Modifier and Type | Method and Description |
---|---|
boolean |
ConformerContainer.add(IAtomContainer atomContainer)
Add a conformer to the end of the list.
|
void |
ConformerContainer.add(int i,
IAtomContainer atomContainer) |
void |
ReactionScheme.add(IReactionScheme scheme)
Add a Scheme of Reactions.
|
boolean |
ConformerContainer.addAll(Collection<? extends IAtomContainer> atomContainers) |
boolean |
ConformerContainer.addAll(int i,
Collection<? extends IAtomContainer> iAtomContainers) |
void |
ConformerContainer.clear()
Get rid of all the conformers but keeps atom and bond information.
|
Object |
ReactionScheme.clone()
Clones this ReactionScheme object and its content.
|
boolean |
Association.contains(IAtom atom)
Returns true if the given atom participates in this Association.
|
boolean |
ConformerContainer.contains(Object o)
Checks to see whether the specified conformer is currently stored.
|
boolean |
ConformerContainer.containsAll(Collection<?> objects) |
IAtomContainer |
ConformerContainer.get(int i)
Get the conformer at a specified position.
|
IAtom |
Association.getAtomAt(int position)
Returns an Atom from this Association.
|
int |
Association.getAtomCount()
Returns the number of Atoms in this Association.
|
IAtom[] |
Association.getAtoms()
Returns the array of atoms making up this Association.
|
Integer |
Association.getElectronCount()
Returns the number of electrons in a Association.
|
int |
ReactionScheme.getReactionSchemeCount()
Returns the number of ReactionScheme in this Scheme.
|
String |
ConformerContainer.getTitle()
Get the title of the conformers.
|
static String |
CDK.getVersion()
Returns the version of this CDK library.
|
int |
ConformerContainer.indexOf(Object o)
Returns the lowest index at which the specific IAtomContainer appears in the list or -1 if is not found.
|
boolean |
ReactionSet.isEmpty() |
boolean |
ConformerContainer.isEmpty()
Checks whether any conformers are stored or not.
|
boolean |
ChemModel.isEmpty() |
boolean |
AtomContainerSet.isEmpty() |
boolean |
AtomContainer.isEmpty() |
Iterator<IAtomContainer> |
ConformerContainer.iterator()
Gets an iterator over the conformers.
|
int |
ConformerContainer.lastIndexOf(Object o)
Returns the highest index at which the specific IAtomContainer appears in the list or -1 if is not found.
|
ListIterator<IAtomContainer> |
ConformerContainer.listIterator() |
ListIterator<IAtomContainer> |
ConformerContainer.listIterator(int i) |
IAtomParity |
AtomParity.map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds) |
Iterable<IReactionScheme> |
ReactionScheme.reactionSchemes()
Returns an Iterable for looping over all IMolecularScheme
in this ReactionScheme.
|
IAtomContainer |
ConformerContainer.remove(int i)
Removes the conformer at the specified position.
|
boolean |
ConformerContainer.remove(Object o)
Remove the specified conformer.
|
boolean |
ConformerContainer.removeAll(Collection<?> objects) |
void |
ReactionScheme.removeAllReactionSchemes()
Removes all IReactionScheme from this chemObject.
|
void |
ReactionScheme.removeReactionScheme(IReactionScheme scheme)
Removes an IReactionScheme from this chemObject.
|
boolean |
ConformerContainer.retainAll(Collection<?> objects) |
IAtomContainer |
ConformerContainer.set(int i,
IAtomContainer atomContainer) |
void |
Association.setAtomAt(IAtom atom,
int position)
Sets an Atom in this Association.
|
void |
Association.setAtoms(IAtom[] atoms)
Sets the array of atoms making up this Association.
|
int |
ConformerContainer.size()
Get the number of conformers stored.
|
void |
AtomContainerSet.sortAtomContainers(Comparator<IAtomContainer> comparator)
Sort the AtomContainers and multipliers using a provided Comparator
|
List<IAtomContainer> |
ConformerContainer.subList(int i,
int i1) |
Object[] |
ConformerContainer.toArray()
Returns the conformers in the form of an array of IAtomContainers.
|
<IAtomContainer> |
ConformerContainer.toArray(IAtomContainer[] ts) |
String |
Association.toString()
Returns a one line string representation of this Container.
|
Constructor and Description |
---|
Association()
Constructs an empty association.
|
Association(IAtom atom1,
IAtom atom2)
Constructs an association between two Atom's.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
DoubleBondAcceptingAromaticityDetector.detectAromaticity(IAtomContainer atomContainer) |
static boolean |
CDKHueckelAromaticityDetector.detectAromaticity(IAtomContainer atomContainer) |
static boolean |
AromaticityCalculator.isAromatic(IRing ring,
IAtomContainer atomContainer)
Tests the
ring in the molecule for aromaticity. |
Modifier and Type | Method and Description |
---|---|
IAtomType[] |
SybylAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer) |
IAtomType[] |
StructGenMatcher.findMatchingAtomType(IAtomContainer atomContainer) |
IAtomType[] |
MMFF94AtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer) |
IAtomType[] |
MM2AtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer) |
IAtomType[] |
EStateAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer) |
IAtomType[] |
CDKAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer) |
IAtomType |
SybylAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atom)
Sybyl atom type perception for a single atom.
|
IAtomType |
EStateAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atom) |
IAtomType |
CDKAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atom) |
static SybylAtomTypeMatcher |
SybylAtomTypeMatcher.getInstance(IChemObjectBuilder builder) |
static CDKAtomTypeMatcher |
CDKAtomTypeMatcher.getInstance(IChemObjectBuilder builder) |
static CDKAtomTypeMatcher |
CDKAtomTypeMatcher.getInstance(IChemObjectBuilder builder,
int mode) |
static boolean |
EStateAtomTypeMatcher.inSameAromaticRing(IAtomContainer m,
IAtom atom1,
IAtom atom2,
IRingSet rs) |
Modifier and Type | Method and Description |
---|---|
static AtomTypeMapper |
AtomTypeMapper.getInstance(String mappingFile)
Instantiates an atom type to atom type mapping, based on the given mapping file.
|
static AtomTypeMapper |
AtomTypeMapper.getInstance(String mappingFile,
InputStream stream) |
String |
AtomTypeMapper.getMapping() |
String |
AtomTypeMapper.mapAtomType(String type) |
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
GasteigerMarsiliPartialCharges.assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer ac,
boolean setCharge)
Main method which assigns Gasteiger Marisili partial sigma charges
|
IAtomContainer |
GasteigerPEPEPartialCharges.assignGasteigerPiPartialCharges(IAtomContainer ac,
boolean setCharge)
Main method which assigns Gasteiger partial pi charges.
|
double[] |
GasteigerMarsiliPartialCharges.assignGasteigerSigmaMarsiliFactors(IAtomContainer ac)
Method which stores and assigns the factors a,b,c and CHI+
|
IAtomContainer |
InductivePartialCharges.assignInductivePartialCharges(IAtomContainer ac)
Main method, set charge as atom properties
|
double[][] |
GasteigerPEPEPartialCharges.assignrPiMarsilliFactors(IAtomContainerSet setAc)
Method which stores and assigns the factors a,b,c and CHI+
|
double |
Polarizability.calculateBondPolarizability(IAtomContainer atomContainer,
IBond bond)
calculate bond polarizability
|
void |
InductivePartialCharges.calculateCharges(IAtomContainer container) |
void |
GasteigerPEPEPartialCharges.calculateCharges(IAtomContainer container) |
void |
GasteigerMarsiliPartialCharges.calculateCharges(IAtomContainer container) |
void |
AtomTypeCharges.calculateCharges(IAtomContainer container) |
double |
Polarizability.calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer,
IAtom atom,
boolean addExplicitH,
int[][] distanceMatrix)
calculate effective atom polarizability
|
double |
Polarizability.calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer,
IAtom atom,
int influenceSphereCutOff,
boolean addExplicitH)
calculate effective atom polarizability
|
double |
Polarizability.calculateKJMeanMolecularPolarizability(IAtomContainer atomContainer)
calculates the mean molecular polarizability as described in paper of Kang and Jhorn
|
double |
PiElectronegativity.calculatePiElectronegativity(IAtomContainer ac,
IAtom atom)
calculate the electronegativity of orbitals pi.
|
double |
PiElectronegativity.calculatePiElectronegativity(IAtomContainer ac,
IAtom atom,
int maxIterations,
int maxResonStruc)
calculate the electronegativity of orbitals pi.
|
double |
StabilizationCharges.calculatePositive(IAtomContainer atomContainer,
IAtom atom)
calculate the stabilization of orbitals when they contain deficiency of charge.
|
double |
Electronegativity.calculateSigmaElectronegativity(IAtomContainer ac,
IAtom atom)
calculate the electronegativity of orbitals sigma.
|
double |
Electronegativity.calculateSigmaElectronegativity(IAtomContainer ac,
IAtom atom,
int maxIterations,
int maxResonStruc)
calculate the electronegativity of orbitals sigma.
|
double |
InductivePartialCharges.getAtomicSoftnessCore(IAtomContainer ac,
int atomPosition)
Gets the atomicSoftnessCore attribute of the InductivePartialCharges object
|
double |
GasteigerMarsiliPartialCharges.getChiCatHydrogen()
Gets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation
|
double |
GasteigerMarsiliPartialCharges.getMaxGasteigerDamp()
Gets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges
object
|
int |
GasteigerPEPEPartialCharges.getMaxGasteigerIters()
Gets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges
object
|
double |
GasteigerMarsiliPartialCharges.getMaxGasteigerIters()
Gets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges
object
|
int |
PiElectronegativity.getMaxIterations()
get the maximal number of Iterations.
|
int |
Electronegativity.getMaxIterations()
get the maximal number of Iterations.
|
int |
PiElectronegativity.getMaxResonStruc()
get the maximal number of resonance structures.
|
int |
Electronegativity.getMaxResonStruc()
get the maximal number of resonance structures.
|
int |
GasteigerPEPEPartialCharges.getMaxResoStruc()
Gets the maximum resonance structures to be searched
|
double[] |
InductivePartialCharges.getPaulingElectronegativities(IAtomContainer ac,
boolean modified)
Gets the paulingElectronegativities attribute of the
InductivePartialCharges object
|
double |
Polarizability.getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer,
IAtom atom)
Gets the polarizabilitiyFactorForAtom
|
int |
GasteigerPEPEPartialCharges.getStepSize()
Get the StepSize attribute of the GasteigerMarsiliPartialCharges
object
|
int |
GasteigerMarsiliPartialCharges.getStepSize()
Get the StepSize attribute of the GasteigerMarsiliPartialCharges
object
|
IAtomContainer |
AtomTypeCharges.setCharges(IAtomContainer atomContainer)
Sets initial charges for atom types
+1 for cationic atom types
-1 for anionic atom types
carboxylic oxygen -0.5
phosphorylic oxygen -0.66
sulfanilic oxygen -0.5
or to formal charge (which must be determined elsewhere or set manually)
polycations are not handled by this approach
|
void |
GasteigerMarsiliPartialCharges.setChiCatHydrogen(double chiCat)
Sets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation
|
void |
GasteigerMarsiliPartialCharges.setMaxGasteigerDamp(double damp)
Sets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges
object
|
void |
GasteigerMarsiliPartialCharges.setMaxGasteigerIters(double iters)
Sets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges
object
|
void |
GasteigerPEPEPartialCharges.setMaxGasteigerIters(int iters)
Sets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges
object
|
void |
PiElectronegativity.setMaxIterations(int maxIterations)
set the maximal number of Iterations.
|
void |
Electronegativity.setMaxIterations(int maxIterations)
set the maximal number of Iterations.
|
void |
PiElectronegativity.setMaxResonStruc(int maxResonStruc)
set the maximal number of resonance structures.
|
void |
Electronegativity.setMaxResonStruc(int maxResonStruc)
set the maximal number of resonance structures.
|
void |
GasteigerPEPEPartialCharges.setMaxResoStruc(int numbReson)
Sets the maximum resonance structures to be searched
|
void |
GasteigerPEPEPartialCharges.setStepSize(int step)
Set the StepSize attribute of the GasteigerMarsiliPartialCharges
object
|
void |
GasteigerMarsiliPartialCharges.setStepSize(int step)
Set the StepSize attribute of the GasteigerMarsiliPartialCharges
object
|
Modifier and Type | Method and Description |
---|---|
IAtom |
IsotopeFactory.configure(IAtom atom)
Configures an atom.
|
IAtom |
AtomTypeFactory.configure(IAtom atom)
Configures an atom.
|
IAtom |
IsotopeFactory.configure(IAtom atom,
IIsotope isotope)
Configures an atom to have all the data of the
given isotope.
|
void |
IsotopeFactory.configureAtoms(IAtomContainer container)
Configures atoms in an AtomContainer to
carry all the correct data according to their element type.
|
IAtomType[] |
AtomTypeFactory.getAllAtomTypes()
Gets the allAtomTypes attribute of the AtomTypeFactory object.
|
IAtomType |
AtomTypeFactory.getAtomType(String identifier)
Get an AtomType with the given ID.
|
IAtomType[] |
AtomTypeFactory.getAtomTypes(String symbol)
Get an array of all atomTypes known to the AtomTypeFactory for the given
element symbol and atomtype class.
|
IElement |
IsotopeFactory.getElement(int atomicNumber)
Returns an element according to a given atomic number.
|
IElement |
IsotopeFactory.getElement(String symbol)
Returns an Element with a given element symbol.
|
String |
IsotopeFactory.getElementSymbol(int atomicNumber)
Returns the symbol matching the element with the given atomic number.
|
static IsotopeFactory |
IsotopeFactory.getInstance(IChemObjectBuilder builder)
Returns an IsotopeFactory instance.
|
static AtomTypeFactory |
AtomTypeFactory.getInstance(IChemObjectBuilder builder)
Method to create a default AtomTypeFactory, using the structgen atom type list.
|
static AtomTypeFactory |
AtomTypeFactory.getInstance(InputStream ins,
String format,
IChemObjectBuilder builder)
Method to create a default AtomTypeFactory, using the given InputStream.
|
static AtomTypeFactory |
AtomTypeFactory.getInstance(String configFile,
IChemObjectBuilder builder)
Method to create a specialized AtomTypeFactory.
|
IIsotope |
IsotopeFactory.getIsotope(String symbol,
int massNumber)
Get isotope based on element symbol and mass number.
|
IIsotope[] |
IsotopeFactory.getIsotopes(String symbol)
Gets an array of all isotopes known to the IsotopeFactory for the given
element symbol.
|
IIsotope |
IsotopeFactory.getMajorIsotope(int atomicNumber)
Returns the most abundant (major) isotope with a given atomic number.
|
IIsotope |
IsotopeFactory.getMajorIsotope(String symbol)
Returns the most abundant (major) isotope whose symbol equals element.
|
double |
IsotopeFactory.getNaturalMass(IElement element)
Gets the natural mass of this element, defined as average of masses of isotopes,
weighted by abundance.
|
int |
IsotopeFactory.getSize()
Returns the number of isotopes defined by this class.
|
int |
AtomTypeFactory.getSize()
Returns the number of atom types in this list.
|
boolean |
IsotopeFactory.isElement(String elementName)
Checks whether the given element exists.
