetBitSet, boolean findAllStructure, boolean findAllMap, boolean shouldMatchBonds)
Deprecated.General Rgraph parsing method (usually not used directly) This method is the entry point for the recursive search adapted to the atom container input. -
Uses of CDKException in org.openscience.cdk.smsd.algorithm.single
Methods in org.openscience.cdk.smsd.algorithm.single that throw CDKException Modifier and Type Method Description protected List<Map<IAtom,IAtom>>
SingleMapping. getOverLaps(IAtomContainer source, IAtomContainer target, boolean removeHydrogen)
Deprecated.Returns single mapping solutions.protected List<Map<IAtom,IAtom>>
SingleMapping. getOverLaps(IQueryAtomContainer source, IAtomContainer target, boolean removeHydrogen)
Deprecated.Returns single mapping solutions. -
Uses of CDKException in org.openscience.cdk.smsd.filters
Methods in org.openscience.cdk.smsd.filters that throw CDKException Modifier and Type Method Description void
ChemicalFilters. sortResultsByEnergies()
Deprecated.Sort MCS solution by bond breaking energy.void
ChemicalFilters. sortResultsByStereoAndBondMatch()
Deprecated.Sort MCS solution by stereo and bond type matches. -
Uses of CDKException in org.openscience.cdk.smsd.interfaces
Methods in org.openscience.cdk.smsd.interfaces that throw CDKException Modifier and Type Method Description abstract void
AbstractMCS. init(IAtomContainer source, IAtomContainer target, boolean removeHydrogen, boolean cleanAndConfigureMolecule)
Deprecated.initialize query and target molecules.abstract void
AbstractMCS. init(IQueryAtomContainer source, IAtomContainer target)
Deprecated.initialize query and target molecules.void
IMCSBase. set(IQueryAtomContainer source, IAtomContainer target)
Deprecated.Initialise the query and target molecule.void
IMCSBase. set(MolHandler source, MolHandler target)
Deprecated.Initialise the query and target molecule. -
Uses of CDKException in org.openscience.cdk.smsd.ring
Methods in org.openscience.cdk.smsd.ring that throw CDKException Modifier and Type Method Description IRingSet
HanserRingFinder. getRingSet(IAtomContainer molecule)
Deprecated.Returns Ring set based on Hanser Ring Finding methodIRingSet
RingFinder. getRingSet(IAtomContainer molecule)
Deprecated.Returns CDK object Ring set based on Hanser Ring Finding method -
Uses of CDKException in org.openscience.cdk.smsd.tools
Methods in org.openscience.cdk.smsd.tools that throw CDKException Modifier and Type Method Description static BondEnergies
BondEnergies. getInstance()
Deprecated.Returns Singleton pattern instance for the Bond Energy classstatic void
ExtAtomContainerManipulator. percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Deprecated.Convenience method to perceive atom types for allIAtom
s in theIAtomContainer
, using theCDKAtomTypeMatcher
. -
Uses of CDKException in org.openscience.cdk.structgen
Methods in org.openscience.cdk.structgen that throw CDKException Modifier and Type Method Description IAtomContainer
SingleStructureRandomGenerator. generate()
Generates a random structure based on the atoms in the given IAtomContainer. -
Uses of CDKException in org.openscience.cdk.structgen.maygen
Methods in org.openscience.cdk.structgen.maygen that throw CDKException Modifier and Type Method Description void
Maygen. degree2graph()
Building a degree 2 graph for a single element type.void
Maygen. distributeSulfurOxygen(String localFormula)
void
Maygen. distributeSymbols(int oxy, int sul, int nextSize, int currentSize, int reversedLength, int leftEquivalents, int rightEquivalents, boolean reversalIsSmaller)
Main function for the distribution of atom symbols: O and S for OnSm form formulae.void
Maygen. distributeSymbolsNextSizeAboveGraphSize(int currentSize, boolean reversalIsSmaller)
void
Maygen. doRun(String localFormula)
void
Maygen. emit(IAtomContainer mol)
Emits a molecule to whomever is listening.int[][]
Maygen. forward(IAtomContainer ac, String[] symbolArrayCopy, int[][] a, int[] indices, int[] degrees, int[] initialPartition, int[][] partitionList, boolean[] callForward, int[] connectivityIndices, boolean[] learningFromConnectivity, int[] nonCanonicalIndices, List<ArrayList<Permutation>> formerPermutations, int[] hydrogens, int[] partSize, int[] r, int[] y, int[] z, int[][][] max, int[][][] l, int[][][] c, int[][] ys, int[][] zs, boolean[] learningFromCanonicalTest)
