| Modifier and Type | Method and 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 a
molecule which this model determined were
aromatic. |
static void |
Kekulization.kekulize(IAtomContainer ac)
Assign a Kekulé representation to the aromatic systems of a compound.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomType |
MMFF94AtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atomInterface)
Deprecated.
Assign the mmff94 atom type to a given atom.
|
IAtomType |
MM2AtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atomInterface)
Deprecated.
Assign the mm2 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 |
IAtomTypeMatcher.findMatchingAtomType(IAtomContainer container,
IAtom atom)
Method that assigns an atom type to a given atom belonging to an atom
container.
|
IAtomType |
CDKAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atom)
Method that assigns an atom type to a given atom belonging to an atom
container.
|
IAtomType |
SybylAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atom)
Sybyl atom type perception for a single atom.
|
IAtomType[] |
MMFF94AtomTypeMatcher.findMatchingAtomTypes(IAtomContainer atomContainer)
Deprecated.
|
IAtomType[] |
MM2AtomTypeMatcher.findMatchingAtomTypes(IAtomContainer atomContainer)
Deprecated.
|
IAtomType[] |
StructGenMatcher.findMatchingAtomTypes(IAtomContainer atomContainer) |
IAtomType[] |
IAtomTypeMatcher.findMatchingAtomTypes(IAtomContainer container)
Method that assigns atom types to atoms in the given atom container.
|
IAtomType[] |
CDKAtomTypeMatcher.findMatchingAtomTypes(IAtomContainer atomContainer)
Method that assigns atom types to atoms in the given atom container.
|
IAtomType[] |
EStateAtomTypeMatcher.findMatchingAtomTypes(IAtomContainer atomContainer) |
IAtomType[] |
SybylAtomTypeMatcher.findMatchingAtomTypes(IAtomContainer atomContainer)
Method that assigns atom types to atoms in the given atom container.
|
List<IAtomType> |
StructGenAtomTypeGuesser.possibleAtomTypes(IAtomContainer atomContainer,
IAtom atom)
Finds the AtomType matching the Atom's element symbol, formal charge and
hybridization state.
|
List<IAtomType> |
IAtomTypeGuesser.possibleAtomTypes(IAtomContainer container,
IAtom atom)
Method that returns an iterator with a suitable list of atom types
given the provided atom.
|
| Modifier and Type | Method and 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 charges
|
void |
MMFF94PartialCharges.calculateCharges(IAtomContainer container) |
void |
IElectronicPropertyCalculator.calculateCharges(IAtomContainer container) |
void |
GasteigerPEPEPartialCharges.calculateCharges(IAtomContainer container) |
void |
AtomTypeCharges.calculateCharges(IAtomContainer container) |
void |
GasteigerMarsiliPartialCharges.calculateCharges(IAtomContainer container) |
void |
InductivePartialCharges.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.
|
| Modifier and Type | Method and Description |
|---|---|
IAtom |
AtomTypeFactory.configure(IAtom atom)
Configures an atom.
|
| Modifier and Type | Method and Description |
|---|---|
Depiction |
DepictionGenerator.depict(IAtomContainer mol)
Depict a single molecule.
|
Depiction |
DepictionGenerator.depict(IReaction rxn)
Depict a reaction.
|
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.
|
| Modifier and Type | Class and 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 |
| Modifier and Type | Method and Description |
|---|---|
void |
CircularFingerprinter.calculate(IAtomContainer mol)
Calculates the fingerprints for the given
IAtomContainer, 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 |
LingoFingerprinter.getBitFingerprint(IAtomContainer iAtomContainer) |
IBitFingerprint |
SignatureFingerprinter.getBitFingerprint(IAtomContainer atomContainer) |
IBitFingerprint |
SubstructureFingerprinter.getBitFingerprint(IAtomContainer atomContainer)
Returns the bit fingerprint for the given
IAtomContainer. |
IBitFingerprint |
CircularFingerprinter.getBitFingerprint(IAtomContainer mol)
Calculates the circular fingerprint for the given
IAtomContainer, and folds the result into a single bitset
(see getSize()). |
IBitFingerprint |
ExtendedFingerprinter.getBitFingerprint(IAtomContainer container)
Generates a fingerprint of the default size for the given
AtomContainer, using path and ring metrics.
|
IBitFingerprint |
MACCSFingerprinter.getBitFingerprint(IAtomContainer container)
Returns the bit fingerprint for the given
IAtomContainer. |
IBitFingerprint |
ShortestPathFingerprinter.getBitFingerprint(IAtomContainer ac)
Generates a shortest path based BitSet fingerprint for the given AtomContainer.
|
IBitFingerprint |
EStateFingerprinter.getBitFingerprint(IAtomContainer atomContainer)
Returns the bit fingerprint for the given
IAtomContainer. |
IBitFingerprint |
AtomPairs2DFingerprinter.getBitFingerprint(IAtomContainer container) |
IBitFingerprint |
PubchemFingerprinter.getBitFingerprint(IAtomContainer atomContainer)
Calculate 881 bit Pubchem fingerprint for a molecule.
|
IBitFingerprint |
Fingerprinter.getBitFingerprint(IAtomContainer container)
Generates a fingerprint of the default size for the given AtomContainer.
|
IBitFingerprint |
IFingerprinter.getBitFingerprint(IAtomContainer container)
Returns the bit fingerprint for the given
IAtomContainer. |
IBitFingerprint |
Fingerprinter.getBitFingerprint(IAtomContainer container,
AllRingsFinder ringFinder)
Generates a fingerprint of the default size for the given AtomContainer.
|
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.