|
List<IAtomType> |
TXTBasedAtomTypeConfigurator.readAtomTypes(IChemObjectBuilder builder)
Reads a text based configuration file.
|
List<IAtomType> |
OWLBasedAtomTypeConfigurator.readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the OWL based atom type list.
|
List<IAtomType> |
CDKBasedAtomTypeConfigurator.readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the CDK based atom type list.
|
void |
TXTBasedAtomTypeConfigurator.setInputStream(InputStream ins)
Sets the file containing the config data.
|
void |
OWLBasedAtomTypeConfigurator.setInputStream(InputStream ins) |
void |
CDKBasedAtomTypeConfigurator.setInputStream(InputStream ins) |
Constructor and Description |
---|
CDKBasedAtomTypeConfigurator() |
OWLBasedAtomTypeConfigurator() |
TXTBasedAtomTypeConfigurator() |
Modifier and Type | Method and Description |
---|---|
void |
OWLAtomTypeMappingHandler.characters(char[] chars,
int start,
int length) |
void |
OWLAtomTypeHandler.characters(char[] chars,
int start,
int length) |
void |
AtomTypeHandler.characters(char[] chars,
int start,
int length) |
void |
OWLAtomTypeMappingHandler.endElement(String uri,
String local,
String raw) |
void |
OWLAtomTypeHandler.endElement(String uri,
String local,
String raw) |
void |
AtomTypeHandler.endElement(String uri,
String local,
String raw) |
Map<String,String> |
OWLAtomTypeMappingHandler.getAtomTypeMappings()
Returns a
Map with atom type mappings. |
List<IAtomType> |
OWLAtomTypeHandler.getAtomTypes()
Returns a List with read IAtomType's.
|
List<IAtomType> |
AtomTypeHandler.getAtomTypes()
Returns a List with read IAtomType's.
|
Map<String,String> |
OWLAtomTypeMappingReader.readAtomTypeMappings()
Reads the atom type mappings from the data file.
|
List<IAtomType> |
OWLAtomTypeReader.readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the data file.
|
List<IAtomType> |
AtomTypeReader.readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the data file.
|
void |
OWLAtomTypeMappingHandler.startDocument() |
void |
OWLAtomTypeHandler.startDocument() |
void |
AtomTypeHandler.startDocument() |
void |
OWLAtomTypeMappingHandler.startElement(String uri,
String local,
String raw,
Attributes atts) |
void |
OWLAtomTypeHandler.startElement(String uri,
String local,
String raw,
Attributes atts) |
void |
AtomTypeHandler.startElement(String uri,
String local,
String raw,
Attributes atts) |
Constructor and Description |
---|
AtomTypeHandler(IChemObjectBuilder build)
Constructs a new AtomTypeHandler and will create IAtomType
implementations using the given IChemObjectBuilder.
|
AtomTypeReader(Reader input)
Instantiates the XML based AtomTypeReader.
|
OWLAtomTypeHandler(IChemObjectBuilder build)
Constructs a new AtomTypeHandler and will create IAtomType
implementations using the given IChemObjectBuilder.
|
OWLAtomTypeMappingHandler()
Constructs a new OWLAtomTypeMappingHandler.
|
OWLAtomTypeMappingReader(Reader input)
Instantiates the XML based AtomTypeReader.
|
OWLAtomTypeReader(Reader input)
Instantiates the XML based AtomTypeReader.
|
Modifier and Type | Method and Description |
---|---|
void |
IsotopeHandler.characters(char[] chars,
int start,
int length) |
void |
IsotopeHandler.endElement(String uri,
String local,
String raw) |
List<IIsotope> |
IsotopeHandler.getIsotopes()
Returns the isotopes read from the XML file.
|
List<IIsotope> |
IsotopeReader.readIsotopes()
Triggers the XML parsing of the data file and returns the read Isotopes.
|
void |
IsotopeHandler.startDocument() |
void |
IsotopeHandler.startElement(String uri,
String local,
String raw,
Attributes atts) |
Constructor and Description |
---|
IsotopeHandler(IChemObjectBuilder builder)
Constructs an IsotopeHandler used by the IsotopeReader.
|
IsotopeReader(InputStream input,
IChemObjectBuilder builder)
Instantiates a new reader that parses the XML from the given
input . |
Modifier and Type | Method and Description |
---|---|
boolean |
DebugReactionSet.isEmpty() |
boolean |
DebugChemModel.isEmpty() |
boolean |
DebugAtomContainerSet.isEmpty() |
boolean |
DebugAtomContainer.isEmpty() |
IAtomParity |
DebugAtomParity.map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds) |
Modifier and Type | Method and Description |
---|---|
String |
DictRef.getReference() |
String |
DictRef.getType() |
String |
DictRef.toString() |
Constructor and Description |
---|
CDKException(String message)
Constructs a new CDKException with the given message.
|
CDKException(String message,
Throwable cause)
Constructs a new CDKException with the given message and the
Exception as cause.
|
NoSuchAtomException(String message)
Constructs a new NoSuchAtomException with the given message.
|
NoSuchAtomTypeException(String message)
Constructs a new NoSuchAtomTypeException.
|
Modifier and Type | Method and Description |
---|---|
static BitSet |
PubchemFingerprinter.decode(String enc)
Returns a fingerprint from a Base64 encoded Pubchem fingerprint.
|
BitSet |
SubstructureFingerprinter.getFingerprint(IAtomContainer atomContainer)
Calculates the substructure fingerprint for the given AtomContainer.
|
BitSet |
PubchemFingerprinter.getFingerprint(IAtomContainer atomContainer)
Calculate 881 bit Pubchem fingerprint for a molecule.
|
BitSet |
MACCSFingerprinter.getFingerprint(IAtomContainer atomContainer)
Calculates the substructure fingerprint for the given AtomContainer.
|
BitSet |
HybridizationFingerprinter.getFingerprint(IAtomContainer container)
Generates a fingerprint of the default size for the given AtomContainer.
|
BitSet |
Fingerprinter.getFingerprint(IAtomContainer container)
Generates a fingerprint of the default size for the given AtomContainer.
|
BitSet |
ExtendedFingerprinter.getFingerprint(IAtomContainer container)
Generates a fingerprint of the default size for the given
AtomContainer, using path and ring metrics.
|
BitSet |
EStateFingerprinter.getFingerprint(IAtomContainer atomContainer)
Calculates the substructure fingerprint for the given AtomContainer.
|
BitSet |
Fingerprinter.getFingerprint(IAtomContainer container,
AllRingsFinder ringFinder)
Generates a fingerprint of the default size for the given AtomContainer.
|
BitSet |
GraphOnlyFingerprinter.getFingerprint(IAtomContainer container,
int size) |
BitSet |
ExtendedFingerprinter.getFingerprint(IAtomContainer atomContainer,
IRingSet ringSet,
List<IRingSet> rslist)
Generates a fingerprint of the default size for the given
AtomContainer, using path and ring metrics.
|
byte[] |
PubchemFingerprinter.getFingerprintAsBytes()
Returns the fingerprint generated for a molecule as a byte[].
|
static String[] |
StandardSubstructureSets.getFunctionalGroupSMARTS() |
int |
HybridizationFingerprinter.getSearchDepth() |
int |
Fingerprinter.getSearchDepth() |
int |
SubstructureFingerprinter.getSize() |
int |
PubchemFingerprinter.getSize()
Get the size of the fingerprint.
|
int |
MACCSFingerprinter.getSize() |
int |
HybridizationFingerprinter.getSize() |
int |
Fingerprinter.getSize() |
int |
ExtendedFingerprinter.getSize() |
int |
EStateFingerprinter.getSize() |
String |
SubstructureFingerprinter.getSubstructure(int bitIndex)
Retrieves the SMARTS representation of a substructure for a given
bit in the fingerprint.
|
static boolean |
FingerprinterTool.isSubset(BitSet bs1,
BitSet bs2)
Checks whether all the positive bits in BitSet bs2 occur in BitSet bs1.
|
static List<Integer> |
FingerprinterTool.listDifferences(BitSet bs1,
BitSet bs2)
This lists all bits set in bs2 and not in bs2 (other way round not considered) in a list and to logger
|
Constructor and Description |
---|
EStateFingerprinter() |
MACCSFingerprinter() |
SubstructureFingerprinter()
Set up the fingerprinter to use the fragments from
StandardSubstructureSets . |
SubstructureFingerprinter(String[] smarts)
Set up the fingerprinter to use a user-defined set of fragments.
|
Modifier and Type | Method and Description |
---|---|
IMolecularFormula |
MolecularFormula.add(IMolecularFormula formula)
Adds an molecularFormula to this MolecularFormula.
|
void |
MolecularFormulaSet.add(IMolecularFormulaSet formulaSet)
Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
|
void |
AdductFormula.add(IMolecularFormulaSet formulaSet)
Adds all molecularFormulas in the AdductFormula to this chemObject.
|
IMolecularFormula |
MolecularFormula.addIsotope(IIsotope isotope)
Adds an Isotope to this MolecularFormula one time.
|
IMolecularFormula |
MolecularFormula.addIsotope(IIsotope isotope,
int count)
Adds an Isotope to this MolecularFormula in a number of occurrences.
|
void |
MolecularFormulaRange.addIsotope(IIsotope isotope,
int countMin,
int countMax)
Adds an Isotope to this MolecularFormulaExpand in a number of
maximum and minimum occurrences allowed.
|
void |
IsotopePattern.addIsotope(IsotopeContainer isoContainer)
Add an isotope object.
|
void |
MolecularFormulaSet.addMolecularFormula(IMolecularFormula formula)
Adds an molecularFormula to this chemObject.
|
void |
AdductFormula.addMolecularFormula(IMolecularFormula formula)
Adds an molecularFormula to this chemObject.
|
Object |
MolecularFormulaSet.clone()
Clones this MolecularFormulaSet object and its content.
|
Object |
MolecularFormulaRange.clone()
Clones this MolecularFormulaExpand object and its content.
|
Object |
MolecularFormula.clone()
Clones this MolecularFormula object and its content.
|
Object |
IsotopePattern.clone()
Clones this IsotopePattern object and its content.
|
Object |
IsotopeContainer.clone()
Clones this IsotopeContainer object and its content.
|
Object |
AdductFormula.clone()
Clones this AdductFormula object and its content.
|
double |
IsotopePatternSimilarity.compare(IsotopePattern isoto1,
IsotopePattern isoto2)
Compare the IMolecularFormula with a isotope
abundance pattern.
|
boolean |
MolecularFormulaRange.contains(IIsotope isotope)
True, if the MolecularFormulaExpand contains the given IIsotope.
|
boolean |
MolecularFormula.contains(IIsotope isotope)
True, if the MolecularFormula contains the given IIsotope object and not
the instance.
|
boolean |
AdductFormula.contains(IIsotope isotope)
True, if the AdductFormula contains the given IIsotope object and not
the instance.
|
boolean |
MolecularFormulaSet.contains(IMolecularFormula formula)
True, if the MolecularFormulaSet contains the given IMolecularFormula object.
|
boolean |
AdductFormula.contains(IMolecularFormula formula)
True, if the AdductFormula contains the given IMolecularFormula object.
|
IMolecularFormulaSet |
MassToFormulaTool.generate(double mass)
Method that actually does the work of extracting the molecular formula.
|
Integer |
MolecularFormula.getCharge()
Returns the partial charge of this IMolecularFormula.
|
double |
IsotopePattern.getCharge()
Get the charge in this pattern.
|
Integer |
AdductFormula.getCharge()
Returns the partial charge of this Adduct.
|
IMolecularFormula |
IsotopeContainer.getFormula()
Get the IMolecularFormula object of this container.
|
double |
IsotopeContainer.getIntensity()
Get the intensity value of this container.
|
IsotopeContainer |
IsotopePattern.getIsotope(int position)
Returns the a isotopes given a specific position.
|
int |
MolecularFormulaRange.getIsotopeCount()
Checks a set of Nodes for the number of different isotopes in the
MolecularFormulaExpand.
|
int |
MolecularFormula.getIsotopeCount()
Checks a set of Nodes for the number of different isotopes in the
IMolecularFormula.
|
int |
AdductFormula.getIsotopeCount()
Checks a set of Nodes for the number of different isotopes in the
adduct formula.
|
int |
MolecularFormula.getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the
IMolecularFormula from a particular isotope.
|
int |
AdductFormula.getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the
adduct formula from a particular isotope.
|
int |
MolecularFormulaRange.getIsotopeCountMax(IIsotope isotope)
Checks a set of Nodes for the maximal occurrence of the isotope in the
MolecularFormulaExpand from a particular isotope.
|
int |
MolecularFormulaRange.getIsotopeCountMin(IIsotope isotope)
Checks a set of Nodes for the minimal occurrence of the isotope in the
MolecularFormulaExpand from a particular isotope.
|
List<IsotopeContainer> |
IsotopePattern.getIsotopes()
Returns the all isotopes that form this isotope pattern.
|
double |
IsotopeContainer.getMass()
Get the mass value of this container.
|
IMolecularFormula |
MolecularFormulaSet.getMolecularFormula(int position)
Returns the MolecularFormula at position
number in the
chemObject. |
IMolecularFormula |
AdductFormula.getMolecularFormula(int position)
Returns the MolecularFormula at position
number in the
chemObject. |
IsotopeContainer |
IsotopePattern.getMonoIsotope()
Returns the mono-isotope peak that form this isotope pattern.
|
int |
IsotopePattern.getNumberOfIsotopes()
Returns the number of isotopes in this pattern.
|
Map<Object,Object> |
MolecularFormula.getProperties()
Returns a Map with the IChemObject's properties.I should
integrate into ChemObject.
|
Object |
MolecularFormula.getProperty(Object description)
Returns a property for the IChemObject.
|
List<IRule> |
MassToFormulaTool.getRestrictions()
Get the restrictions that must be presents in the molecular formula.
|
List<IRule> |
MolecularFormulaChecker.getRules()
Get the IRules to be applied to validate the IMolecularFormula.
|
double |
IsotopePatternSimilarity.getTolerance()
Get the tolerance of the mass accuracy.
|
Iterable<IIsotope> |
MolecularFormulaRange.isotopes()
Returns an Iterator for looping over all isotopes in this MolecularFormulaExpand.
|
Iterable<IIsotope> |
MolecularFormula.isotopes()
Returns an Iterator for looping over all isotopes in this IMolecularFormula.
|
Iterable<IIsotope> |
AdductFormula.isotopes()
Returns an Iterator for looping over all isotopes in this adduct formula.
|
IMolecularFormula |
MolecularFormulaChecker.isValid(IMolecularFormula formula)
Validate if a IMolecularFormula is valid.
|
Double |
MolecularFormulaChecker.isValidSum(IMolecularFormula formula)
Validate if a IMolecularFormula is valid.
|
Iterator<IMolecularFormula> |
MolecularFormulaSet.iterator()
Returns an Iterator for looping over all IMolecularFormula
in this MolecularFormulaSet.
|
Iterator<IMolecularFormula> |
AdductFormula.iterator()
Returns an Iterator for looping over all IMolecularFormula
in this adduct formula.
|
Iterable<IMolecularFormula> |
MolecularFormulaSet.molecularFormulas()
Returns an Iterable for looping over all IMolecularFormula
in this MolecularFormulaSet.