Setting successor indices entry if there is a possible filling.int[][]
Maygen. forward(IAtomContainer ac, String[] symbolArrayCopy, int lInverse, int cInverse, int maximalX, int i, int j, int[][] a, int[] indices, int[] initialPartition, int[][] partitionList, boolean[] callForward, int[] connectivityIndices, boolean[] learningFromConnectivity, int[] nonCanonicalIndices, List<ArrayList<Permutation>> formerPermutations, int[] hydrogens, int[] partSize, int[] r, int[] y, int[] z, int[][][] max, int[][][] l, int[][][] c, int[][] ys, int[][] zs, boolean[] learningFromCanonicalTest)
void
Maygen. generate(IAtomContainer ac, String[] symbolArrayCopy, int[] degreeList, int[] initialPartition, int[][] partitionList, int[] connectivityIndices, boolean[] learningFromConnectivity, int[] nonCanonicalIndices, List<ArrayList<Permutation>> formerPermutations, int[] hydrogens, int[] partSize, int[] r, int[] y, int[] z, int[][] ys, int[][] zs, boolean[] learningFromCanonicalTest)
Initialization of global variables for the generate of structures for given degree list.void
Maygen. nextStep(IAtomContainer ac, String[] symbolArrayCopy, int[][] a, int[] indices, int[] degrees, int[] initialPartition, int[][] partitionList, boolean[] callForward, int[] connectivityIndices, boolean[] learningFromConnectivity, int[] nonCanonicalIndices, List<ArrayList<Permutation>> formerPermutations, int[] hydrogens, int[] partSize, int[] r, int[] y, int[] z, int[][][] max, int[][][] l, int[][][] c, int[][] ys, int[][] zs, boolean[] learningFromCanonicalTest, boolean[] flag)
Calling foward or backward function in a nextstep function.void
Maygen. processFormula(String normalizedLocalFormula, long startTime)
void
Maygen. processRun(String normalizedLocalFormula, long startTime)
void
Maygen. run()
Main function to initialize the global variables and calling the generate function.void
Maygen. runDistributeSymbols(int nextSize, int currentSize, int reversedLength, int leftEquivalents, int rightEquivalents, boolean reversalIsSmaller, int oxy2, int sul2, int reverse)
void
Maygen. runDistributeSymbolsCheckNodeLabels(int oxy, int sul, int nextSize, int currentSize, int reversedLength, int leftEquivalents, boolean reversalIsSmaller)
void
Maygen. writeSingleAtom(int[] hydrogens)
Writing the single atom molecule in a output file. -
Uses of CDKException in org.openscience.cdk.structgen.stochastic
Methods in org.openscience.cdk.structgen.stochastic that throw CDKException Modifier and Type Method Description IAtomContainer
PartialFilledStructureMerger. generate(IAtomContainerSet atomContainers)
Randomly generates a single, connected, correctly bonded structure from a number of fragments. -
Uses of CDKException in org.openscience.cdk.structgen.stochastic.operator
Methods in org.openscience.cdk.structgen.stochastic.operator that throw CDKException Modifier and Type Method Description List<IAtomContainer>
CrossoverMachine. doCrossover(IAtomContainer dad, IAtomContainer mom)
Performs the n point crossover of twoIAtomContainer
. -
Uses of CDKException in org.openscience.cdk.tautomers
Methods in org.openscience.cdk.tautomers that throw CDKException Modifier and Type Method Description List<IAtomContainer>
InChITautomerGenerator. getTautomers(IAtomContainer mol)
Public method to get tautomers for an input molecule, based on the InChI which will be calculated by JNI-InChI.List<IAtomContainer>
InChITautomerGenerator. getTautomers(IAtomContainer mol, String inchi)
Deprecated.useInChITautomerGenerator.getTautomers(IAtomContainer)
directly -
Uses of CDKException in org.openscience.cdk.tools
Methods in org.openscience.cdk.tools that throw CDKException Modifier and Type Method Description void
CDKHydrogenAdder. addImplicitHydrogens(IAtomContainer container)
Sets implicit hydrogen counts for all atoms in the given IAtomContainer.void
CDKHydrogenAdder. addImplicitHydrogens(IAtomContainer container, IAtom atom)
Sets the implicit hydrogen count for the indicated IAtom in the given IAtomContainer.boolean
LonePairElectronChecker. allSaturated(IAtomContainer ac)
Determines of all atoms on the AtomContainer have the right number the lone pair electrons.boolean