|
ICountFingerprint |
LingoFingerprinter.getCountFingerprint(IAtomContainer container) |
ICountFingerprint |
SignatureFingerprinter.getCountFingerprint(IAtomContainer container) |
ICountFingerprint |
SubstructureFingerprinter.getCountFingerprint(IAtomContainer atomContainer)
Returns the count fingerprint for the given
IAtomContainer. |
ICountFingerprint |
CircularFingerprinter.getCountFingerprint(IAtomContainer mol)
Calculates the circular fingerprint for the given
IAtomContainer, and returns a datastructure that enumerates all
of the fingerprints, and their counts (i.e. |
ICountFingerprint |
ExtendedFingerprinter.getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the given
IAtomContainer. |
ICountFingerprint |
MACCSFingerprinter.getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the given
IAtomContainer. |
ICountFingerprint |
ShortestPathFingerprinter.getCountFingerprint(IAtomContainer iac) |
ICountFingerprint |
EStateFingerprinter.getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the given
IAtomContainer. |
ICountFingerprint |
AtomPairs2DFingerprinter.getCountFingerprint(IAtomContainer mol) |
ICountFingerprint |
PubchemFingerprinter.getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the given
IAtomContainer. |
ICountFingerprint |
Fingerprinter.getCountFingerprint(IAtomContainer container) |
ICountFingerprint |
IFingerprinter.getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the given
IAtomContainer. |
BitSet |
ExtendedFingerprinter.getFingerprint(IAtomContainer mol) |
BitSet |
AbstractFingerprinter.getFingerprint(IAtomContainer mol)
Generate a binary fingerprint as a bit.
|
BitSet |
IFingerprinter.getFingerprint(IAtomContainer mol)
Generate a binary fingerprint as a bit.
|
Map<String,Integer> |
LingoFingerprinter.getRawFingerprint(IAtomContainer atomContainer) |
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.
|
Map<String,Integer> |
CircularFingerprinter.getRawFingerprint(IAtomContainer mol)
Invalid: it is not appropriate to convert the integer hash codes into strings.
|
Map<String,Integer> |
ExtendedFingerprinter.getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.
|
Map<String,Integer> |
MACCSFingerprinter.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> |
EStateFingerprinter.getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.
|
Map<String,Integer> |
AtomPairs2DFingerprinter.getRawFingerprint(IAtomContainer mol) |
Map<String,Integer> |
PubchemFingerprinter.getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.
|
Map<String,Integer> |
Fingerprinter.getRawFingerprint(IAtomContainer iAtomContainer)
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.
|
| Modifier and Type | Method and 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.
|
| Modifier and Type | Method and Description |
|---|---|
void |
MassToFormulaTool.setRestrictions(List<IRule> rulesNew)
Deprecated.
Set the restrictions that must be presents in the molecular formula.
|
| Modifier and Type | Method and 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 |
NitrogenRule.setParameters(Object[] params)
Sets the parameters attribute of the NitrogenRule object.
|
void |
MMElementRule.setParameters(Object[] params)
Sets the parameters attribute of the MMElementRule object.
|
void |
IRule.setParameters(Object[] params)
Sets the parameters for this rule.
|
void |
RDBERule.setParameters(Object[] params)
Sets the parameters attribute of the RDBE object.
|
void |
IsotopePatternRule.setParameters(Object[] params)
Sets the parameters attribute of the IsotopePatternRule 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 |
NitrogenRule.validate(IMolecularFormula formula)
Validate the nitrogen rule of this IMolecularFormula.
|
double |
MMElementRule.validate(IMolecularFormula formula)
Validate the occurrence of this IMolecularFormula.
|
double |
IRule.validate(IMolecularFormula formula)
Analyze the validity for the given IMolecularFormula.
|
double |
RDBERule.validate(IMolecularFormula formula)
Validate the RDBRule of this IMolecularFormula.
|
double |
IsotopePatternRule.validate(IMolecularFormula formula)
Validate the isotope pattern of this IMolecularFormula.
|
double |
ToleranceRangeRule.validate(IMolecularFormula formula)
Validate the Tolerance Range of this IMolecularFormula.
|
boolean |
RDBERule.validate(IMolecularFormula formula,
double value)
Validate the ion state.
|
| Modifier and Type | Method and 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.
|
| Modifier and Type | Method and 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.
|
| Constructor and 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.
|
| Modifier and Type | Method and 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.
|
| Modifier and Type | Method and Description |
|---|---|
static double |
VABCVolume.calculate(IAtomContainer molecule)
Calculates the volume for the given
IAtomContainer. |
| Modifier and Type | Method and 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.
|
| Modifier and Type | Method and 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).
|
| Modifier and Type | Method and Description |
|---|---|
void |
RebondTool.rebond(IAtomContainer container)
Rebonding using a Binary Space Partition Tree.
|
| Modifier and Type | Method and Description |
|---|---|
protected void |
InChIToStructure.generateAtomContainerFromInchi(IChemObjectBuilder builder)
Gets structure from InChI, and converts InChI library data structure
into an IAtomContainer.
|
InChIGenerator |
InChIGeneratorFactory.getInChIGenerator(IAtomContainer container)
Gets an Standard InChI generator for a
IAtomContainer. |
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,
List<INCHI_OPTION> options)
|
InChIGenerator |
InChIGeneratorFactory.getInChIGenerator(IAtomContainer container,
String options)
Gets InChI generator for CDK IAtomContainer.
|
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,
List<String> options)
Gets structure generator for an InChI string.
|
InChIToStructure |
InChIGeneratorFactory.getInChIToStructure(String inchi,
IChemObjectBuilder builder,
String options)
Gets structure generator for an InChI string.
|
static InChIGeneratorFactory |
InChIGeneratorFactory.getInstance()
Gives the one
InChIGeneratorFactory instance,
if needed also creates it. |
| Constructor and Description |
|---|
InChIGenerator(IAtomContainer atomContainer,
boolean ignoreAromaticBonds)
Constructor.
|
InChIGenerator(IAtomContainer atomContainer,
io.github.dan2097.jnainchi.InchiOptions options,
boolean ignoreAromaticBonds) |
InChIGenerator(IAtomContainer atomContainer,
List<INCHI_OPTION> opts,
boolean ignoreAromaticBonds)
Deprecated.
|
InChIGenerator(IAtomContainer atomContainer,
String optStr,
boolean ignoreAromaticBonds)
Constructor.