|
Iterable<IMolecularFormula> |
AdductFormula.molecularFormulas()
Returns an Iterable for looping over all IMolecularFormula
in this adduct formula.
|
static IsotopePattern |
IsotopePatternManipulator.normalize(IsotopePattern isotopeP)
Return the isotope pattern normalized to the highest abundance
|
void |
MolecularFormulaRange.removeAllIsotopes()
Removes all isotopes of this molecular formula.
|
void |
MolecularFormula.removeAllIsotopes()
Removes all isotopes of this molecular formula.
|
void |
MolecularFormulaSet.removeAllMolecularFormulas()
Removes all IMolecularFormula from this chemObject.
|
void |
AdductFormula.removeAllMolecularFormulas()
Removes all IMolecularFormula from this chemObject.
|
void |
MolecularFormulaRange.removeIsotope(IIsotope isotope)
Removes the given isotope from the MolecularFormulaExpand.
|
void |
MolecularFormula.removeIsotope(IIsotope isotope)
Removes the given isotope from the MolecularFormula.
|
void |
MolecularFormulaSet.removeMolecularFormula(IMolecularFormula formula)
Removes an IMolecularFormula from this chemObject.
|
void |
AdductFormula.removeMolecularFormula(IMolecularFormula formula)
Removes an IMolecularFormula from this chemObject.
|
void |
MolecularFormulaSet.removeMolecularFormula(int position)
Removes an MolecularFormula from this chemObject.
|
void |
AdductFormula.removeMolecularFormula(int position)
Removes an MolecularFormula from this chemObject.
|
void |
MolecularFormula.removeProperty(Object description)
Removes a property for a IChemObject.
|
void |
IsotopePattern.setCharge(double charge)
Set the charge in this pattern.
|
void |
MolecularFormula.setCharge(Integer charge)
Sets the partial charge of this IMolecularFormula.
|
void |
AdductFormula.setCharge(Integer charge)
Deprecated.
|
void |
MassToFormulaTool.setDefaultRestrictions()
Set the default restrictions that must be presents in the molecular formula.
|
void |
IsotopeContainer.setFormula(IMolecularFormula formula)
Set IMolecularFormula object of this container.
|
void |
IsotopeContainer.setIntensity(double intensity)
Set the intensity value of this container.
|
void |
IsotopeContainer.setMass(double mass)
Set the mass value of this container.
|
void |
IsotopePattern.setMonoIsotope(IsotopeContainer isoContainer)
Set the mono isotope object.
|
void |
IsotopePatternSimilarity.seTolerance(double tolerance)
Set the tolerance of the mass accuracy.
|
void |
MolecularFormula.setProperties(Map<Object,Object> properties)
Sets the properties of this object.
|
void |
MolecularFormula.setProperty(Object description,
Object property)
Sets a property for a IChemObject.
|
void |
MassToFormulaTool.setRestrictions(List<IRule> rulesNew)
Set the restrictions that must be presents in the molecular formula.
|
int |
MolecularFormulaSet.size()
Returns the number of MolecularFormulas in this MolecularFormulaSet.
|
int |
AdductFormula.size()
Returns the number of MolecularFormulas in this AdductFormula.
|
static IsotopePattern |
IsotopePatternManipulator.sortAndNormalizedByIntensity(IsotopePattern isotopeP)
Return the isotope pattern sorted and normalized by intensity
to the highest abundance.
|
static IsotopePattern |
IsotopePatternManipulator.sortByIntensity(IsotopePattern isotopeP)
Return the isotope pattern sorted by intensity
to the highest abundance.
|
static IsotopePattern |
IsotopePatternManipulator.sortByMass(IsotopePattern isotopeP)
Return the isotope pattern sorted by mass
to the highest abundance.
|
Constructor and Description |
---|
IsotopeContainer(double mass,
double intensity)
Constructor of the IsotopeContainer object setting a mass
and intensity value.
|
IsotopeContainer(IMolecularFormula formula,
double intensity)
Constructor of the IsotopeContainer object setting a IMolecularFormula
object and intensity value.
|
Modifier and Type | Method and Description |
---|---|
void |
MurckoFragmenter.generateFragments(IAtomContainer atomContainer)
Perform the fragmentation procedure.
|
void |
ExhaustiveFragmenter.generateFragments(IAtomContainer atomContainer)
Generate fragments for the input molecule.
|
String[] |
MurckoFragmenter.getFragments()
This returns the frameworks and ring systems from a Murcko fragmentation.
|
String[] |
ExhaustiveFragmenter.getFragments()
Get the fragments generated as SMILES strings.
|
IAtomContainer[] |
ExhaustiveFragmenter.getFragmentsAsContainers()
Get the fragments generated as
IAtomContainer objects.. |
String[] |
MurckoFragmenter.getFrameworks()
Get frameworks as SMILES strings.
|
String[] |
MurckoFragmenter.getRingSystems()
Get the ring system fragments as SMILES strings.
|
IAtomContainer[] |
MurckoFragmenter.getRingSystemsAsContainers()
Get rings systems as
IAtomContainer objects. |
void |
ExhaustiveFragmenter.setMinimumFragmentSize(int minFragSize)
Set the minimum fragment size.
|
Constructor and Description |
---|
ExhaustiveFragmenter()
Instantiate fragmenter with default minimum fragment size.
|
ExhaustiveFragmenter(int minFragSize)
Instantiate fragmenter with user specified minimum fragment size.
|
MurckoFragmenter()
Instantiate Murcko fragmenter.
|
MurckoFragmenter(boolean singleFrameworkOnly,
int minimumFragmentSize)
Instantiate Murcko fragmenter.
|
Modifier and Type | Method and Description |
---|---|
static javax.vecmath.Vector3d[] |
CrystalGeometryTools.calcInvertedAxes(javax.vecmath.Vector3d aAxis,
javax.vecmath.Vector3d bAxis,
javax.vecmath.Vector3d cAxis)
Inverts three cell axes.
|
static javax.vecmath.Point3d |
CrystalGeometryTools.cartesianToFractional(javax.vecmath.Vector3d aAxis,
javax.vecmath.Vector3d bAxis,
javax.vecmath.Vector3d cAxis,
javax.vecmath.Point3d cartPoint) |
static double[] |
CrystalGeometryTools.cartesianToNotional(javax.vecmath.Vector3d aAxis,
javax.vecmath.Vector3d bAxis,
javax.vecmath.Vector3d cAxis) |
static boolean |
BondTools.closeEnoughToBond(IAtom atom1,
IAtom atom2,
double distanceFudgeFactor)
Returns true if the two atoms are within the distance fudge
factor of each other.
|
static javax.vecmath.Point3d |
CrystalGeometryTools.fractionalToCartesian(javax.vecmath.Vector3d aAxis,
javax.vecmath.Vector3d bAxis,
javax.vecmath.Vector3d cAxis,
javax.vecmath.Point3d frac) |
static double |
BondTools.giveAngle(IAtom from,
IAtom to1,
IAtom to2)
Calls giveAngleBothMethods with bool = true
|
static double |
BondTools.giveAngleBothMethods(IAtom from,
IAtom to1,
IAtom to2,
boolean bool)
Gives the angle between two lines starting at atom from and going to to1
and to2.
|
static double |
BondTools.giveAngleBothMethods(javax.vecmath.Point2d from,
javax.vecmath.Point2d to1,
javax.vecmath.Point2d to2,
boolean bool) |
static double |
BondTools.giveAngleFromMiddle(IAtom from,
IAtom to1,
IAtom to2)
Calls giveAngleBothMethods with bool = false
|
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 boolean |
BondTools.isLeft(IAtom whereIs,
IAtom viewFrom,
IAtom viewTo)
Says if an atom is on the left side of a another atom seen from a certain
atom or not
|
static boolean |
BondTools.isSquarePlanar(IAtomContainer container,
IAtom atom)
Says if an atom as a center of a square planar chirality.
|
static boolean |
BondTools.isStereo(IAtomContainer container,
IAtom stereoAtom)
Says if an atom as a center of any valid stereo configuration or not.
|
static int |
BondTools.isTetrahedral(IAtomContainer container,
IAtom atom,
boolean strict)
Says if an atom as a center of a tetrahedral chirality.
|
static int |
BondTools.isTrigonalBipyramidalOrOctahedral(IAtomContainer container,
IAtom atom)
Says if an atom as a center of a trigonal-bipyramidal or actahedral
chirality.
|
static boolean |
BondTools.isValidDoubleBondConfiguration(IAtomContainer container,
IBond bond)
Tells if a certain bond is center of a valid double bond configuration.
|
static void |
BondTools.makeUpDownBonds(IAtomContainer container) |
static javax.vecmath.Vector3d[] |
CrystalGeometryTools.notionalToCartesian(double alength,
double blength,
double clength,
double alpha,
double beta,
double gamma)
Calculates cartesian vectors for unit cell axes from axes lengths and angles
between axes.
|
static boolean |
BondTools.stereosAreOpposite(IAtomContainer container,
IAtom atom)
Says if of four atoms connected two one atom the up and down bonds are
opposite or not, i.
|
Modifier and Type | Method and Description |
---|---|
void |
KabschAlignment.align()
Perform an alignment.
|
double |
KabschAlignment.getRMSD()
Returns the RMSD from the alignment.
|
double[][] |
KabschAlignment.getRotationMatrix()
Returns the rotation matrix (u).
|
Constructor and Description |
---|
KabschAlignment(IAtomContainer ac1,
IAtomContainer ac2)
Sets up variables for the alignment algorithm.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
CIPTool.checkIfAllLigandsAreDifferent(ILigand[] ligands)
Checks if each next
ILigand is different from the previous
one according to the CIPLigandRule . |
static org.openscience.cdk.geometry.cip.LigancyFourChirality |
CIPTool.defineLigancyFourChirality(IAtomContainer container,
int chiralAtom,
int ligand1,
int ligand2,
int ligand3,
int ligand4,
ITetrahedralChirality.Stereo stereo)
Creates a ligancy four chirality around a single chiral atom, where the involved
atoms are identified by there index in the
IAtomContainer . |
static ILigand |
CIPTool.defineLigand(IAtomContainer container,
VisitedAtoms visitedAtoms,
int chiralAtom,
int ligandAtom)
Creates a ligand attached to a single chiral atom, where the involved
atoms are identified by there index in the
IAtomContainer . |
IAtomContainer |
Ligand.getAtomContainer()
IAtomContainer of which this ligand is part. |
IAtom |
Ligand.getCentralAtom()
|
static CIPTool.CIP_CHIRALITY |
CIPTool.getCIPChirality(IAtomContainer container,
ITetrahedralChirality stereoCenter)
Returns the R or S chirality according to the CIP rules, based on the given
chirality information.
|
static CIPTool.CIP_CHIRALITY |
CIPTool.getCIPChirality(org.openscience.cdk.geometry.cip.LigancyFourChirality stereoCenter)
Returns the R or S chirality according to the CIP rules, based on the given
chirality information.
|
IAtom |
Ligand.getLigandAtom()
|
static ILigand[] |
CIPTool.getLigandLigands(ILigand ligand)
Returns a CIP-expanded array of side chains of a ligand.
|
VisitedAtoms |
Ligand.getVisitedAtoms() |
boolean |
VisitedAtoms.isVisited(IAtom atom)
Returns true if the given atom already has been visited.
|
boolean |
Ligand.isVisited(IAtom atom) |
static ILigand[] |
CIPTool.order(ILigand[] ligands)
Reorders the
ILigand objects in the array according to the CIP rules. |
void |
VisitedAtoms.visited(IAtom atom)
Marks the given atom as visited.
|
void |
VisitedAtoms.visited(VisitedAtoms visitedAtoms)
Adds all atoms from the
visitedAtoms list to the current
list. |
Constructor and Description |
---|
ImplicitHydrogenLigand(IAtomContainer container,
VisitedAtoms visitedAtoms,
IAtom centralAtom) |
Ligand(IAtomContainer container,
VisitedAtoms visitedAtoms,
IAtom centralAtom,
IAtom ligandAtom) |
VisitedAtoms()
Creates a new empty list of visited
IAtom s. |
Modifier and Type | Method and Description |
---|---|
int |
CIPLigandRule.compare(ILigand ligand1,
ILigand ligand2)
Compares two ligands according to the particular sequence sub rule.
|
Modifier and Type | Method and Description |
---|---|
List |
BiconnectivityInspector.biconnectedSets()
Returns a list of
Set s, where each set contains all edge that are
in the same biconnected component. |
static void |
PathTools.breadthFirstSearch(IAtomContainer atomContainer,
List<IAtom> sphere,
IMolecule molecule)
Performs a breadthFirstSearch in an AtomContainer starting with a
particular sphere, which usually consists of one start atom.
|
static void |
PathTools.breadthFirstSearch(IAtomContainer atomContainer,
List<IAtom> sphere,
IMolecule molecule,
int max)
Performs a breadthFirstSearch in an AtomContainer starting with a
particular sphere, which usually consists of one start atom.
|
static int |
PathTools.breadthFirstTargetSearch(IAtomContainer atomContainer,
List<IAtom> sphere,
IAtom target,
int pathLength,
int cutOff)
Performs a breadthFirstTargetSearch in an AtomContainer starting with a
particular sphere, which usually consists of one start atom.
|
static int[][] |
PathTools.computeFloydAPSP(double[][] costMatrix)
All-Pairs-Shortest-Path computation based on Floyd's
algorithm .
|
static int[][] |
PathTools.computeFloydAPSP(int[][] costMatrix)
All-Pairs-Shortest-Path computation based on Floyd's
algorithm .
|
static boolean |
PathTools.depthFirstTargetSearch(IAtomContainer molecule,
IAtom root,
IAtom target,
IAtomContainer path)
Recursivly perfoms a depth first search in a molecular graphs contained in
the AtomContainer molecule, starting at the root atom and returning when it
hits the target atom.
|
static IAtom[] |
PathTools.findClosestByBond(IAtomContainer atomContainer,
IAtom atom,
int max)
Returns the atoms which are closest to an atom in an AtomContainer by bonds.
|
static List<org._3pq.jgrapht.Edge> |
BFSShortestPath.findPathBetween(org._3pq.jgrapht.Graph graph,
Object startVertex,
Object endVertex) |
static List<List<IAtom>> |
PathTools.getAllPaths(IAtomContainer atomContainer,
IAtom start,
IAtom end)
Get a list of all the paths between two atoms.
|
IRingSet |
SpanningTree.getAllRings() |
IRingSet |
SpanningTree.getBasicRings() |
int |
SpanningTree.getBondsAcyclicCount() |
int |
SpanningTree.getBondsCyclicCount() |
IAtomContainer |
SpanningTree.getCyclicFragmentsContainer()
Returns an IAtomContainer which contains all the atoms and bonds which
are involved in ring systems.
|
static int[] |
PathTools.getInt2DColumnSum(int[][] apsp)
Sums up the columns in a 2D int matrix
|
static int |
PathTools.getMolecularGraphDiameter(IAtomContainer atomContainer)
Returns the diameter of the molecular graph.
|
static int |
PathTools.getMolecularGraphRadius(IAtomContainer atomContainer)
Returns the radius of the molecular graph.