SaturationChecker. allSaturated(IAtomContainer ac)
boolean
SmilesValencyChecker. allSaturated(IAtomContainer ac)
boolean
AtomTypeAwareSaturationChecker. bondOrderCanBeIncreased(IBond bond, IAtomContainer atomContainer)
Check if the bond order can be increased.int
SaturationChecker. calculateNumberOfImplicitHydrogens(IAtom atom)
int
SaturationChecker. calculateNumberOfImplicitHydrogens(IAtom atom, double bondOrderSum, double singleElectronSum, List<IBond> connectedBonds, boolean throwExceptionForUnknowAtom)
Calculate the number of missing hydrogens by subtracting the number of bonds for the atom from the expected number of bonds.int
SaturationChecker. calculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container)
Calculate the number of missing hydrogens by subtracting the number of bonds for the atom from the expected number of bonds.int
SaturationChecker. calculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container, boolean throwExceptionForUnknowAtom)
int
SmilesValencyChecker. calculateNumberOfImplicitHydrogens(IAtom atom, double bondOrderSum, IBond.Order maxBondOrder, int neighbourCount)
Calculates the number of hydrogens that can be added to the given atom to fullfil the atom's valency.int
SmilesValencyChecker. calculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container)
static IBioPolymer
ProteinBuilderTool. createProtein(String sequence)
Creates a BioPolymer from a sequence of amino acid as identified by a the sequence of their one letter codes.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.void
AtomTypeAwareSaturationChecker. decideBondOrder(IAtomContainer atomContainer)
This method decides the bond order on bonds that has theSINGLE_OR_DOUBLE
-flag raised.void
AtomTypeAwareSaturationChecker. decideBondOrder(IAtomContainer atomContainer, boolean atomsSaturated)
This method decides the bond order on bonds that has theSINGLE_OR_DOUBLE
-flag raised.protected AtomTypeFactory
SaturationChecker. getAtomTypeFactory(IChemObjectBuilder builder)
protected AtomTypeFactory
SmilesValencyChecker. getAtomTypeFactory(IChemObjectBuilder builder)
double
BremserOneSphereHOSECodePredictor. getConfidenceLimit(String hoseCode)
double
SaturationChecker. getCurrentMaxBondOrder(IAtom atom, IAtomContainer ac)
Returns the currently maximum formable bond order for this atom.String
HOSECodeGenerator. getHOSECode(IAtomContainer ac, IAtom root, int noOfSpheres)
String
HOSECodeGenerator. getHOSECode(IAtomContainer ac, IAtom root, int noOfSpheres, boolean ringsize)
double
AtomTypeAwareSaturationChecker. getMaxNoOfBonds(IAtom atom)
This method calculates the number of bonds that anIAtom
can have.static double[]
IonizationPotentialTool. getQSARs(IAtomContainer container, IAtom atom)
Deprecated.Get the results of 7 qsar descriptors been applied.static double[]
IonizationPotentialTool. getQSARs(IAtomContainer container, IBond bond)
Deprecated.Get the results of 7 qsar descriptors been applied.List<IAtom>[]
HOSECodeGenerator. getSpheres(IAtomContainer ac, IAtom root, int noOfSpheres, boolean ringsize)
This method is intended to be used to get the atoms around an atom in spheres.boolean
SaturationChecker. hasPerfectConfiguration(IAtom atom, IAtomContainer ac)
boolean
SaturationChecker. isOverSaturated(IAtom atom, IAtomContainer ac)
Checks if the current atom has exceeded its bond order sum value.boolean
AtomTypeAwareSaturationChecker. isSaturated(IAtomContainer container)
boolean
AtomTypeAwareSaturationChecker. isSaturated(IAtom atom, IAtomContainer container)
boolean
CDKValencyChecker. isSaturated(IAtomContainer atomContainer)
boolean
CDKValencyChecker. isSaturated(IAtom atom, IAtomContainer container)
boolean
IValencyChecker. isSaturated(IAtomContainer ac)
boolean
IValencyChecker. isSaturated(IAtom atom, IAtomContainer container)
boolean
LonePairElectronChecker. isSaturated(IAtomContainer container)
Determines of all atoms on the AtomContainer have the right number the lone pair electrons.boolean
LonePairElectronChecker. isSaturated(IAtom atom, IAtomContainer ac)
Checks if an Atom is saturated their lone pair electrons by comparing it with known AtomTypes.boolean
SaturationChecker. isSaturated(IAtomContainer container)