|
InChIToStructure(String inchi,
IChemObjectBuilder builder)
Constructor.
|
InChIToStructure(String inchi,
IChemObjectBuilder builder,
io.github.dan2097.jnainchi.InchiOptions options)
Constructor.
|
InChIToStructure(String inchi,
IChemObjectBuilder builder,
List<String> options)
Constructor.
|
InChIToStructure(String inchi,
IChemObjectBuilder builder,
String options)
Constructor.
|
| Modifier and Type | Method and Description |
|---|---|
void |
DefaultChemObjectReader.handleError(String message)
Redirects an error message to the
IChemObjectReaderErrorHandler. |
void |
IChemObjectReader.handleError(String message)
Redirects an error message to the
IChemObjectReaderErrorHandler. |
void |
DefaultChemObjectReader.handleError(String message,
Exception exception)
Redirects an error message to the
IChemObjectReaderErrorHandler. |
void |
IChemObjectReader.handleError(String message,
Exception exception)
Redirects an error message to the
IChemObjectReaderErrorHandler. |
void |
DefaultChemObjectReader.handleError(String message,
int row,
int colStart,
int colEnd)
Redirects an error message to the
IChemObjectReaderErrorHandler. |
void |
IChemObjectReader.handleError(String message,
int row,
int colStart,
int colEnd)
Redirects an error message to the
IChemObjectReaderErrorHandler. |
void |
DefaultChemObjectReader.handleError(String message,
int row,
int colStart,
int colEnd,
Exception exception)
Redirects an error message to the
IChemObjectReaderErrorHandler. |
void |
IChemObjectReader.handleError(String message,
int row,
int colStart,
int colEnd,
Exception exception)
Redirects an error message to the
IChemObjectReaderErrorHandler. |
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> |
MoSSOutputReader.read(T object)
Read a
IAtomContainerSet from the input source. |
<T extends IChemObject> |
SMILESReader.read(T object)
Reads the content from a XYZ input.
|
<T extends IChemObject> |
PDBReader.read(T oObj)
Takes an object which subclasses IChemObject, e.g.
|
<T extends IChemObject> |
PCSubstanceXMLReader.read(T object) |
<T extends IChemObject> |
XYZReader.read(T object)
reads the content from a XYZ input.
|
<T extends IChemObject> |
CMLReader.read(T object)
Read a IChemObject from input.
|
<T extends IChemObject> |
PCCompoundASNReader.read(T object) |
<T extends IChemObject> |
GhemicalMMReader.read(T object) |
<T extends IChemObject> |
PCCompoundXMLReader.read(T object) |
<T extends IChemObject> |
ShelXReader.read(T object)
Read a ChemFile from input.
|
<T extends IChemObject> |
CIFReader.read(T object)
Read a ChemFile from input.
|
<T extends IChemObject> |
PMPReader.read(T object)
reads the content from a PMP input.
|
<T extends IChemObject> |
HINReader.read(T object)
Reads the content from a HIN input.
|
<T extends IChemObject> |
Gaussian03Reader.read(T object) |
<T extends IChemObject> |
CTXReader.read(T object) |
<T extends IChemObject> |
Gaussian98Reader.read(T object) |
<T extends IChemObject> |
Mol2Reader.read(T object) |
<T extends IChemObject> |
Mopac7Reader.read(T object) |
<T extends IChemObject> |
MDLV2000Reader.read(T object)
Takes an object which subclasses IChemObject, e.g.
|
<T extends IChemObject> |
MDLRXNReader.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> |
MDLV3000Reader.read(T object) |
<T extends IChemObject> |
MDLRXNV3000Reader.read(T object) |
<T extends IChemObject> |
MDLRXNV2000Reader.read(T object)
Takes an object which subclasses IChemObject, e.g.Molecule, and will read
this (from file, database, internet etc).
|
<T extends IChemObject> |
RGroupQueryReader.read(T object)
Check input IChemObject and proceed to parse.
|
<T extends IChemObject> |
MDLReader.read(T object)
Deprecated.
Takes an object which subclasses IChemObject, e.g.
|
<T extends IChemObject> |
CrystClustReader.read(T object) |
<T extends IChemObject> |
ZMatrixReader.read(T object)
Returns a IChemObject of type object bye reading from
the input.
|
<T extends IChemObject> |
INChIPlainTextReader.read(T object)
Reads a IChemObject of type object from input.
|
<T extends IChemObject> |
VASPReader.read(T object) |
<T extends IChemObject> |
INChIReader.read(T object)
Reads a IChemObject of type object from input.
|
<T extends IChemObject> |
GamessReader.read(T object) |
<T extends IChemObject> |
ISimpleChemObjectReader.read(T object)
Reads an IChemObject of type "object" from input.
|
void |
MDLV3000Reader.readAtomBlock(IAtomContainer readData)
Reads the atoms, coordinates and charges.
|
void |
MDLV3000Reader.readBondBlock(IAtomContainer readData)
Reads the bond atoms, order and stereo configuration.
|
IAtomContainer |
MDLV3000Reader.readConnectionTable(IChemObjectBuilder builder) |
String |
MDLV3000Reader.readHeader(IAtomContainer readData) |
String |
MDLV3000Reader.readLine() |
IAtomContainer |
MDLV3000Reader.readMolecule(IChemObjectBuilder builder) |
void |
MDLV3000Reader.readSGroup(IAtomContainer readData)
Reads labels.
|
void |
MoSSOutputReader.setReader(InputStream input)
Sets the InputStream from which this ChemObjectReader should read
the contents.