|
static org._3pq.jgrapht.graph.SimpleGraph |
MoleculeGraphs.getMoleculeGraph(IAtomContainer molecule)
Creates a molecule graph for use with jgrapht.
|
IAtomContainer |
SpanningTree.getPath(IAtomContainer spt,
IAtom a1,
IAtom a2) |
static List<List<IAtom>> |
PathTools.getPathsOfLength(IAtomContainer atomContainer,
IAtom start,
int length)
Get the paths starting from an atom of specified length.
|
static List<List<IAtom>> |
PathTools.getPathsOfLengthUpto(IAtomContainer atomContainer,
IAtom start,
int length)
Get all the paths starting from an atom of length 0 upto the specified length.
|
static List<IAtom> |
PathTools.getShortestPath(IAtomContainer atomContainer,
IAtom start,
IAtom end)
Returns a list of atoms in the shortest path between two atoms.
|
IAtomContainer |
SpanningTree.getSpanningTree() |
int |
SpanningTree.getSpanningTreeSize() |
static int |
PathTools.getVertexCountAtDistance(IAtomContainer atomContainer,
int distance)
Returns the number of vertices that are a distance 'd' apart.
|
boolean |
MinimalPathIterator.hasNext() |
static boolean |
ConnectivityChecker.isConnected(IAtomContainer atomContainer)
Check whether a set of atoms in an
IAtomContainer is connected. |
boolean |
SpanningTree.isDisconnected() |
Object |
MinimalPathIterator.next() |
static IMoleculeSet |
ConnectivityChecker.partitionIntoMolecules(IAtomContainer atomContainer)
Partitions the atoms in an AtomContainer into covalently connected components.
|
void |
MinimalPathIterator.remove() |
Constructor and Description |
---|
SpanningTree(IAtomContainer atomContainer) |
Modifier and Type | Method and Description |
---|---|
void |
CanonicalLabeler.canonLabel(IAtomContainer atomContainer)
Canonically label the fragment.
|
static IAtomContainerSet |
ConjugatedPiSystemsDetector.detect(IAtomContainer ac)
Detect all conjugated pi systems in an AtomContainer.
|
static long[] |
MorganNumbersTools.getMorganNumbers(IAtomContainer atomContainer)
Makes an array containing the morgan numbers of the atoms of atomContainer.
|
static String[] |
MorganNumbersTools.getMorganNumbersWithElementSymbol(IAtomContainer atomContainer)
Makes an array containing the morgan numbers+element symbol of the atoms of atomContainer.
|
static long[] |
InChINumbersTools.getNumbers(IAtomContainer atomContainer)
Makes an array containing the InChI atom numbers of the non-hydrogen
atoms in the atomContainer.
|
Modifier and Type | Method and Description |
---|---|
static double[][] |
ConnectionMatrix.getMatrix(IAtomContainer container)
Returns the connection matrix representation of this AtomContainer.
|
static int[][] |
AdjacencyMatrix.getMatrix(IAtomContainer container)
Returns the adjacency matrix for the given AtomContainer.
|
Modifier and Type | Method and Description |
---|---|
double |
Point.getDimValue(int dim) |
void |
RebondTool.rebond(IAtomContainer container)
Rebonding using a Binary Space Partition Tree.
|
String |
Point.toString() |
String |
Bspt.toString() |
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
InChIToStructure.getAtomContainer()
Returns generated molecule.
|
String |
InChIGenerator.getAuxInfo()
Gets auxillary information.
|
String |
InChIGenerator.getInchi()
Gets generated InChI string.
|
InChIGenerator |
InChIGeneratorFactory.getInChIGenerator(IAtomContainer container)
Gets an Standard InChI generator for a
IAtomContainer . |
InChIGenerator |
InChIGeneratorFactory.getInChIGenerator(IAtomContainer container,
List<net.sf.jniinchi.INCHI_OPTION> options)
Gets InChI generator for CDK IAtomContainer.
|
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. |
String |
InChIToStructure.getLog()
Gets generated log.
|
String |
InChIGenerator.getLog()
Gets generated log.
|
String |
InChIToStructure.getMessage()
Gets generated (error/warning) messages.
|
String |
InChIGenerator.getMessage()
Gets generated (error/warning) messages.
|
net.sf.jniinchi.INCHI_RET |
InChIToStructure.getReturnStatus()
Gets return status from InChI process.
|
net.sf.jniinchi.INCHI_RET |
InChIGenerator.getReturnStatus()
Gets return status from InChI process.
|
long[][] |
InChIToStructure.getWarningFlags()
Returns warning flags, see INCHIDIFF in inchicmp.h.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
CASNumber.isValid(String casNumber)
Checks whether the registry number is valid.
|
Modifier and Type | Method and Description |
---|---|
boolean |
ZMatrixReader.accepts(Class classObject) |
boolean |
XYZWriter.accepts(Class classObject) |
boolean |
VASPReader.accepts(Class classObject) |
boolean |
SMILESWriter.accepts(Class classObject) |
boolean |
SMILESReader.accepts(Class classObject) |
boolean |
ShelXWriter.accepts(Class classObject) |
boolean |
ShelXReader.accepts(Class classObject) |
boolean |
SDFWriter.accepts(Class classObject) |
boolean |
RssWriter.accepts(Class classObject) |
boolean |
RGroupQueryWriter.accepts(Class classObject)
Returns true for accepted input types.
|
boolean |
RGroupQueryReader.accepts(Class classObject) |
boolean |
PDBWriter.accepts(Class classObject) |
boolean |
PCSubstanceXMLReader.accepts(Class classObject) |
boolean |
PCCompoundXMLReader.accepts(Class classObject) |
boolean |
PCCompoundASNReader.accepts(Class classObject) |
boolean |
MoSSOutputReader.accepts(Class testClass)
Returns whether the given
IChemObject can be read or written. |
boolean |
Mol2Writer.accepts(Class classObject) |
boolean |
Mol2Reader.accepts(Class classObject) |
boolean |
MDLV3000Reader.accepts(Class classObject) |
boolean |
MDLV2000Writer.accepts(Class classObject) |
boolean |
MDLRXNWriter.accepts(Class classObject) |
boolean |
MDLRXNV3000Reader.accepts(Class classObject) |
boolean |
MDLRXNV2000Reader.accepts(Class classObject) |
boolean |
MDLRXNReader.accepts(Class classObject) |
boolean |
MDLReader.accepts(Class classObject) |
boolean |
INChIReader.accepts(Class classObject) |
boolean |
INChIPlainTextReader.accepts(Class classObject) |
boolean |
HINWriter.accepts(Class classObject) |
boolean |
HINReader.accepts(Class classObject) |
boolean |
GhemicalMMReader.accepts(Class classObject) |
boolean |
Gaussian98Reader.accepts(Class classObject) |
boolean |
Gaussian03Reader.accepts(Class classObject) |
boolean |
GamessReader.accepts(Class classObject) |
boolean |
CTXReader.accepts(Class classObject) |
boolean |
CrystClustWriter.accepts(Class classObject) |
boolean |
CrystClustReader.accepts(Class classObject) |
boolean |
CMLWriter.accepts(Class classObject) |
boolean |
CMLReader.accepts(Class classObject) |
boolean |
CIFReader.accepts(Class testClass) |
boolean |
CDKSourceCodeWriter.accepts(Class classObject) |
boolean |
XYZReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
PMPReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
PDBReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
MDLV2000Reader.accepts(Class<? extends IChemObject> classObject) |
boolean |
Mol2Reader.accepts(IChemObject object) |
boolean |
MDLRXNV3000Reader.accepts(IChemObject object) |
boolean |
MDLRXNV2000Reader.accepts(IChemObject object) |
boolean |
MDLRXNReader.accepts(IChemObject object) |
void |
ZMatrixReader.close() |
void |
XYZWriter.close()
Flushes the output and closes this object.
|
void |
XYZReader.close() |
void |
VASPReader.close() |
void |
SMILESWriter.close()
Flushes the output and closes this object
|
void |
SMILESReader.close() |
void |
ShelXWriter.close()
Flushes the output and closes this object
|
void |
ShelXReader.close() |
void |
SDFWriter.close()
Flushes the output and closes this object.
|
void |
RssWriter.close()
Flushes the output and closes this object.
|
void |
RGroupQueryWriter.close()
Flushes the output and closes this object.
|
void |
RGroupQueryReader.close() |
void |
PMPReader.close() |
void |
PDBWriter.close()
Flushes the output and closes this object.
|
void |
PDBReader.close() |
void |
PCSubstanceXMLReader.close() |
void |
PCCompoundXMLReader.close() |
void |
PCCompoundASNReader.close() |
void |
MoSSOutputReader.close()
Closes this IChemObjectIO's resources.
|
void |
Mol2Writer.close()
Flushes the output and closes this object.
|
void |
Mol2Reader.close() |
void |
MDLV3000Reader.close() |
void |
MDLV2000Writer.close()
Flushes the output and closes this object.
|
void |
MDLV2000Reader.close() |
void |
MDLRXNWriter.close()
Flushes the output and closes this object.
|
void |
MDLRXNV3000Reader.close() |
void |
MDLRXNV2000Reader.close() |
void |
MDLRXNReader.close() |
void |
MDLReader.close() |
void |
INChIReader.close() |
void |
INChIPlainTextReader.close() |
void |
IChemObjectIO.close()
Closes this IChemObjectIO's resources.
|
void |
HINWriter.close()
Flushes the output and closes this object.
|
void |
HINReader.close() |
void |
GhemicalMMReader.close() |
void |
Gaussian98Reader.close() |
void |
Gaussian03Reader.close() |
void |
GamessReader.close() |
void |
CTXReader.close() |
void |
CrystClustWriter.close()
Flushes the output and closes this object
|
void |
CrystClustReader.close() |
void |
CMLWriter.close()
Flushes the output and closes this object
|
void |
CMLReader.close() |
void |
CIFReader.close() |
void |
CDKSourceCodeWriter.close()
Flushes the output and closes this object.
|
IResourceFormat |
ZMatrixReader.getFormat() |
IResourceFormat |
XYZWriter.getFormat() |
IResourceFormat |
XYZReader.getFormat() |
IResourceFormat |
VASPReader.getFormat() |
IResourceFormat |
SMILESWriter.getFormat() |
IResourceFormat |
SMILESReader.getFormat() |
IResourceFormat |
ShelXWriter.getFormat() |
IResourceFormat |
ShelXReader.getFormat() |
IResourceFormat |
SDFWriter.getFormat() |
IResourceFormat |
RssWriter.getFormat() |
IResourceFormat |
RGroupQueryWriter.getFormat()
Returns output format.
|
IResourceFormat |
RGroupQueryReader.getFormat() |
IResourceFormat |
PMPReader.getFormat() |
IResourceFormat |
PDBWriter.getFormat() |
IResourceFormat |
PDBReader.getFormat() |
IResourceFormat |
PCSubstanceXMLReader.getFormat() |
IResourceFormat |
PCCompoundXMLReader.getFormat() |
IResourceFormat |
PCCompoundASNReader.getFormat() |
IResourceFormat |
MoSSOutputReader.getFormat()
Returns the
IResourceFormat class for this IO class. |
IResourceFormat |
Mol2Writer.getFormat() |
IResourceFormat |
Mol2Reader.getFormat() |
IResourceFormat |
MDLV3000Reader.getFormat() |
IResourceFormat |
MDLV2000Writer.getFormat() |
IResourceFormat |
MDLV2000Reader.getFormat() |
IResourceFormat |
MDLRXNWriter.getFormat() |
IResourceFormat |
MDLRXNV3000Reader.getFormat() |
IResourceFormat |
MDLRXNV2000Reader.getFormat() |
IResourceFormat |
MDLRXNReader.getFormat() |
IResourceFormat |
MDLReader.getFormat() |
IResourceFormat |
INChIReader.getFormat() |
IResourceFormat |
INChIPlainTextReader.getFormat() |
IResourceFormat |
HINWriter.getFormat() |
IResourceFormat |
HINReader.getFormat() |
IResourceFormat |
GhemicalMMReader.getFormat() |
IResourceFormat |
Gaussian98Reader.getFormat() |
IResourceFormat |
Gaussian03Reader.getFormat() |
IResourceFormat |
GamessReader.getFormat() |
IResourceFormat |
CTXReader.getFormat() |
IResourceFormat |
CrystClustWriter.getFormat() |
IResourceFormat |
CrystClustReader.getFormat() |
IResourceFormat |
CMLWriter.getFormat() |
IResourceFormat |
CMLReader.getFormat() |
IResourceFormat |
CIFReader.getFormat() |
IResourceFormat |
CDKSourceCodeWriter.getFormat() |
IChemFormat |
FormatFactory.guessFormat(InputStream input) |
<T extends IChemObject> |
XYZReader.read(T object)
reads the content from a XYZ input.
|
<T extends IChemObject> |
SMILESReader.read(T object)
reads the content from a XYZ input.
|
<T extends IChemObject> |
MDLRXNV3000Reader.read(T object) |
void |
ZMatrixReader.setReader(InputStream input) |
void |
XYZReader.setReader(InputStream input) |
void |
VASPReader.setReader(InputStream input) |
void |
SMILESReader.setReader(InputStream input) |
void |
ShelXReader.setReader(InputStream input) |
void |
RGroupQueryReader.setReader(InputStream input) |
void |
PMPReader.setReader(InputStream input) |
void |
PDBReader.setReader(InputStream input) |
void |
PCSubstanceXMLReader.setReader(InputStream input) |
void |
PCCompoundXMLReader.setReader(InputStream input) |
void |
PCCompoundASNReader.setReader(InputStream input) |
void |
MoSSOutputReader.setReader(InputStream input)
Sets the InputStream from which this ChemObjectReader should read
the contents.
|
void |
Mol2Reader.setReader(InputStream input) |
void |
MDLV3000Reader.setReader(InputStream input) |
void |
MDLV2000Reader.setReader(InputStream input) |
void |
MDLRXNV3000Reader.setReader(InputStream input) |
void |
MDLRXNV2000Reader.setReader(InputStream input) |
void |
MDLRXNReader.setReader(InputStream input) |
void |
MDLReader.setReader(InputStream input) |
void |
INChIReader.setReader(InputStream input) |
void |
INChIPlainTextReader.setReader(InputStream input) |
void |
HINReader.setReader(InputStream input) |
void |
GhemicalMMReader.setReader(InputStream input) |
void |
Gaussian98Reader.setReader(InputStream input) |
void |
Gaussian03Reader.setReader(InputStream input) |
void |
GamessReader.setReader(InputStream input) |
void |
CTXReader.setReader(InputStream input) |
void |
CrystClustReader.setReader(InputStream input) |
void |
CMLReader.setReader(InputStream input) |
void |
CIFReader.setReader(InputStream input) |
void |
ZMatrixReader.setReader(Reader input) |
void |
XYZReader.setReader(Reader input) |
void |
VASPReader.setReader(Reader input) |
void |
SMILESReader.setReader(Reader input) |
void |
ShelXReader.setReader(Reader input) |
void |
RGroupQueryReader.setReader(Reader input)
Sets the input Reader.
|
void |
PMPReader.setReader(Reader input) |
void |
PDBReader.setReader(Reader input) |
void |
PCSubstanceXMLReader.setReader(Reader input) |
void |
PCCompoundXMLReader.setReader(Reader input) |
void |
PCCompoundASNReader.setReader(Reader input) |
void |
MoSSOutputReader.setReader(Reader reader)
Sets the Reader from which this ChemObjectReader should read
the contents.