Determines of all atoms on the AtomContainer are saturated.boolean
SaturationChecker. isSaturated(IAtom atom, IAtomContainer ac)
Checks whether an Atom is saturated by comparing it with known AtomTypes.boolean
SaturationChecker. isSaturated(IBond bond, IAtomContainer atomContainer)
Returns whether a bond is saturated.boolean
SmilesValencyChecker. isSaturated(IAtomContainer container)
Determines of all atoms on the AtomContainer are saturated.boolean
SmilesValencyChecker. isSaturated(IAtom atom, IAtomContainer container)
Checks whether an Atom is saturated by comparing it with known AtomTypes.boolean
SmilesValencyChecker. isSaturated(IBond bond, IAtomContainer atomContainer)
Returns whether a bond is saturated.boolean
SaturationChecker. isUnsaturated(IBond bond, IAtomContainer atomContainer)
Returns whether a bond is unsaturated.boolean
SmilesValencyChecker. isUnsaturated(IBond bond, IAtomContainer atomContainer)
Returns whether a bond is unsaturated.void
SaturationChecker. newSaturate(IAtomContainer atomContainer)
Saturates a molecule by setting appropriate bond orders.boolean
SaturationChecker. newSaturate(IBond[] bonds, IAtomContainer atomContainer)
Saturates a set of Bonds in an AtomContainer.boolean
SaturationChecker. newSaturate(IBond bond, IAtomContainer atomContainer)
Saturate atom by adjusting its bond orders.double
BremserOneSphereHOSECodePredictor. predict(String hoseCode)
String
BremserOneSphereHOSECodePredictor. predictFull(String hoseCode)
static double
IonizationPotentialTool. predictIP(IAtomContainer container, IAtom atom)
Deprecated.Method which is predict the Ionization Potential from given atom.static double
IonizationPotentialTool. predictIP(IAtomContainer container, IBond bond)
Deprecated.Method which is predict the Ionization Potential from given atom.void
AtomTypeAwareSaturationChecker. saturate(IAtomContainer container)
void
IDeduceBondOrderTool. saturate(IAtomContainer ac)
void
LonePairElectronChecker. saturate(IAtomContainer atomContainer)
Saturates a molecule by setting appropriate number lone pair electrons.void
LonePairElectronChecker. saturate(IAtom atom, IAtomContainer ac)
Saturates an IAtom by adding the appropriate number lone pairs.void
SaturationChecker. saturate(IAtomContainer atomContainer)
The method is known to fail for certain compounds.void
SmilesValencyChecker. saturate(IAtomContainer atomContainer)
Saturates a molecule by setting appropriate bond orders.boolean
SmilesValencyChecker. saturate(IBond[] bonds, IAtomContainer atomContainer)
Saturates a set of Bonds in an AtomContainer.boolean
SmilesValencyChecker. saturateByIncreasingBondOrder(IBond bond, IAtomContainer atomContainer)
Tries to saturate a bond by increasing its bond orders by 1.0.void
SaturationChecker. saturateRingSystems(IAtomContainer atomContainer)
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Uses of CDKException in org.openscience.cdk.tools.manipulator
Methods in org.openscience.cdk.tools.manipulator that throw CDKException Modifier and Type Method Description static void
AminoAcidManipulator. addAcidicOxygen(IAminoAcid acid)
Adds the singly bonded oxygen from the acid group of the AminoAcid.static IAtom
AtomContainerManipulator. getAtomById(IAtomContainer ac, String id)
Returns an atom in an atomcontainer identified by idstatic double
MolecularFormulaManipulator. getDBE(IMolecularFormula formula)
Returns the number of double bond equivalents in this molecule.static void
ReactionManipulator. perceiveAtomTypesAndConfigureAtoms(IReaction reaction)
static void
ReactionManipulator. perceiveAtomTypesAndConfigureUnsetProperties(IReaction reaction)
static void
AtomContainerManipulator. percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Convenience method to perceive atom types for allIAtom
s in theIAtomContainer
, using theCDKAtomTypeMatcher
.static void
AtomContainerManipulator. percieveAtomTypesAndConfigureUnsetProperties(IAtomContainer container)
Convenience method to perceive atom types for allIAtom
s in theIAtomContainer
, using theCDKAtomTypeMatcher
.static void
AminoAcidManipulator. removeAcidicOxygen(IAminoAcid acid)
Removes the singly bonded oxygen from the acid group of the AminoAcid.
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