|
void |
SMILESReader.setReader(InputStream input) |
void |
PDBReader.setReader(InputStream input) |
void |
PCSubstanceXMLReader.setReader(InputStream input) |
void |
XYZReader.setReader(InputStream input) |
void |
CMLReader.setReader(InputStream input) |
void |
PCCompoundASNReader.setReader(InputStream input) |
void |
GhemicalMMReader.setReader(InputStream input) |
void |
PCCompoundXMLReader.setReader(InputStream input) |
void |
ShelXReader.setReader(InputStream input) |
void |
CIFReader.setReader(InputStream input) |
void |
PMPReader.setReader(InputStream input) |
void |
HINReader.setReader(InputStream input) |
void |
Gaussian03Reader.setReader(InputStream input) |
void |
CTXReader.setReader(InputStream input) |
void |
Gaussian98Reader.setReader(InputStream input) |
void |
Mol2Reader.setReader(InputStream input) |
void |
Mopac7Reader.setReader(InputStream input) |
void |
MDLV2000Reader.setReader(InputStream input) |
void |
MDLRXNReader.setReader(InputStream input)
Deprecated.
|
void |
MDLV3000Reader.setReader(InputStream input) |
void |
MDLRXNV3000Reader.setReader(InputStream input) |
void |
MDLRXNV2000Reader.setReader(InputStream input) |
void |
RGroupQueryReader.setReader(InputStream input) |
void |
MDLReader.setReader(InputStream input)
Deprecated.
|
void |
CrystClustReader.setReader(InputStream input) |
void |
ZMatrixReader.setReader(InputStream input) |
void |
INChIPlainTextReader.setReader(InputStream input) |
void |
VASPReader.setReader(InputStream input) |
void |
INChIReader.setReader(InputStream input) |
void |
GamessReader.setReader(InputStream input) |
void |
IChemObjectReader.setReader(InputStream reader)
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 |
SMILESReader.setReader(Reader input) |
void |
PDBReader.setReader(Reader input) |
void |
PCSubstanceXMLReader.setReader(Reader input) |
void |
XYZReader.setReader(Reader input) |
void |
CMLReader.setReader(Reader reader)
This method must not be used; XML reading requires the use of an InputStream.
|
void |
PCCompoundASNReader.setReader(Reader input) |
void |
GhemicalMMReader.setReader(Reader input) |
void |
PCCompoundXMLReader.setReader(Reader input) |
void |
ShelXReader.setReader(Reader input) |
void |
CIFReader.setReader(Reader reader) |
void |
PMPReader.setReader(Reader input) |
void |
HINReader.setReader(Reader input) |
void |
Gaussian03Reader.setReader(Reader reader) |
void |
CTXReader.setReader(Reader reader) |
void |
Gaussian98Reader.setReader(Reader input)
Sets the reader attribute of the Gaussian98Reader object.
|
void |
Mol2Reader.setReader(Reader input) |
void |
Mopac7Reader.setReader(Reader input) |
void |
MDLV2000Reader.setReader(Reader input) |
void |
MDLRXNReader.setReader(Reader input)
Deprecated.
|
void |
MDLV3000Reader.setReader(Reader input) |
void |
MDLRXNV3000Reader.setReader(Reader input) |
void |
MDLRXNV2000Reader.setReader(Reader input) |
void |
RGroupQueryReader.setReader(Reader input)
Sets the input Reader.
|
void |
MDLReader.setReader(Reader input)
Deprecated.
|
void |
CrystClustReader.setReader(Reader reader) |
void |
ZMatrixReader.setReader(Reader input) |
void |
VASPReader.setReader(Reader input) |
void |
INChIReader.setReader(Reader reader)
This method must not be used; XML reading requires the use of an InputStream.
|
void |
GamessReader.setReader(Reader reader) |
void |
IChemObjectReader.setReader(Reader reader)
Sets the Reader from which this ChemObjectReader should read
the contents.
|
void |
SMILESWriter.setWriter(OutputStream output) |
void |
PDBWriter.setWriter(OutputStream output) |
void |
CMLWriter.setWriter(OutputStream output) |
void |
RssWriter.setWriter(OutputStream output) |
void |
Mol2Writer.setWriter(OutputStream output) |
void |
HINWriter.setWriter(OutputStream output) |
void |
CDKSourceCodeWriter.setWriter(OutputStream output) |
void |
XYZWriter.setWriter(OutputStream output) |
void |
RGroupQueryWriter.setWriter(OutputStream output)
Sets the writer to given output stream.
|
void |
MDLV3000Writer.setWriter(OutputStream writer)
Sets the OutputStream from which this ChemObjectWriter should write
the contents.
|
void |
MDLRXNWriter.setWriter(OutputStream output) |
void |
SDFWriter.setWriter(OutputStream output) |
void |
MDLV2000Writer.setWriter(OutputStream output) |
void |
ShelXWriter.setWriter(OutputStream output) |
void |
CrystClustWriter.setWriter(OutputStream output) |
void |
IChemObjectWriter.setWriter(OutputStream writer)
Sets the OutputStream from which this ChemObjectWriter should write
the contents.
|
void |
SMILESWriter.setWriter(Writer out) |
void |
PDBWriter.setWriter(Writer out) |
void |
CMLWriter.setWriter(Writer writer) |
void |
RssWriter.setWriter(Writer out) |
void |
Mol2Writer.setWriter(Writer out) |
void |
HINWriter.setWriter(Writer out) |
void |
CDKSourceCodeWriter.setWriter(Writer out) |
void |
XYZWriter.setWriter(Writer out) |
void |
RGroupQueryWriter.setWriter(Writer out)
Sets the writer.
|
void |
MDLV3000Writer.setWriter(Writer writer)
Sets the Writer from which this ChemObjectWriter should write
the contents.
|
void |
MDLRXNWriter.setWriter(Writer out) |
void |
SDFWriter.setWriter(Writer out) |
void |
MDLV2000Writer.setWriter(Writer out) |
void |
ShelXWriter.setWriter(Writer out) |
void |
CrystClustWriter.setWriter(Writer out) |
void |
IChemObjectWriter.setWriter(Writer writer)
Sets the Writer from which this ChemObjectWriter should write
the contents.
|
void |
SMILESWriter.write(IChemObject object)
Writes the content from object to output.
|
void |
PDBWriter.write(IChemObject object) |
void |
CMLWriter.write(IChemObject object)
Serializes the IChemObject to CML and redirects it to the output Writer.
|
void |
RssWriter.write(IChemObject object)
Writes a IChemObject to the MDL molfile formated output.