|
void |
Mol2Reader.setReader(Reader input) |
void |
MDLV3000Reader.setReader(Reader input) |
void |
MDLV2000Reader.setReader(Reader input) |
void |
MDLRXNV3000Reader.setReader(Reader input) |
void |
MDLRXNV2000Reader.setReader(Reader input) |
void |
MDLRXNReader.setReader(Reader input) |
void |
MDLReader.setReader(Reader input) |
void |
INChIReader.setReader(Reader reader)
This method must not be used; XML reading requires the use of an InputStream.
|
void |
INChIPlainTextReader.setReader(Reader input) |
void |
HINReader.setReader(Reader input) |
void |
GhemicalMMReader.setReader(Reader input) |
void |
Gaussian98Reader.setReader(Reader input)
Sets the reader attribute of the Gaussian98Reader object
|
void |
Gaussian03Reader.setReader(Reader reader) |
void |
GamessReader.setReader(Reader reader) |
void |
CTXReader.setReader(Reader reader) |
void |
CrystClustReader.setReader(Reader reader) |
void |
CMLReader.setReader(Reader reader)
This method must not be used; XML reading requires the use of an InputStream.
|
void |
CIFReader.setReader(Reader reader) |
Modifier and Type | Method and Description |
---|---|
String |
CMLStack.current()
Returns the last added entry.
|
boolean |
CMLStack.endsWith(String lastElement)
Convenience method to check the last added elements.
|
boolean |
CMLStack.endsWith(String oneButLast,
String lastElement)
Convenience method to check the last two added elements.
|
boolean |
CMLStack.endsWith(String twoButLast,
String oneButLast,
String lastElement)
Convenience method to check the last three added elements.
|
String |
CMLStack.pop()
Retrieves and deletes to last added entry.
|
void |
CMLStack.push(String item)
Adds an entry to the stack.
|
Modifier and Type | Method and Description |
---|---|
void |
IteratingSMILESReader.close()
Close the reader.
|
void |
IteratingPCSubstancesXMLReader.close() |
void |
IteratingPCCompoundXMLReader.close() |
void |
IteratingPCCompoundASNReader.close() |
void |
IteratingMDLReader.close() |
IResourceFormat |
IteratingSMILESReader.getFormat()
Get the format for this reader.
|
IResourceFormat |
IteratingPCSubstancesXMLReader.getFormat() |
IResourceFormat |
IteratingPCCompoundXMLReader.getFormat() |
IResourceFormat |
IteratingPCCompoundASNReader.getFormat() |
IResourceFormat |
IteratingMDLReader.getFormat() |
boolean |
IteratingSMILESReader.hasNext()
Checks whether there is another molecule to read.
|
boolean |
IteratingMDLConformerReader.hasNext() |
IAtomContainer |
IteratingSMILESReader.next()
Get the next molecule from the stream.
|
Object |
IteratingMDLConformerReader.next() |
void |
IteratingSMILESReader.remove() |
void |
IteratingMDLConformerReader.remove() |
void |
IteratingSMILESReader.setReader(InputStream reader) |
void |
IteratingPCSubstancesXMLReader.setReader(InputStream reader) |
void |
IteratingPCCompoundXMLReader.setReader(InputStream reader) |
void |
IteratingPCCompoundASNReader.setReader(InputStream reader) |
void |
IteratingMDLReader.setReader(InputStream reader) |
void |
IteratingSMILESReader.setReader(Reader reader) |
void |
IteratingPCSubstancesXMLReader.setReader(Reader reader) |
void |
IteratingPCCompoundXMLReader.setReader(Reader reader) |
void |
IteratingPCCompoundASNReader.setReader(Reader reader) |
void |
IteratingMDLReader.setReader(Reader reader) |
Constructor and Description |
---|
IteratingMDLConformerReader(InputStream in,
IChemObjectBuilder builder) |
IteratingMDLConformerReader(Reader in,
IChemObjectBuilder builder) |
IteratingSMILESReader(InputStream in)
Constructs a new IteratingSMILESReader that can read Molecule from a given InputStream.
|
IteratingSMILESReader(Reader in,
IChemObjectBuilder builder)
Constructs a new IteratingSMILESReader that can read Molecule from a given Reader.
|
Modifier and Type | Method and Description |
---|---|
void |
EventCMLReader.close() |
IResourceFormat |
EventCMLReader.getFormat() |
void |
EventCMLReader.setReader(Reader reader) |
Modifier and Type | Method and Description |
---|---|
boolean |
GaussianInputWriter.accepts(Class classObject) |
void |
GaussianInputWriter.close() |
IResourceFormat |
GaussianInputWriter.getFormat() |
void |
GaussianInputWriter.write(IChemObject object) |
Modifier and Type | Method and Description |
---|---|
boolean |
RandomAccessSDFReader.accepts(Class classObject) |
void |
RandomAccessReader.close() |
IResourceFormat |
RandomAccessSDFReader.getFormat() |
void |
RandomAccessSDFReader.setReader(InputStream reader) |
void |
RandomAccessSDFReader.setReader(Reader reader) |
Modifier and Type | Method and Description |
---|---|
boolean |
CDKOWLWriter.accepts(Class classObject)
Returns whether the given
IChemObject can be read or written. |
boolean |
CDKOWLReader.accepts(Class<? extends IChemObject> classObject)
Returns whether the given
IChemObject can be read or written. |
void |
CDKOWLReader.close()
Closes this IChemObjectIO's resources.
|
IResourceFormat |
CDKOWLReader.getFormat()
Returns the
IResourceFormat for this reader. |
void |
CDKOWLReader.setReader(InputStream input)
Sets the InputStream from which this ChemObjectReader should read
the contents.
|
void |
CDKOWLReader.setReader(Reader reader)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
boolean |
IsomorphismTester.isIsomorphic(IMolecule mol2)
Checks whether a given molecule is isomorphic with the one
that has been assigned to this IsomorphismTester at contruction time
|
boolean |
IsomorphismTester.isIsomorphic(IMolecule mol1,
IMolecule mol2)
Checks whether a given molecule is isomorphic with the one
that has been assigned to this IsomorphismTester at contruction time
|
Modifier and Type | Method and Description |
---|---|
void |
TemplateHandler.addMolecule(IAtomContainer molecule)
Adds a Molecule to the list of templates use by this TemplateHandler.
|
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.
|
int |
TemplateHandler.getTemplateCount()
Gets the templateCount attribute of the TemplateHandler object
|
void |
TemplateHandler.loadTemplates(IChemObjectBuilder builder)
Loads all existing templates into memory.
|
boolean |
TemplateHandler.mapTemplates(IAtomContainer molecule)
Checks if one of the loaded templates is a substructure in the given
Molecule.
|
void |
AtomPlacer.populatePolygonCorners(List<IAtom> atomsToDraw,
javax.vecmath.Point2d rotationCenter,
double startAngle,
double addAngle,
double radius)
Populates the corners of a polygon with atoms.
|
IAtomContainer |
TemplateHandler.removeMolecule(IAtomContainer molecule) |
Constructor and Description |
---|
AtomPlacer()
Constructor for the AtomPlacer object
|
TemplateHandler(IChemObjectBuilder builder)
Creates a new TemplateHandler.
|
Modifier and Type | Method and Description |
---|---|
static double |
FortranFormat.atof(String s)
Converts a string of digits to an double
|
static double |
RandomNumbersTool.exponentialDouble(double mean)
Generates a random double from an Exponential distribution with the specified
mean value.
|
static boolean |
RandomNumbersTool.flipCoin(double p)
Returns a boolean value based on a biased coin toss.
|
static double |
RandomNumbersTool.gaussianDouble(double dev)
Generates a random double from a Gaussian distribution with the specified
deviation.
|
static float |
RandomNumbersTool.gaussianFloat(float dev)
Generates a random float from a Gaussian distribution with the specified
deviation.
|
static int |
Primes.getPrimeAt(int index)
Returns the i-th prime number in the sequence of
all prime numbers below 19700.
|
static Random |
RandomNumbersTool.getRandom()
Returns the instance of Random used by this class.
|
static long |
RandomNumbersTool.getRandomSeed()
Returns the seed being used by this random number generator.
|
static boolean |
MathTools.isEven(int intValue) |
static boolean |
MathTools.isOdd(int intValue) |
static double |
MathTools.max(double[] values)
Analog of Math.max that returns the largest double value in an array of dpubles.
|
static int |
MathTools.max(int[] values)
Analog of Math.max that returns the largest int value in an array of ints
|
static double |
MathTools.min(double[] values)
Analog of Math.min that returns the largest double value in an array of double.
|
static int |
MathTools.min(int[] values)
Analog of Math.max that returns the largest int value in an array of ints
|
static int |
RandomNumbersTool.randomBit()
Generates a random bit: either
0 or 1 . |
static boolean |
RandomNumbersTool.randomBoolean()
Generates a random boolean.
|
static double |
RandomNumbersTool.randomDouble()
Generates a random double between
0 and 1 . |
static double |
RandomNumbersTool.randomDouble(double lo,
double hi)
Generates a random double between the specified values.
|
static float |
RandomNumbersTool.randomFloat()
Generates a random float between
0 and 1 . |
static float |
RandomNumbersTool.randomFloat(float lo,
float hi)
Generates a random float between the specified values.
|
static int |
RandomNumbersTool.randomInt()
Generates a random integer between
0 and 1 . |
static int |
RandomNumbersTool.randomInt(int lo,
int hi)
Generates a random integer between the specified values.
|
static long |
RandomNumbersTool.randomLong()
Generates a random long between
0 and 1 . |
static long |
RandomNumbersTool.randomLong(long lo,
long hi)
Generates a random long between the specified values.
|
static void |
RandomNumbersTool.setRandom(Random base_random)
Sets the base generator to be used by this class.
|
static void |
RandomNumbersTool.setRandomSeed(long new_seed)
Sets the seed of this random number generator using a single
long seed. |
Modifier and Type | Method and Description |
---|---|
IAtomParity |
NNAtomParity.map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
static void |
SMSDNormalizer.aromatizeMolecule(IAtomContainer mol)
This function finds rings and uses aromaticity detection code to
aromatize the molecule.
|
static IAtomContainer |
SMSDNormalizer.convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
Returns IAtomContainer without Hydrogen.
|
static int |
SMSDNormalizer.getExplicitHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
Returns The number of explicit hydrogens for a given IAtom.
|
static int |
SMSDNormalizer.getHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
The summed implicit + explicit hydrogens of the given IAtom.
|
static int |
SMSDNormalizer.getImplicitHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
Returns The number of Implicit Hydrogen Count for a given IAtom.
|
static IMolecule |
SMSDNormalizer.makeDeepCopy(IAtomContainer container)
Returns deep copy of the molecule
|
static boolean |
Normalizer.normalize(IAtomContainer ac,
Document doc)
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)
Convenience method to perceive atom types for all
IAtom s in the
IAtomContainer , using the CDKAtomTypeMatcher . |
static IAtomContainer |
SMSDNormalizer.removeHydrogensAndPreserveAtomID(IAtomContainer atomContainer)
Returns IAtomContainer without Hydrogen.
|
Modifier and Type | Method and Description |
---|---|
boolean |
PharmacophoreAtom.equals(Object o) |
double |
PharmacophoreBond.getBondLength()
Get the distance between the two pharmacophore groups that make up the constraint.
|
double |
PharmacophoreAngleBond.getBondLength()
Get the angle between the three pharmacophore groups that make up the constraint.
|
double |
PharmacophoreQueryBond.getLower() |
double |
PharmacophoreQueryAngleBond.getLower() |
int[] |
PharmacophoreAtom.getMatchingAtoms()
Get the atoms of a target molecule that correspond to this group.
|
List<List<PharmacophoreAtom>> |
PharmacophoreMatcher.getMatchingPharmacophoreAtoms()
Get the matching pharmacophore groups.
|
List<List<IBond>> |
PharmacophoreMatcher.getMatchingPharmacophoreBonds()
Get the matching pharmacophore constraints.
|
PharmacophoreQuery |
PharmacophoreMatcher.getPharmacophoreQuery()
Get the query pharmacophore
|
String |
PharmacophoreQueryAtom.getSmarts()
Get the SMARTS pattern for this pharmacophore group.
|
String |
PharmacophoreAtom.getSmarts()
Get the SMARTS for the group.
|
List<HashMap<IBond,IBond>> |
PharmacophoreMatcher.getTargetQueryBondMappings()
Return a list of HashMap's that allows one to get the query constraint for a given pharmacophore bond.
|
List<List<PharmacophoreAtom>> |
PharmacophoreMatcher.getUniqueMatchingPharmacophoreAtoms()
Get the uniue matching pharmacophore groups.
|
double |
PharmacophoreQueryBond.getUpper() |
double |
PharmacophoreQueryAngleBond.getUpper() |
boolean |
PharmacophoreQueryAtom.matches(IAtom atom)
Checks whether this query atom matches a target atom.
|
boolean |
PharmacophoreMatcher.matches(IAtomContainer atomContainer)
Performs the pharmacophore matching.
|
boolean |
PharmacophoreMatcher.matches(IAtomContainer atomContainer,
boolean initializeTarget)
Performs the pharmacophore matching.
|
boolean |
PharmacophoreQueryBond.matches(IBond bond)
Checks whether the query distance constraint matches a target distance.
|
boolean |
PharmacophoreQueryAngleBond.matches(IBond bond)
Checks whether the query angle constraint matches a target distance.
|
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.
|
void |
PharmacophoreAtom.setMatchingAtoms(int[] atomIndices)
Set the atoms of a target molecule that correspond to this group.
|
void |
PharmacophoreQueryAtom.setOperator(String ID) |
void |
PharmacophoreMatcher.setPharmacophoreQuery(PharmacophoreQuery query)
Set a pharmacophore query
|
void |
PharmacophoreAtom.setSmarts(String smarts)
Set the SMARTS for the group.
|
String |
PharmacophoreQueryBond.toString()
String representation of a distance constraint.
|
String |
PharmacophoreQueryAtom.toString()
String representation of this pharmacophore group.
|
String |
PharmacophoreQueryAngleBond.toString()
String representation of an angle constraint.
|
String |
PharmacophoreQuery.toString()
String representation of this query.
|
static void |
PharmacophoreUtils.writePharmacophoreDefinition(List<PharmacophoreQuery> queries,
OutputStream out)
Write out one or more pharmacophore queries in the CDK XML format.
|
static void |
PharmacophoreUtils.writePharmacophoreDefinition(PharmacophoreQuery[] queries,
OutputStream out)
Write out one or more pharmacophore queries in the CDK XML format.
|
static void |
PharmacophoreUtils.writePharmacophoreDefinition(PharmacophoreQuery query,
OutputStream out)
Write out one or more pharmacophore queries in the CDK XML format.
|
Modifier and Type | Method and Description |
---|---|
String[] |
DescriptorEngine.getAvailableDictionaryClasses()
Get the all the unique dictionary classes that the descriptors belong to.
|
List<IDescriptor> |
DescriptorEngine.getDescriptorInstances()
Returns a List containing the instantiated descriptor classes.
|
String[] |
DescriptorEngine.getDictionaryClass(DescriptorSpecification descriptorSpecification)
Returns the class(es) of the descriptor as defined in the descriptor dictionary.
|
String[] |
DescriptorEngine.getDictionaryClass(String identifier)
Returns the class(es) of the decsriptor as defined in the descriptor dictionary.
|
String |
DescriptorEngine.getDictionaryType(DescriptorSpecification descriptorSpecification)
Returns the type of the descriptor as defined in the descriptor dictionary.
|
String |
DescriptorEngine.getDictionaryType(String identifier)
Returns the type of the descriptor as defined in the descriptor dictionary.
|
Exception |
DescriptorValue.getException() |
String |
DescriptorSpecification.getImplementationIdentifier() |
String |
DescriptorSpecification.getImplementationTitle() |
String |
DescriptorSpecification.getImplementationVendor() |
String[] |
DescriptorValue.getNames()
Returns an array of names for each descriptor value calculated.
|
String[] |
DescriptorValue.getParameterNames() |
Object[] |
DescriptorValue.getParameters() |
DescriptorSpecification |
DescriptorValue.getSpecification() |
String |
DescriptorSpecification.getSpecificationReference() |
IDescriptorResult |
DescriptorValue.getValue() |
Constructor and Description |
---|
DescriptorEngine(int type)
Constructor that generates a list of descriptors to calculate.
|
Modifier and Type | Method and Description |
---|---|
DescriptorValue |
VdWRadiusDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculate the Van der Waals radius of an atom.
|
DescriptorValue |
StabilizationPlusChargeDescriptor.calculate(IAtom atom,
IAtomContainer container)
The method calculates the stabilization of charge of a given atom
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
|
DescriptorValue |
SigmaElectronegativityDescriptor.calculate(IAtom atom,
IAtomContainer ac)
The method calculates the sigma electronegativity of a given atom
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
|
DescriptorValue |
RDFProtonDescriptor_GSR.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
DescriptorValue |
RDFProtonDescriptor_GHR_topol.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
DescriptorValue |
RDFProtonDescriptor_GHR.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
DescriptorValue |
RDFProtonDescriptor_GDR.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
DescriptorValue |
RDFProtonDescriptor_G3R.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
DescriptorValue |
ProtonTotalPartialChargeDescriptor.calculate(IAtom atom,
IAtomContainer ac)
The method returns partial charges assigned to an heavy atom and its protons through Gasteiger Marsili
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
|
DescriptorValue |
ProtonAffinityHOSEDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the protonation affinity of an atom.
|
DescriptorValue |
PiElectronegativityDescriptor.calculate(IAtom atom,
IAtomContainer atomContainer)
The method calculates the pi electronegativity of a given atom
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
|
DescriptorValue |
PeriodicTablePositionDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the period of an atom.
|
DescriptorValue |
PartialTChargePEOEDescriptor.calculate(IAtom atom,
IAtomContainer ac)
The method returns partial total charges assigned to an heavy atom through PEOE method.
|
DescriptorValue |
PartialTChargeMMFF94Descriptor.calculate(IAtom atom,
IAtomContainer ac)
The method returns partial charges assigned to an heavy atom through MMFF94 method.
|
DescriptorValue |
PartialSigmaChargeDescriptor.calculate(IAtom atom,
IAtomContainer ac)
The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
|
DescriptorValue |
PartialPiChargeDescriptor.calculate(IAtom atom,
IAtomContainer ac)
The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
|
DescriptorValue |
IsProtonInConjugatedPiSystemDescriptor.calculate(IAtom atom,
IAtomContainer atomContainer)
The method is a proton descriptor that evaluates if a proton is joined to a conjugated system.
|
DescriptorValue |
IsProtonInAromaticSystemDescriptor.calculate(IAtom atom,
IAtomContainer atomContainer)
The method is a proton descriptor that evaluate if a proton is bonded to an aromatic system or if there is distance of 2 bonds.
|
DescriptorValue |
IPAtomicLearningDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the ionization potential of an atom.
|
DescriptorValue |
IPAtomicHOSEDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the ionization potential of an atom.
|
DescriptorValue |
InductiveAtomicSoftnessDescriptor.calculate(IAtom atom,
IAtomContainer ac)
It is needed to call the addExplicitHydrogensToSatisfyValency method from
the class tools.HydrogenAdder, and 3D coordinates.
|
DescriptorValue |
InductiveAtomicHardnessDescriptor.calculate(IAtom atom,
IAtomContainer ac)
It is needed to call the addExplicitHydrogensToSatisfyValency method from
the class tools.HydrogenAdder, and 3D coordinates.
|
DescriptorValue |
EffectiveAtomPolarizabilityDescriptor.calculate(IAtom atom,
IAtomContainer ac)
The method calculates the Effective Atom Polarizability of a given atom
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
|
DescriptorValue |
DistanceToAtomDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculate the 3D distance between two atoms.
|
DescriptorValue |
CovalentRadiusDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculate the Covalent radius of an atom.
|
DescriptorValue |
BondsToAtomDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculate the number of bonds on the shortest path between two atoms.
|
DescriptorValue |
AtomValenceDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the valence of an atom.
|
DescriptorValue |
AtomHybridizationVSEPRDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the hybridization of an atom.
|
DescriptorValue |
AtomHybridizationDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the hybridization of an atom.
|
DescriptorValue |
AtomDegreeDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the number of not-H substituents of an atom.
|
DescriptorValue |
RDFProtonDescriptor_GSR.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_GHR_topol.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_GHR.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_GDR.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_G3R.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
String[] |
VdWRadiusDescriptor.getDescriptorNames() |
String[] |
StabilizationPlusChargeDescriptor.getDescriptorNames() |
String[] |
SigmaElectronegativityDescriptor.getDescriptorNames() |
String[] |
RDFProtonDescriptor_GSR.getDescriptorNames() |
String[] |
RDFProtonDescriptor_GHR_topol.getDescriptorNames() |
String[] |
RDFProtonDescriptor_GHR.getDescriptorNames() |
String[] |
RDFProtonDescriptor_GDR.getDescriptorNames() |
String[] |
RDFProtonDescriptor_G3R.getDescriptorNames() |
String[] |
ProtonTotalPartialChargeDescriptor.getDescriptorNames() |
String[] |
ProtonAffinityHOSEDescriptor.getDescriptorNames() |
String[] |
PiElectronegativityDescriptor.getDescriptorNames() |
String[] |
PeriodicTablePositionDescriptor.getDescriptorNames() |
String[] |
PartialTChargePEOEDescriptor.getDescriptorNames() |
String[] |
PartialTChargeMMFF94Descriptor.getDescriptorNames() |
String[] |
PartialSigmaChargeDescriptor.getDescriptorNames() |
String[] |
PartialPiChargeDescriptor.getDescriptorNames() |
String[] |
IsProtonInConjugatedPiSystemDescriptor.getDescriptorNames() |
String[] |
IsProtonInAromaticSystemDescriptor.getDescriptorNames() |
String[] |
IPAtomicLearningDescriptor.getDescriptorNames() |
String[] |
IPAtomicHOSEDescriptor.getDescriptorNames() |
String[] |
InductiveAtomicSoftnessDescriptor.getDescriptorNames() |
String[] |
InductiveAtomicHardnessDescriptor.getDescriptorNames() |
String[] |
EffectiveAtomPolarizabilityDescriptor.getDescriptorNames() |
String[] |
DistanceToAtomDescriptor.getDescriptorNames() |
String[] |
CovalentRadiusDescriptor.getDescriptorNames() |
String[] |
BondsToAtomDescriptor.getDescriptorNames() |
String[] |
AtomValenceDescriptor.getDescriptorNames() |
String[] |
AtomHybridizationVSEPRDescriptor.getDescriptorNames() |
String[] |
AtomHybridizationDescriptor.getDescriptorNames() |
String[] |
AtomDegreeDescriptor.getDescriptorNames() |
String[] |
VdWRadiusDescriptor.getParameterNames()
Gets the parameterNames attribute of the VdWRadiusDescriptor object.
|
String[] |
StabilizationPlusChargeDescriptor.getParameterNames()
Gets the parameterNames attribute of the StabilizationPlusChargeDescriptor
object
|
String[] |
SigmaElectronegativityDescriptor.getParameterNames()
Gets the parameterNames attribute of the SigmaElectronegativityDescriptor
object
|
String[] |
RDFProtonDescriptor_GSR.getParameterNames()
Gets the parameterNames attribute of the RDFProtonDescriptor
object
|
String[] |
RDFProtonDescriptor_GHR_topol.getParameterNames()
Gets the parameterNames attribute of the RDFProtonDescriptor
object
|
String[] |
RDFProtonDescriptor_GHR.getParameterNames()
Gets the parameterNames attribute of the RDFProtonDescriptor
object
|
String[] |
RDFProtonDescriptor_GDR.getParameterNames()
Gets the parameterNames attribute of the RDFProtonDescriptor
object
|
String[] |
RDFProtonDescriptor_G3R.getParameterNames()
Gets the parameterNames attribute of the RDFProtonDescriptor object
|
String[] |
ProtonTotalPartialChargeDescriptor.getParameterNames()
Gets the parameterNames attribute of the ProtonTotalPartialChargeDescriptor
object
|
String[] |
ProtonAffinityHOSEDescriptor.getParameterNames()
Gets the parameterNames attribute of the ProtonAffinityDescriptor object.
|
String[] |
PiElectronegativityDescriptor.getParameterNames()
Gets the parameterNames attribute of the SigmaElectronegativityDescriptor
object
|
String[] |
PeriodicTablePositionDescriptor.getParameterNames()
Gets the parameterNames attribute of the PeriodicTablePositionDescriptor object
|
String[] |
PartialTChargePEOEDescriptor.getParameterNames()
Gets the parameterNames attribute of the PartialTChargePEOEDescriptor
object
|
String[] |
PartialTChargeMMFF94Descriptor.getParameterNames()
Gets the parameterNames attribute of the PartialTChargeMMFF94Descriptor
object
|
String[] |
PartialSigmaChargeDescriptor.getParameterNames()
Gets the parameterNames attribute of the PartialSigmaChargeDescriptor
object
|
String[] |
PartialPiChargeDescriptor.getParameterNames()
Gets the parameterNames attribute of the PartialPiChargeDescriptor
object
|
String[] |
IsProtonInConjugatedPiSystemDescriptor.getParameterNames()
Gets the parameterNames attribute of the
IsProtonInConjugatedPiSystemDescriptor object
|
String[] |
IsProtonInAromaticSystemDescriptor.getParameterNames()
Gets the parameterNames attribute of the IsProtonInAromaticSystemDescriptor
object
|
String[] |
IPAtomicLearningDescriptor.getParameterNames()
Gets the parameterNames attribute of the IPAtomicLearningDescriptor object.
|
String[] |
IPAtomicHOSEDescriptor.getParameterNames()
Gets the parameterNames attribute of the IPAtomicHOSEDescriptor object.
|
String[] |
InductiveAtomicSoftnessDescriptor.getParameterNames()
Gets the parameterNames attribute of the InductiveAtomicSoftnessDescriptor object.
|
String[] |
InductiveAtomicHardnessDescriptor.getParameterNames()
Gets the parameterNames attribute of the InductiveAtomicHardnessDescriptor
object
|
String[] |
EffectiveAtomPolarizabilityDescriptor.getParameterNames()
Gets the parameterNames attribute of the EffectiveAtomPolarizabilityDescriptor
object
|
String[] |
DistanceToAtomDescriptor.getParameterNames()
Gets the parameterNames attribute of the DistanceToAtomDescriptor object
|
String[] |
CovalentRadiusDescriptor.getParameterNames()
Gets the parameterNames attribute of the VdWRadiusDescriptor object.
|
String[] |
BondsToAtomDescriptor.getParameterNames()
Gets the parameterNames attribute of the BondsToAtomDescriptor object
|
String[] |
AtomValenceDescriptor.getParameterNames()
Gets the parameterNames attribute of the VdWRadiusDescriptor object.
|
String[] |
AtomHybridizationVSEPRDescriptor.getParameterNames()
Gets the parameterNames attribute of the AtomHybridizationVSEPRDescriptor object
|
String[] |
AtomHybridizationDescriptor.getParameterNames()
Gets the parameterNames attribute of the VdWRadiusDescriptor object.
|
String[] |
AtomDegreeDescriptor.getParameterNames()
Gets the parameterNames attribute of the AtomDegreeDescriptor object.
|
Object[] |
VdWRadiusDescriptor.getParameters()
Gets the parameters attribute of the VdWRadiusDescriptor object.
|
Object[] |
StabilizationPlusChargeDescriptor.getParameters()
Gets the parameters attribute of the StabilizationPlusChargeDescriptor
object
|
Object[] |
SigmaElectronegativityDescriptor.getParameters()
Gets the parameters attribute of the SigmaElectronegativityDescriptor
object
|
Object[] |
RDFProtonDescriptor_GSR.getParameters()
Gets the parameters attribute of the RDFProtonDescriptor
object
|
Object[] |
RDFProtonDescriptor_GHR_topol.getParameters()
Gets the parameters attribute of the RDFProtonDescriptor
object
|
Object[] |
RDFProtonDescriptor_GHR.getParameters()
Gets the parameters attribute of the RDFProtonDescriptor
object
|
Object[] |
RDFProtonDescriptor_GDR.getParameters()
Gets the parameters attribute of the RDFProtonDescriptor
object
|
Object[] |
RDFProtonDescriptor_G3R.getParameters()
Gets the parameters attribute of the RDFProtonDescriptor object
|
Object[] |
ProtonTotalPartialChargeDescriptor.getParameters()
Gets the parameters attribute of the ProtonTotalPartialChargeDescriptor
object
|
Object[] |
ProtonAffinityHOSEDescriptor.getParameters()
Gets the parameters attribute of the ProtonAffinityDescriptor object.
|
Object[] |
PiElectronegativityDescriptor.getParameters()
Gets the parameters attribute of the PiElectronegativityDescriptor
object
|
Object[] |
PeriodicTablePositionDescriptor.getParameters()
Gets the parameters attribute of the PeriodicTablePositionDescriptor object
|
Object[] |
PartialTChargePEOEDescriptor.getParameters()
Gets the parameters attribute of the PartialTChargePEOEDescriptor
object
|
Object[] |
PartialTChargeMMFF94Descriptor.getParameters()
Gets the parameters attribute of the PartialTChargeMMFF94Descriptor
object
|
Object[] |
PartialSigmaChargeDescriptor.getParameters()
Gets the parameters attribute of the PartialSigmaChargeDescriptor object
|
Object[] |
PartialPiChargeDescriptor.getParameters()
Gets the parameters attribute of the PartialPiChargeDescriptor object
|
Object[] |
IsProtonInConjugatedPiSystemDescriptor.getParameters()
Gets the parameters attribute of the IsProtonInConjugatedPiSystemDescriptor
object
|
Object[] |
IsProtonInAromaticSystemDescriptor.getParameters()
Gets the parameters attribute of the IsProtonInAromaticSystemDescriptor
object
|
Object[] |
IPAtomicLearningDescriptor.getParameters()
Gets the parameters attribute of the IPAtomicLearningDescriptor object.