|
void |
Mol2Writer.write(IChemObject object) |
void |
HINWriter.write(IChemObject object) |
void |
CDKSourceCodeWriter.write(IChemObject object) |
void |
XYZWriter.write(IChemObject object) |
void |
RGroupQueryWriter.write(IChemObject object)
The actual writing of the output.
|
void |
MDLV3000Writer.write(IChemObject object)
Writes a molecule to the V3000 format.
|
void |
MDLRXNWriter.write(IChemObject object)
Writes a IChemObject to the MDL RXN file formated output.
|
void |
SDFWriter.write(IChemObject object)
Writes a IChemObject to the MDL SD file formated output.
|
void |
MDLV2000Writer.write(IChemObject object)
Writes a
IChemObject to the MDL molfile formated output. |
void |
ShelXWriter.write(IChemObject object)
Serializes the IChemObject to ShelX and redirects it to the output Writer.
|
void |
IChemObjectWriter.write(IChemObject object)
Writes the content of "object" to output.
|
void |
PDBWriter.writeCrystal(ICrystal crystal) |
void |
PDBWriter.writeMolecule(IAtomContainer molecule)
Writes a single frame in PDB format to the Writer.
|
| Constructor and Description |
|---|
MDLV3000Writer(OutputStream out)
Create a new V3000 writer, output to the provided JDK output stream.
|
| Modifier and Type | Method and Description |
|---|---|
void |
DefaultIteratingChemObjectReader.handleError(String message)
Redirects an error message to the
IChemObjectReaderErrorHandler. |
void |
DefaultIteratingChemObjectReader.handleError(String message,
Exception exception)
Redirects an error message to the
IChemObjectReaderErrorHandler. |
void |
DefaultIteratingChemObjectReader.handleError(String message,
int row,
int colStart,
int colEnd)
Redirects an error message to the
IChemObjectReaderErrorHandler. |
void |
DefaultIteratingChemObjectReader.handleError(String message,
int row,
int colStart,
int colEnd,
Exception exception)
Redirects an error message to the
IChemObjectReaderErrorHandler. |
void |
IteratingPCSubstancesXMLReader.setReader(InputStream reader) |
void |
IteratingPCCompoundXMLReader.setReader(InputStream reader) |
void |
IteratingPCSubstancesXMLReader.setReader(Reader reader) |
void |
IteratingPCCompoundXMLReader.setReader(Reader reader) |
| Modifier and Type | Method and Description |
|---|---|
void |
EventCMLReader.process()
Starts the reading of the CML file.
|
void |
EventCMLReader.setReader(Reader reader) |
| Modifier and Type | Method and Description |
|---|---|
void |
Mopac7Writer.setWriter(OutputStream writer) |
void |
GaussianInputWriter.setWriter(OutputStream output) |
void |
Mopac7Writer.setWriter(Writer writer) |
void |
GaussianInputWriter.setWriter(Writer out) |
void |
Mopac7Writer.write(IChemObject arg0)
Writes the content of "object" to output.
|
void |
GaussianInputWriter.write(IChemObject object) |
| Modifier and Type | Method and Description |
|---|---|
protected IChemObject |
RandomAccessSDFReader.processContent() |
protected IChemObject |
RandomAccessReader.processContent()
The reader is already set to read the record buffer.
|
protected String |
RandomAccessReader.readContent(int record)
Reads the record text content into a String.
|
void |
RandomAccessSDFReader.setReader(InputStream reader) |
void |
RandomAccessSDFReader.setReader(Reader reader) |
| Modifier and Type | Method and Description |
|---|---|
<T extends IChemObject> |
CDKOWLReader.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.
|
| Modifier and Type | Method and Description |
|---|---|
void |
OptionIOSetting.setSetting(int setting)
Sets the setting for a certain question.
|
void |
StringIOSetting.setSetting(String setting)
Sets the setting for a certain question.
|
void |
IntegerIOSetting.setSetting(String setting)
Sets the setting for a certain question.
|
void |
BooleanIOSetting.setSetting(String setting)
Sets the setting for a certain question.
|
void |
OptionIOSetting.setSetting(String setting)
Sets the setting for a certain question.
|
void |
IOSetting.setSetting(String setting)
Sets the setting for a certain question.
|
| Modifier and Type | Method and Description |
|---|---|
static RGraph |
UniversalIsomorphismTester.buildRGraph(IAtomContainer g1,
IAtomContainer g2)
Builds the
RGraph ( 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 module
|
static 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)
General
RGraph parsing method (usually not used directly)
This method is the entry point for the recursive search
adapted to the atom container input. |
| Modifier and Type | Method and Description |
|---|---|
List<IAtomContainer> |
RGroupQuery.getAllConfigurations() |
void |
RGroupList.setOccurrence(String occurrence)
Picky setter for occurrence fields.
|
| Constructor and Description |
|---|
RGroupList(int rGroupNumber,
boolean restH,
String occurrence,
int requiredRGroupNumber)
Constructor with attributes given.
|
| Modifier and Type | Method and 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.
|
| Modifier and Type | Method and 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(IAtomContainer mol)
Convenience method for generating 2D coordinates.
|
void |
StructureDiagramGenerator.generateCoordinates(IReaction reaction)
Convenience method to generate 2D coordinates for a reaction.
|
void |
StructureDiagramGenerator.generateCoordinates(javax.vecmath.Vector2d firstBondVector)
The main method of this StructurDiagramGenerator.
|
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) |
| Modifier and Type | Method and 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 TemplateHandler3D |
TemplateHandler3D.getInstance() |
static ModelBuilder3D |
ModelBuilder3D.getInstance(IChemObjectBuilder builder) |
static ModelBuilder3D |
ModelBuilder3D.getInstance(TemplateHandler3D templateHandler,
String ffname,
IChemObjectBuilder chemObjectBuilder) |
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 object
|
void |
ForceFieldConfigurator.setMM2Parameters(IChemObjectBuilder builder)
Sets the parameters attribute of the ForceFieldConfigurator object, default is mm2 force field
|
| Modifier and Type | Method and 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 all
IAtoms in the
IAtomContainer, using the CDKAtomTypeMatcher. |
| Modifier and Type | Method and 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.
|
| Modifier and Type | Class and Description |
|---|---|
class |
DescriptorException
Exception that is thrown by descriptor routines when a problem has occurred.
|
| Modifier and Type | Method and 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.
|
| Modifier and Type | Method and Description |
|---|---|
void |
IPAtomicLearningDescriptor.setParameters(Object[] params)
Deprecated.