|
Object[] |
IPAtomicHOSEDescriptor.getParameters()
Gets the parameters attribute of the IPAtomicHOSEDescriptor object.
|
Object[] |
InductiveAtomicSoftnessDescriptor.getParameters()
Gets the parameters attribute of the InductiveAtomicSoftnessDescriptor
object
|
Object[] |
InductiveAtomicHardnessDescriptor.getParameters()
Gets the parameters attribute of the InductiveAtomicHardnessDescriptor
object
|
Object[] |
EffectiveAtomPolarizabilityDescriptor.getParameters()
Gets the parameters attribute of the EffectiveAtomPolarizabilityDescriptor
object
|
Object[] |
DistanceToAtomDescriptor.getParameters()
Gets the parameters attribute of the DistanceToAtomDescriptor object
|
Object[] |
CovalentRadiusDescriptor.getParameters()
Gets the parameters attribute of the VdWRadiusDescriptor object.
|
Object[] |
BondsToAtomDescriptor.getParameters()
Gets the parameters attribute of the BondsToAtomDescriptor object
|
Object[] |
AtomValenceDescriptor.getParameters()
Gets the parameters attribute of the VdWRadiusDescriptor object.
|
Object[] |
AtomHybridizationVSEPRDescriptor.getParameters()
Gets the parameters attribute of the AtomHybridizationVSEPRDescriptor object
|
Object[] |
AtomHybridizationDescriptor.getParameters()
Gets the parameters attribute of the VdWRadiusDescriptor object.
|
Object[] |
AtomDegreeDescriptor.getParameters()
Gets the parameters attribute of the AtomDegreeDescriptor object.
|
Object |
VdWRadiusDescriptor.getParameterType(String name)
Gets the parameterType attribute of the VdWRadiusDescriptor object.
|
Object |
StabilizationPlusChargeDescriptor.getParameterType(String name)
Gets the parameterType attribute of the StabilizationPlusChargeDescriptor
object
|
Object |
SigmaElectronegativityDescriptor.getParameterType(String name)
Gets the parameterType attribute of the SigmaElectronegativityDescriptor
object
|
Object |
RDFProtonDescriptor_GSR.getParameterType(String name)
Gets the parameterType attribute of the RDFProtonDescriptor
object
|
Object |
RDFProtonDescriptor_GHR_topol.getParameterType(String name)
Gets the parameterType attribute of the RDFProtonDescriptor
object
|
Object |
RDFProtonDescriptor_GHR.getParameterType(String name)
Gets the parameterType attribute of the RDFProtonDescriptor
object
|
Object |
RDFProtonDescriptor_GDR.getParameterType(String name)
Gets the parameterType attribute of the RDFProtonDescriptor
object
|
Object |
RDFProtonDescriptor_G3R.getParameterType(String name)
Gets the parameterType attribute of the RDFProtonDescriptor object
|
Object |
ProtonTotalPartialChargeDescriptor.getParameterType(String name)
Gets the parameterType attribute of the ProtonTotalPartialChargeDescriptor
object
|
Object |
ProtonAffinityHOSEDescriptor.getParameterType(String name)
Gets the parameterType attribute of the ProtonAffinityDescriptor object.
|
Object |
PiElectronegativityDescriptor.getParameterType(String name)
Gets the parameterType attribute of the SigmaElectronegativityDescriptor
object
|
Object |
PeriodicTablePositionDescriptor.getParameterType(String name)
Gets the parameterType attribute of the PeriodicTablePositionDescriptor object
|
Object |
PartialTChargePEOEDescriptor.getParameterType(String name)
Gets the parameterType attribute of the PartialTChargePEOEDescriptor
object
|
Object |
PartialTChargeMMFF94Descriptor.getParameterType(String name)
Gets the parameterType attribute of the PartialTChargeMMFF94Descriptor
object
|
Object |
PartialSigmaChargeDescriptor.getParameterType(String name)
Gets the parameterType attribute of the PartialSigmaChargeDescriptor
object
|
Object |
PartialPiChargeDescriptor.getParameterType(String name)
Gets the parameterType attribute of the PartialPiChargeDescriptor
object
|
Object |
IsProtonInConjugatedPiSystemDescriptor.getParameterType(String name)
Gets the parameterType attribute of the
IsProtonInConjugatedPiSystemDescriptor object
|
Object |
IsProtonInAromaticSystemDescriptor.getParameterType(String name)
Gets the parameterType attribute of the IsProtonInAromaticSystemDescriptor
object
|
Object |
IPAtomicLearningDescriptor.getParameterType(String name)
Gets the parameterType attribute of the IPAtomicLearningDescriptor object.
|
Object |
IPAtomicHOSEDescriptor.getParameterType(String name)
Gets the parameterType attribute of the IPAtomicHOSEDescriptor object.
|
Object |
InductiveAtomicSoftnessDescriptor.getParameterType(String name)
Gets the parameterType attribute of the InductiveAtomicSoftnessDescriptor object.
|
Object |
InductiveAtomicHardnessDescriptor.getParameterType(String name)
Gets the parameterType attribute of the InductiveAtomicHardnessDescriptor
object
|
Object |
EffectiveAtomPolarizabilityDescriptor.getParameterType(String name)
Gets the parameterType attribute of the EffectiveAtomPolarizabilityDescriptor
object
|
Object |
DistanceToAtomDescriptor.getParameterType(String name)
Gets the parameterType attribute of the DistanceToAtomDescriptor object
|
Object |
CovalentRadiusDescriptor.getParameterType(String name)
Gets the parameterType attribute of the VdWRadiusDescriptor object.
|
Object |
BondsToAtomDescriptor.getParameterType(String name)
Gets the parameterType attribute of the BondsToAtomDescriptor object
|
Object |
AtomValenceDescriptor.getParameterType(String name)
Gets the parameterType attribute of the VdWRadiusDescriptor object.
|
Object |
AtomHybridizationVSEPRDescriptor.getParameterType(String name)
Gets the parameterType attribute of the AtomHybridizationVSEPRDescriptor object
|
Object |
AtomHybridizationDescriptor.getParameterType(String name)
Gets the parameterType attribute of the VdWRadiusDescriptor object.
|
Object |
AtomDegreeDescriptor.getParameterType(String name)
Gets the parameterType attribute of the AtomDegreeDescriptor object.
|
DescriptorSpecification |
VdWRadiusDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
StabilizationPlusChargeDescriptor.getSpecification()
Gets the specification attribute of the StabilizationPlusChargeDescriptor
object
|
DescriptorSpecification |
SigmaElectronegativityDescriptor.getSpecification()
Gets the specification attribute of the SigmaElectronegativityDescriptor
object
|
DescriptorSpecification |
RDFProtonDescriptor_GSR.getSpecification()
Gets the specification attribute of the RDFProtonDescriptor_GSR
object
|
DescriptorSpecification |
RDFProtonDescriptor_GHR_topol.getSpecification()
Gets the specification attribute of the RDFProtonDescriptor_GHR_topol
object
|
DescriptorSpecification |
RDFProtonDescriptor_GHR.getSpecification()
Gets the specification attribute of the RDFProtonDescriptor_GHR
object
|
DescriptorSpecification |
RDFProtonDescriptor_GDR.getSpecification()
Gets the specification attribute of the RDFProtonDescriptor_GDR
object
|
DescriptorSpecification |
RDFProtonDescriptor_G3R.getSpecification()
Gets the specification attribute of the RDFProtonDescriptor_G3R object
|
DescriptorSpecification |
ProtonTotalPartialChargeDescriptor.getSpecification()
Gets the specification attribute of the ProtonTotalPartialChargeDescriptor
object
|
DescriptorSpecification |
ProtonAffinityHOSEDescriptor.getSpecification()
Gets the specification attribute of the ProtonAffinityDescriptor object
|
DescriptorSpecification |
PiElectronegativityDescriptor.getSpecification()
Gets the specification attribute of the PiElectronegativityDescriptor
object
|
DescriptorSpecification |
PeriodicTablePositionDescriptor.getSpecification()
Gets the specification attribute of the PeriodicTablePositionDescriptor object
|
DescriptorSpecification |
PartialTChargePEOEDescriptor.getSpecification()
Gets the specification attribute of the PartialTChargePEOEDescriptor object
|
DescriptorSpecification |
PartialTChargeMMFF94Descriptor.getSpecification()
Gets the specification attribute of the PartialTChargeMMFF94Descriptor object
|
DescriptorSpecification |
PartialSigmaChargeDescriptor.getSpecification()
Gets the specification attribute of the PartialSigmaChargeDescriptor
object
|
DescriptorSpecification |
PartialPiChargeDescriptor.getSpecification()
Gets the specification attribute of the PartialPiChargeDescriptor
object
|
DescriptorSpecification |
IsProtonInConjugatedPiSystemDescriptor.getSpecification()
Gets the specification attribute of the
IsProtonInConjugatedPiSystemDescriptor object
|
DescriptorSpecification |
IsProtonInAromaticSystemDescriptor.getSpecification()
Gets the specification attribute of the IsProtonInAromaticSystemDescriptor
object
|
DescriptorSpecification |
IPAtomicLearningDescriptor.getSpecification()
Gets the specification attribute of the IPAtomicLearningDescriptor object
|
DescriptorSpecification |
IPAtomicHOSEDescriptor.getSpecification()
Gets the specification attribute of the IPAtomicHOSEDescriptor object
|
DescriptorSpecification |
InductiveAtomicSoftnessDescriptor.getSpecification()
Gets the specification attribute of the InductiveAtomicSoftnessDescriptor
object
|
DescriptorSpecification |
InductiveAtomicHardnessDescriptor.getSpecification()
Gets the specification attribute of the InductiveAtomicHardnessDescriptor
object
|
DescriptorSpecification |
EffectiveAtomPolarizabilityDescriptor.getSpecification()
Gets the specification attribute of the EffectiveAtomPolarizabilityDescriptor
object
|
DescriptorSpecification |
DistanceToAtomDescriptor.getSpecification()
Gets the specification attribute of the DistanceToAtomDescriptor object
|
DescriptorSpecification |
CovalentRadiusDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
BondsToAtomDescriptor.getSpecification()
Gets the specification attribute of the BondsToAtomDescriptor object
|
DescriptorSpecification |
AtomValenceDescriptor.getSpecification()
Gets the specification attribute of the AtomValenceDescriptor object
|
DescriptorSpecification |
AtomHybridizationVSEPRDescriptor.getSpecification()
Gets the specification attribute of the AtomHybridizationVSEPRDescriptor object
|
DescriptorSpecification |
AtomHybridizationDescriptor.getSpecification()
Gets the specification attribute of the AtomHybridizationDescriptor object
|
DescriptorSpecification |
AtomDegreeDescriptor.getSpecification() |
void |
VdWRadiusDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
StabilizationPlusChargeDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the StabilizationPlusChargeDescriptor
object
|
void |
SigmaElectronegativityDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the SigmaElectronegativityDescriptor
object
|
void |
RDFProtonDescriptor_GSR.setParameters(Object[] params)
Sets the parameters attribute of the RDFProtonDescriptor
object
|
void |
RDFProtonDescriptor_GHR_topol.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 |
RDFProtonDescriptor_GDR.setParameters(Object[] params)
Sets the parameters attribute of the RDFProtonDescriptor
object
|
void |
RDFProtonDescriptor_G3R.setParameters(Object[] params)
Sets the parameters attribute of the RDFProtonDescriptor object
|
void |
ProtonTotalPartialChargeDescriptor.setParameters(Object[] params)
This descriptor does not have any parameter to be set.
|
void |
ProtonAffinityHOSEDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
PiElectronegativityDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the PiElectronegativityDescriptor
object
|
void |
PeriodicTablePositionDescriptor.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 |
PartialTChargeMMFF94Descriptor.setParameters(Object[] params)
This descriptor does not have any parameter to be set.
|
void |
PartialSigmaChargeDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the PartialSigmaChargeDescriptor
object
|
void |
PartialPiChargeDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the PartialPiChargeDescriptor
object
|
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 |
IPAtomicLearningDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
IPAtomicHOSEDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
InductiveAtomicSoftnessDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
InductiveAtomicHardnessDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
EffectiveAtomPolarizabilityDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
DistanceToAtomDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the DistanceToAtomDescriptor object
|
void |
CovalentRadiusDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
BondsToAtomDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the BondsToAtomDescriptor object
|
void |
AtomValenceDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
AtomHybridizationVSEPRDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
AtomHybridizationDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
AtomDegreeDescriptor.setParameters(Object[] params)
This descriptor does not have any parameter to be set.
|
Modifier and Type | Method and Description |
---|---|
String[] |
PiContactDetectionDescriptor.getDescriptorNames() |
Modifier and Type | Method and Description |
---|---|
DescriptorValue |
IPBondLearningDescriptor.calculate(IBond bond,
IAtomContainer atomContainer)
This method calculates the ionization potential of a bond.
|
DescriptorValue |
BondSigmaElectronegativityDescriptor.calculate(IBond aBond,
IAtomContainer atomContainer)
The method calculates the sigma electronegativity of a given bond
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
|
DescriptorValue |
BondPartialTChargeDescriptor.calculate(IBond bond,
IAtomContainer ac)
The method calculates the bond total Partial charge of a given bond
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
|
DescriptorValue |
BondPartialSigmaChargeDescriptor.calculate(IBond bond,
IAtomContainer ac)
The method calculates the bond-sigma Partial charge of a given bond
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
|
DescriptorValue |
BondPartialPiChargeDescriptor.calculate(IBond bond,
IAtomContainer ac)
The method calculates the bond-pi Partial charge of a given bond
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
|
DescriptorValue |
AtomicNumberDifferenceDescriptor.calculate(IBond bond,
IAtomContainer ac) |
String[] |
IPBondLearningDescriptor.getDescriptorNames() |
String[] |
BondSigmaElectronegativityDescriptor.getDescriptorNames() |
String[] |
BondPartialTChargeDescriptor.getDescriptorNames() |
String[] |
BondPartialSigmaChargeDescriptor.getDescriptorNames() |
String[] |
BondPartialPiChargeDescriptor.getDescriptorNames() |
String[] |
AtomicNumberDifferenceDescriptor.getDescriptorNames() |
String[] |
IPBondLearningDescriptor.getParameterNames()
Gets the parameterNames attribute of the IPBondLearningDescriptor object.
|
String[] |
BondSigmaElectronegativityDescriptor.getParameterNames()
Gets the parameterNames attribute of the BondSigmaElectronegativityDescriptor object.
|
String[] |
BondPartialTChargeDescriptor.getParameterNames()
Gets the parameterNames attribute of the BondPartialTChargeDescriptor object.
|
String[] |
BondPartialSigmaChargeDescriptor.getParameterNames()
Gets the parameterNames attribute of the BondPartialSigmaChargeDescriptor object.
|
String[] |
BondPartialPiChargeDescriptor.getParameterNames()
Gets the parameterNames attribute of the BondPartialPiChargeDescriptor object.
|
String[] |
AtomicNumberDifferenceDescriptor.getParameterNames() |
Object[] |
IPBondLearningDescriptor.getParameters()
Gets the parameters attribute of the IPBondLearningDescriptor object.
|
Object[] |
BondSigmaElectronegativityDescriptor.getParameters()
Gets the parameters attribute of the BondSigmaElectronegativityDescriptor object.