This descriptor does have any parameter.
|
void |
PartialTChargeMMFF94Descriptor.setParameters(Object[] params)
This descriptor does not have any parameter to be set.
|
void |
IPAtomicHOSEDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
CovalentRadiusDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
RDFProtonDescriptor_GDR.setParameters(Object[] params)
Sets the parameters attribute of the RDFProtonDescriptor
object
|
void |
RDFProtonDescriptor_GHR.setParameters(Object[] params)
Sets the parameters attribute of the RDFProtonDescriptor
object
|
void |
AtomValenceDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
PartialSigmaChargeDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the PartialSigmaChargeDescriptor
object
|
void |
EffectiveAtomPolarizabilityDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
AtomHybridizationDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
IsProtonInConjugatedPiSystemDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the IsProtonInConjugatedPiSystemDescriptor
object
|
void |
IsProtonInAromaticSystemDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the IsProtonInAromaticSystemDescriptor
object
|
void |
DistanceToAtomDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the DistanceToAtomDescriptor object
|
void |
VdWRadiusDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
InductiveAtomicHardnessDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
BondsToAtomDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the BondsToAtomDescriptor object
|
void |
PiElectronegativityDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the PiElectronegativityDescriptor
object
|
void |
RDFProtonDescriptor_GSR.setParameters(Object[] params)
Sets the parameters attribute of the RDFProtonDescriptor
object
|
void |
StabilizationPlusChargeDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the StabilizationPlusChargeDescriptor
object
|
void |
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 |
SigmaElectronegativityDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the SigmaElectronegativityDescriptor
object
|
void |
RDFProtonDescriptor_GHR_topol.setParameters(Object[] params)
Sets the parameters attribute of the RDFProtonDescriptor
object
|
void |
PeriodicTablePositionDescriptor.setParameters(Object[] params)
This descriptor does not have any parameter to be set.
|
void |
AtomHybridizationVSEPRDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
InductiveAtomicSoftnessDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
AtomDegreeDescriptor.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 object
|
void |
PartialPiChargeDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the PartialPiChargeDescriptor
object
|
void |
PartialTChargePEOEDescriptor.setParameters(Object[] params)
This descriptor does not have any parameter to be set.
|
| Modifier and Type | Method and Description |
|---|---|
void |
PiContactDetectionDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the PiContactDetectionDescriptor object.
|
| Modifier and Type | Method and Description |
|---|---|
void |
IPBondLearningDescriptor.setParameters(Object[] params)
Deprecated.
This descriptor does have any parameter.
|
void |
AtomicNumberDifferenceDescriptor.setParameters(Object[] params) |
void |
BondPartialTChargeDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
BondPartialSigmaChargeDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
BondSigmaElectronegativityDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
BondPartialPiChargeDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
| Modifier and Type | Method and Description |
|---|---|
DescriptorValue |
IPMolecularLearningDescriptor.calculatePlus(IAtomContainer container)
Deprecated.
It calculates the 1,2,..
|
void |
IPMolecularLearningDescriptor.setParameters(Object[] params)
Deprecated.
Sets the parameters attribute of the IPMolecularLearningDescriptor object
|
void |
AminoAcidCountDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the AminoAcidsCountDescriptor object.
|
void |
BondCountDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the BondCountDescriptor object
|
void |
HBondAcceptorCountDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the HBondAcceptorCountDescriptor object.
|
void |
AutocorrelationDescriptorPolarizability.setParameters(Object[] params) |
void |
AromaticAtomsCountDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the AromaticAtomsCountDescriptor object.
|
void |
KappaShapeIndicesDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the
KappaShapeIndicesDescriptor object
|
void |
FragmentComplexityDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the FragmentComplexityDescriptor object.
|
void |
AutocorrelationDescriptorMass.setParameters(Object[] params) |
void |
LargestPiSystemDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the LargestPiSystemDescriptor object.
|
void |
FractionalPSADescriptor.setParameters(Object[] params)
Sets the parameters for this descriptor.
|
void |
ChiPathClusterDescriptor.setParameters(Object[] params) |
void |
CarbonTypesDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the GravitationalIndexDescriptor object.
|
void |
ChiChainDescriptor.setParameters(Object[] params) |
void |
LengthOverBreadthDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the PetitjeanNumberDescriptor object
|
void |
GravitationalIndexDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the GravitationalIndexDescriptor object.
|
void |
CPSADescriptor.setParameters(Object[] params)
Sets the parameters attribute of the CPSADescriptor object.
|
void |
AutocorrelationDescriptorCharge.setParameters(Object[] params) |
void |
TPSADescriptor.setParameters(Object[] params)
Sets the parameters attribute of the TPSADescriptor object.
|
void |
FMFDescriptor.setParameters(Object[] params)
Sets the parameters for this descriptor.
|
void |
MomentOfInertiaDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the MomentOfInertiaDescriptor object.
|
void |
RotatableBondsCountDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the RotatableBondsCountDescriptor object
|
void |
ChiPathDescriptor.setParameters(Object[] params) |
void |
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 |
ZagrebIndexDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the ZagrebIndexDescriptor object.
|
void |
RuleOfFiveDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the RuleOfFiveDescriptor object.
|
void |
APolDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the APolDescriptor object.
|
void |
XLogPDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the XLogPDescriptor object.
|
void |
AcidicGroupCountDescriptor.setParameters(Object[] params)
Sets the parameters for this descriptor.
|
void |
LargestChainDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the LargestChain object.
|
void |
JPlogPDescriptor.setParameters(Object[] params) |
void |
VAdjMaDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the VAdjMaDescriptor object
|
void |
EccentricConnectivityIndexDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the EccentricConnectivityIndexDescriptor object
|
void |
VABCDescriptor.setParameters(Object[] params)
Sets the parameters for this descriptor.
|
void |
BPolDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the BPolDescriptor object
|
void |
SpiroAtomCountDescriptor.setParameters(Object[] params)
Sets the parameters for this descriptor.
|
void |
PetitjeanShapeIndexDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the PetitjeanShapeIndexDescriptor object.
|
void |
PetitjeanNumberDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the PetitjeanNumberDescriptor object
|
void |
FractionalCSP3Descriptor.setParameters(Object[] params)
Sets the parameters for this descriptor.
|
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 |
HBondDonorCountDescriptor.setParameters(Object[] params)
Sets the parameter of this HBondDonorCountDescriptor instance.
|
void |
KierHallSmartsDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the descriptor.
|
void |
WHIMDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the WHIMDescriptor object.
|
void |
ALOGPDescriptor.setParameters(Object[] params) |
void |
MDEDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the WeightDescriptor object.
|
void |
LongestAliphaticChainDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the LongestAliphaticChainDescriptor 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 |
HybridizationRatioDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the HybridizationRatioDescriptor object.
|
void |
ChiClusterDescriptor.setParameters(Object[] params) |
void |
SmallRingDescriptor.setParameters(Object[] params)
Set parameters: ignored, there are none.
|
void |
MannholdLogPDescriptor.setParameters(Object[] params)
This
IDescriptor does not have any parameters. |
void |
WienerNumbersDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the WienerNumbersDescriptor object.
|
| Constructor and Description |
|---|
ALOGPDescriptor() |
| Modifier and Type | Method and Description |
|---|---|
void |
TaeAminoAcidDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the TaeAminoAcidDescriptor object.
|
| Modifier and Type | Method and Description |
|---|---|
void |
OxygenAtomCountDescriptor.setParameters(Object[] parameters)
Sets the parameters for this descriptor.
|
| Modifier and Type | Method and 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 |
ReactionEngine.setParameterList(List<IParameterReact> params)
Returns the current parameter Map for this reaction.
|
void |
IReactionProcess.setParameterList(List<IParameterReact> params)
Sets the parameters for this reaction.
|
| Modifier and Type | Method and Description |
|---|---|
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.
|
IReaction |
RemovingSEofNBMechanism.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 |
RadicalSiteIonizationMechanism.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 |
AdductionPBMechanism.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 |
AdductionLPMechanism.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.
|
| Modifier and Type | Method and Description |
|---|---|
IReactionSet |
RadicalSiteRrAlphaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RearrangementRadicalReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteInitiationReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
PiBondingMovementReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
HyperconjugationReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RearrangementCationReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteRrDeltaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RearrangementLonePairReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
AdductionProtonPBReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteHrAlphaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
ElectronImpactNBEReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalChargeSiteInitiationReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
SharingChargeDBReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
SharingAnionReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteHrDeltaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
ElectronImpactSDBReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteRrBetaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteHrBetaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RearrangementAnionReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
HeterolyticCleavagePBReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteRrGammaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
SharingLonePairReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalChargeSiteInitiationHReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
AdductionSodiumLPReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
TautomerizationReaction.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 |
RadicalSiteHrGammaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
CarbonylEliminationReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
ElectronImpactPDBReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
SharingChargeSBReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
AdductionProtonLPReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteInitiationHReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
| Modifier and Type | Method and Description |
|---|---|
void |
AllRingsFinder.checkTimeout()
Deprecated.
timeout not used
|
IRingSet |
AllRingsFinder.findAllRings(IAtomContainer container)
Compute all rings in the given
IAtomContainer. |
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 given
IAtomContainer. |
IRingSet |
AllRingsFinder.findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer,
int maxRingSize)
Compute all rings up to an including the maxRingSize.
|
| Modifier and Type | Method and Description |
|---|---|
static float |
Tanimoto.calculate(BitSet bitset1,
BitSet bitset2)
Evaluates Tanimoto coefficient for two bit sets.
|
static float |
Tanimoto.calculate(double[] features1,
double[] features2)
Evaluates the continuous Tanimoto coefficient for two real valued vectors.
|
static float |
DistanceMoment.calculate(IAtomContainer query,
IAtomContainer target)
Evaluate the 3D similarity between two molecules.
|
static float[] |
DistanceMoment.generateMoments(IAtomContainer atomContainer)
Evaluate the 12 descriptors used to characterize the 3D shape of a molecule.
|
| Modifier and Type | Method and Description |
|---|---|
String |
SmilesGenerator.create(IAtomContainer molecule)
Generate SMILES for the provided
molecule. |
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.
|
| Modifier and Type | Method and 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.
|
| Modifier and Type | Method and Description |
|---|---|
void |
Isomorphism.init(IAtomContainer reactant,
IAtomContainer product,
boolean removeHydrogen,
boolean cleanAndConfigureMolecule)
Deprecated.
initialize query and target molecules.
|
void |
Isomorphism.init(IQueryAtomContainer reactant,
IAtomContainer product)
Deprecated.
|
void |
Isomorphism.init(String sourceMolFileName,
String targetMolFileName,
boolean removeHydrogen,
boolean cleanAndConfigureMolecule)
Deprecated.
Initialize the query and targetAtomCount mol via mol files
|
| Modifier and Type | Method and Description |
|---|---|
protected List<List<Integer>> |
MCSPlus.getOverlaps(IAtomContainer ac1,
IAtomContainer ac2,
boolean shouldMatchBonds)
Deprecated.
|
| Modifier and Type | Method and 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
Fingerprint
|
void |
CDKRMapHandler.calculateOverlapsAndReduce(IAtomContainer molecule1,
IAtomContainer molecule2,
boolean shouldMatchBonds)
Deprecated.
This function calculates all the possible combinations of MCS
|
void |
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
Fingerprint
|
void |
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
Fingerprint
|
static List<CDKRMap> |
CDKMCS.checkSingleAtomCases(IAtomContainer sourceGraph,
IAtomContainer targetGraph)
Deprecated.
Checks for single atom cases before doing subgraph/isomorphism search
|
static 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 |
CDKSubGraphHandler.getUncommon(IAtomContainer mol,
IAtomContainer mcss,
boolean shouldMatchBonds)
Deprecated.
|
protected IAtomContainerSet |
CDKMCSHandler.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.
|
| Modifier and Type | Method and 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.
|
| Modifier and Type | Method and 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.
|
| Modifier and Type | Method and 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.
|
| Modifier and Type | Method and Description |
|---|---|
IRingSet |
RingFinder.getRingSet(IAtomContainer molecule)
Deprecated.
Returns CDK object Ring set based on Hanser Ring Finding method
|
IRingSet |
HanserRingFinder.getRingSet(IAtomContainer molecule)
Deprecated.
Returns Ring set based on Hanser Ring Finding method
|
| Modifier and Type | Method and Description |
|---|---|
static BondEnergies |
BondEnergies.getInstance()
Deprecated.
Returns Singleton pattern instance for the Bond Energy class
|
static void |
ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Deprecated.
Convenience method to perceive atom types for all
IAtoms in the
IAtomContainer, using the CDKAtomTypeMatcher. |
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
SingleStructureRandomGenerator.generate()
Generates a random structure based on the atoms in the given IAtomContainer.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
PartialFilledStructureMerger.generate(IAtomContainerSet atomContainers)
Randomly generates a single, connected, correctly bonded structure from
a number of fragments.
|
| Modifier and Type | Method and Description |
|---|---|
List<IAtomContainer> |
CrossoverMachine.doCrossover(IAtomContainer dad,
IAtomContainer mom)
Performs the n point crossover of two
IAtomContainer. |
| Modifier and Type | Method and 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.
use
InChITautomerGenerator.getTautomers(IAtomContainer) directly |
| Modifier and Type | Method and 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 |
SmilesValencyChecker.allSaturated(IAtomContainer ac) |
boolean |
SaturationChecker.allSaturated(IAtomContainer ac) |
boolean |
LonePairElectronChecker.allSaturated(IAtomContainer ac)
Determines of all atoms on the AtomContainer have
the right number the lone pair electrons.
|
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 |
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) |
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) |
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 the
SINGLE_OR_DOUBLE-flag raised. |
void |
AtomTypeAwareSaturationChecker.decideBondOrder(IAtomContainer atomContainer,
boolean atomsSaturated)
This method decides the bond order on bonds that has the
SINGLE_OR_DOUBLE-flag raised. |
protected AtomTypeFactory |
SmilesValencyChecker.getAtomTypeFactory(IChemObjectBuilder builder) |
protected AtomTypeFactory |
SaturationChecker.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 an
IAtom
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 |
IValencyChecker.isSaturated(IAtomContainer ac) |
boolean |
AtomTypeAwareSaturationChecker.isSaturated(IAtomContainer container) |
boolean |
SmilesValencyChecker.isSaturated(IAtomContainer container)
Determines of all atoms on the AtomContainer are saturated.
|
boolean |
SaturationChecker.isSaturated(IAtomContainer container)
Determines of all atoms on the AtomContainer are saturated.
|
boolean |
CDKValencyChecker.isSaturated(IAtomContainer atomContainer) |
boolean |
LonePairElectronChecker.isSaturated(IAtomContainer container)
Determines of all atoms on the AtomContainer have the
right number the lone pair electrons.
|
boolean |
IValencyChecker.isSaturated(IAtom atom,
IAtomContainer container) |
boolean |
AtomTypeAwareSaturationChecker.isSaturated(IAtom atom,
IAtomContainer container) |
boolean |
SmilesValencyChecker.isSaturated(IAtom atom,
IAtomContainer container)
Checks whether an Atom is saturated by comparing it with known AtomTypes.
|
boolean |
SaturationChecker.isSaturated(IAtom atom,
IAtomContainer ac)
Checks whether an Atom is saturated by comparing it with known AtomTypes.
|
boolean |
CDKValencyChecker.isSaturated(IAtom atom,
IAtomContainer container) |
boolean |
LonePairElectronChecker.isSaturated(IAtom atom,
IAtomContainer ac)
Checks if an Atom is saturated their lone pair electrons
by comparing it with known AtomTypes.
|
boolean |
SmilesValencyChecker.isSaturated(IBond bond,
IAtomContainer atomContainer)
Returns whether a bond is saturated.
|
boolean |
SaturationChecker.isSaturated(IBond bond,
IAtomContainer atomContainer)
Returns whether a bond is saturated.
|
boolean |
SmilesValencyChecker.isUnsaturated(IBond bond,
IAtomContainer atomContainer)
Returns whether a bond is unsaturated.
|
boolean |
SaturationChecker.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 |
SmilesValencyChecker.saturate(IAtomContainer atomContainer)
Saturates a molecule by setting appropriate bond orders.
|
void |
SaturationChecker.saturate(IAtomContainer atomContainer)
The method is known to fail for certain compounds.
|
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.
|
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) |
| Modifier and Type | Method and 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 id
|
static double |
MolecularFormulaManipulator.getDBE(IMolecularFormula formula)
Returns the number of double bond equivalents in this molecule.
|
static void |
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Convenience method to perceive atom types for all
IAtoms in the
IAtomContainer, using the CDKAtomTypeMatcher. |
static void |
AtomContainerManipulator.percieveAtomTypesAndConfigureUnsetProperties(IAtomContainer container)
Convenience method to perceive atom types for all
IAtoms in the
IAtomContainer, using the CDKAtomTypeMatcher. |
static void |
AminoAcidManipulator.removeAcidicOxygen(IAminoAcid acid)
Removes the singly bonded oxygen from the acid group of the AminoAcid.
|
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