|
Object[] |
BondPartialTChargeDescriptor.getParameters()
Gets the parameters attribute of the BondPartialTChargeDescriptor object.
|
Object[] |
BondPartialSigmaChargeDescriptor.getParameters()
Gets the parameters attribute of the BondPartialSigmaChargeDescriptor object.
|
Object[] |
BondPartialPiChargeDescriptor.getParameters()
Gets the parameters attribute of the BondPartialPiChargeDescriptor object.
|
Object[] |
AtomicNumberDifferenceDescriptor.getParameters() |
Object |
IPBondLearningDescriptor.getParameterType(String name)
Gets the parameterType attribute of the IPBondLearningDescriptor object.
|
Object |
BondSigmaElectronegativityDescriptor.getParameterType(String name)
Gets the parameterType attribute of the BondSigmaElectronegativityDescriptor object.
|
Object |
BondPartialTChargeDescriptor.getParameterType(String name)
Gets the parameterType attribute of the BondPartialTChargeDescriptor object.
|
Object |
BondPartialSigmaChargeDescriptor.getParameterType(String name)
Gets the parameterType attribute of the BondPartialSigmaChargeDescriptor object.
|
Object |
BondPartialPiChargeDescriptor.getParameterType(String name)
Gets the parameterType attribute of the BondPartialPiChargeDescriptor object.
|
Object |
AtomicNumberDifferenceDescriptor.getParameterType(String name) |
DescriptorSpecification |
IPBondLearningDescriptor.getSpecification()
Gets the specification attribute of the IPBondLearningDescriptor object
|
DescriptorSpecification |
BondSigmaElectronegativityDescriptor.getSpecification()
Gets the specification attribute of the BondSigmaElectronegativityDescriptor
object
|
DescriptorSpecification |
BondPartialTChargeDescriptor.getSpecification()
Gets the specification attribute of the BondPartialTChargeDescriptor
object
|
DescriptorSpecification |
BondPartialSigmaChargeDescriptor.getSpecification()
Gets the specification attribute of the BondPartialSigmaChargeDescriptor
object
|
DescriptorSpecification |
BondPartialPiChargeDescriptor.getSpecification()
Gets the specification attribute of the BondPartialPiChargeDescriptor
object
|
DescriptorSpecification |
AtomicNumberDifferenceDescriptor.getSpecification() |
void |
IPBondLearningDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
BondSigmaElectronegativityDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
BondPartialTChargeDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
BondPartialSigmaChargeDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
BondPartialPiChargeDescriptor.setParameters(Object[] params)
This descriptor does have any parameter.
|
void |
AtomicNumberDifferenceDescriptor.setParameters(Object[] params) |
Modifier and Type | Method and Description |
---|---|
DescriptorValue |
ZagrebIndexDescriptor.calculate(IAtomContainer atomContainer)
Evaluate the Zagreb Index for a molecule.
|
DescriptorValue |
XLogPDescriptor.calculate(IAtomContainer atomContainer)
Calculates the xlogP for an atom container.
|
DescriptorValue |
WienerNumbersDescriptor.calculate(IAtomContainer atomContainer)
Calculate the Wiener numbers.
|
DescriptorValue |
WHIMDescriptor.calculate(IAtomContainer container)
Calculates 11 directional and 6 non-directional WHIM descriptors for.
|
DescriptorValue |
WeightedPathDescriptor.calculate(IAtomContainer container)
Calculates the weighted path descriptors.
|
DescriptorValue |
WeightDescriptor.calculate(IAtomContainer container)
Calculate the weight of specified element type in the supplied
IAtomContainer . |
DescriptorValue |
VAdjMaDescriptor.calculate(IAtomContainer atomContainer)
calculates the VAdjMa descriptor for an atom container
|
DescriptorValue |
VABCDescriptor.calculate(IAtomContainer atomContainer)
Calculates the descriptor value using the
VABCVolume class. |
DescriptorValue |
TPSADescriptor.calculate(IAtomContainer atomContainer)
Calculates the TPSA for an atom container.
|
DescriptorValue |
RuleOfFiveDescriptor.calculate(IAtomContainer mol)
the method take a boolean checkAromaticity: if the boolean is true, it means that
aromaticity has to be checked.
|
DescriptorValue |
RotatableBondsCountDescriptor.calculate(IAtomContainer ac)
The method calculates the number of rotatable bonds of an atom container.
|
DescriptorValue |
PetitjeanShapeIndexDescriptor.calculate(IAtomContainer container)
Calculates the two Petitjean shape indices.
|
DescriptorValue |
PetitjeanNumberDescriptor.calculate(IAtomContainer atomContainer)
Evaluate the descriptor for the molecule.
|
DescriptorValue |
MomentOfInertiaDescriptor.calculate(IAtomContainer container)
Calculates the 3 MI's, 3 ration and the R_gyr value.
|
DescriptorValue |
MDEDescriptor.calculate(IAtomContainer container)
Calculate the weight of specified element type in the supplied
IAtomContainer . |
DescriptorValue |
MannholdLogPDescriptor.calculate(IAtomContainer atomContainer)
Calculates the Mannhold LogP for an atom container.
|
DescriptorValue |
LongestAliphaticChainDescriptor.calculate(IAtomContainer atomContainer)
Calculate the count of atoms of the longest aliphatic chain in the supplied
AtomContainer . |
DescriptorValue |
LengthOverBreadthDescriptor.calculate(IAtomContainer atomContainer)
Evaluate the descriptor for the molecule.
|
DescriptorValue |
LargestPiSystemDescriptor.calculate(IAtomContainer container)
Calculate the count of atoms of the largest pi system in the supplied
AtomContainer . |
DescriptorValue |
LargestChainDescriptor.calculate(IAtomContainer atomContainer)
Calculate the count of atoms of the largest chain in the supplied
IAtomContainer . |
DescriptorValue |
KierHallSmartsDescriptor.calculate(IAtomContainer container)
This method calculates occurrences of the Kier & Hall E-state fragments.
|
DescriptorValue |
KappaShapeIndicesDescriptor.calculate(IAtomContainer container)
calculates the kier shape indices for an atom container
|
DescriptorValue |
IPMolecularLearningDescriptor.calculate(IAtomContainer atomContainer)
It calculates the first ionization energy of a molecule.
|
DescriptorValue |
HybridizationRatioDescriptor.calculate(IAtomContainer container)
Calculate sp3/sp2 hybridization ratio in the supplied
IAtomContainer . |
DescriptorValue |
HBondDonorCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the number of H bond donors.
|
DescriptorValue |
HBondAcceptorCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the number of H bond acceptors.
|
DescriptorValue |
GravitationalIndexDescriptor.calculate(IAtomContainer container)
Calculates the 9 gravitational indices.
|
DescriptorValue |
FragmentComplexityDescriptor.calculate(IAtomContainer container)
Calculate the complexity in the supplied
AtomContainer . |
DescriptorValue |
FMFDescriptor.calculate(IAtomContainer container)
Calculates the FMF descriptor value for the given
IAtomContainer . |
DescriptorValue |
EccentricConnectivityIndexDescriptor.calculate(IAtomContainer container)
Calculates the eccentric connectivity
|
DescriptorValue |
CPSADescriptor.calculate(IAtomContainer atomContainer)
Evaluates the 29 CPSA descriptors using Gasteiger-Marsilli charges.
|
DescriptorValue |
ChiPathDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
ChiPathClusterDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
ChiClusterDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
ChiChainDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
CarbonTypesDescriptor.calculate(IAtomContainer container)
Calculates the 9 carbon types descriptors
|
DescriptorValue |
BPolDescriptor.calculate(IAtomContainer container)
This method calculate the sum of the absolute value of
the difference between atomic polarizabilities of all bonded atoms in the molecule
|
DescriptorValue |
BondCountDescriptor.calculate(IAtomContainer container)
This method calculate the number of bonds of a given type in an atomContainer
|
DescriptorValue |
BCUTDescriptor.calculate(IAtomContainer container)
Calculates the three classes of BCUT descriptors.
|
DescriptorValue |
BasicGroupCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the descriptor value for the given IAtomContainer.
|
DescriptorValue |
AutocorrelationDescriptorPolarizability.calculate(IAtomContainer container)
This method calculate the ATS Autocorrelation descriptor.
|
DescriptorValue |
AutocorrelationDescriptorMass.calculate(IAtomContainer atomContainer)
This method calculate the ATS Autocorrelation descriptor.
|
DescriptorValue |
AutocorrelationDescriptorCharge.calculate(IAtomContainer atomContainer) |
DescriptorValue |
AtomCountDescriptor.calculate(IAtomContainer container)
This method calculate the number of atoms of a given type in an
IAtomContainer . |
DescriptorValue |
AromaticBondsCountDescriptor.calculate(IAtomContainer atomContainer)
Calculate the count of aromatic atoms in the supplied
IAtomContainer . |
DescriptorValue |
AromaticAtomsCountDescriptor.calculate(IAtomContainer atomContainer)
Calculate the count of aromatic atoms in the supplied
IAtomContainer . |
DescriptorValue |
APolDescriptor.calculate(IAtomContainer container)
Calculate the sum of atomic polarizabilities in an
IAtomContainer . |
DescriptorValue |
AminoAcidCountDescriptor.calculate(IAtomContainer ac)
Determine the number of amino acids groups the supplied
IAtomContainer . |
DescriptorValue |
ALOGPDescriptor.calculate(IAtomContainer atomContainer)
The AlogP descriptor.
|
DescriptorValue |
AcidicGroupCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the descriptor value for the given IAtomContainer.
|
DescriptorValue |
IPMolecularLearningDescriptor.calculatePlus(IAtomContainer container)
It calculates the 1,2,..
|
String[] |
ZagrebIndexDescriptor.getDescriptorNames() |
String[] |
XLogPDescriptor.getDescriptorNames() |
String[] |
WienerNumbersDescriptor.getDescriptorNames() |
String[] |
WHIMDescriptor.getDescriptorNames() |
String[] |
WeightedPathDescriptor.getDescriptorNames() |
String[] |
WeightDescriptor.getDescriptorNames() |
String[] |
VAdjMaDescriptor.getDescriptorNames() |
String[] |
VABCDescriptor.getDescriptorNames() |
String[] |
TPSADescriptor.getDescriptorNames() |
String[] |
RuleOfFiveDescriptor.getDescriptorNames() |
String[] |
RotatableBondsCountDescriptor.getDescriptorNames() |
String[] |
PetitjeanShapeIndexDescriptor.getDescriptorNames() |
String[] |
PetitjeanNumberDescriptor.getDescriptorNames() |
String[] |
MomentOfInertiaDescriptor.getDescriptorNames() |
String[] |
MDEDescriptor.getDescriptorNames() |
String[] |
MannholdLogPDescriptor.getDescriptorNames() |
String[] |
LongestAliphaticChainDescriptor.getDescriptorNames() |
String[] |
LengthOverBreadthDescriptor.getDescriptorNames() |
String[] |
LargestPiSystemDescriptor.getDescriptorNames() |
String[] |
LargestChainDescriptor.getDescriptorNames() |
String[] |
KierHallSmartsDescriptor.getDescriptorNames() |
String[] |
KappaShapeIndicesDescriptor.getDescriptorNames() |
String[] |
IPMolecularLearningDescriptor.getDescriptorNames() |
String[] |
HybridizationRatioDescriptor.getDescriptorNames() |
String[] |
HBondDonorCountDescriptor.getDescriptorNames() |
String[] |
HBondAcceptorCountDescriptor.getDescriptorNames() |
String[] |
GravitationalIndexDescriptor.getDescriptorNames() |
String[] |
FragmentComplexityDescriptor.getDescriptorNames() |
String[] |
EccentricConnectivityIndexDescriptor.getDescriptorNames() |
String[] |
CPSADescriptor.getDescriptorNames() |
String[] |
ChiPathDescriptor.getDescriptorNames() |
String[] |
ChiPathClusterDescriptor.getDescriptorNames() |
String[] |
ChiClusterDescriptor.getDescriptorNames() |
String[] |
ChiChainDescriptor.getDescriptorNames() |
String[] |
CarbonTypesDescriptor.getDescriptorNames() |
String[] |
BPolDescriptor.getDescriptorNames() |
String[] |
BondCountDescriptor.getDescriptorNames() |
String[] |
BCUTDescriptor.getDescriptorNames() |
String[] |
BasicGroupCountDescriptor.getDescriptorNames()
Returns an array of names for each descriptor value calculated.
|
String[] |
AutocorrelationDescriptorPolarizability.getDescriptorNames() |
String[] |
AutocorrelationDescriptorMass.getDescriptorNames() |
String[] |
AutocorrelationDescriptorCharge.getDescriptorNames() |
String[] |
AtomCountDescriptor.getDescriptorNames() |
String[] |
AromaticBondsCountDescriptor.getDescriptorNames() |
String[] |
AromaticAtomsCountDescriptor.getDescriptorNames() |
String[] |
APolDescriptor.getDescriptorNames() |
String[] |
AminoAcidCountDescriptor.getDescriptorNames() |
String[] |
ALOGPDescriptor.getDescriptorNames() |
String[] |
AcidicGroupCountDescriptor.getDescriptorNames()
Returns an array of names for each descriptor value calculated.
|
IDescriptorResult |
ZagrebIndexDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
XLogPDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
WienerNumbersDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
WHIMDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
WeightedPathDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
WeightDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
VAdjMaDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
VABCDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
TPSADescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
RuleOfFiveDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
RotatableBondsCountDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
PetitjeanShapeIndexDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
PetitjeanNumberDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
MomentOfInertiaDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
MDEDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
MannholdLogPDescriptor.getDescriptorResultType()
Returns a type of return value calculated by this descriptor.
|
IDescriptorResult |
LongestAliphaticChainDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
LengthOverBreadthDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
LargestPiSystemDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
LargestChainDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
KierHallSmartsDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
KappaShapeIndicesDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
IPMolecularLearningDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
HybridizationRatioDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
HBondDonorCountDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
HBondAcceptorCountDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
GravitationalIndexDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
FragmentComplexityDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
EccentricConnectivityIndexDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
CPSADescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
ChiPathDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
ChiPathClusterDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
ChiClusterDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
ChiChainDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
CarbonTypesDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
BPolDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
BondCountDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
BCUTDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
BasicGroupCountDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
AutocorrelationDescriptorPolarizability.getDescriptorResultType() |
IDescriptorResult |
AutocorrelationDescriptorMass.getDescriptorResultType() |
IDescriptorResult |
AutocorrelationDescriptorCharge.getDescriptorResultType() |
IDescriptorResult |
AtomCountDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
AromaticBondsCountDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
AromaticAtomsCountDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
APolDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
AminoAcidCountDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
ALOGPDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
IDescriptorResult |
AcidicGroupCountDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
String[] |
ZagrebIndexDescriptor.getParameterNames()
Gets the parameterNames attribute of the ZagrebIndexDescriptor object.
|
String[] |
XLogPDescriptor.getParameterNames()
Gets the parameterNames attribute of the XLogPDescriptor object.
|
String[] |
WienerNumbersDescriptor.getParameterNames()
Gets the parameterNames attribute of the WienerNumbersDescriptor object.
|
String[] |
WHIMDescriptor.getParameterNames()
Gets the parameterNames attribute of the WHIMDescriptor object.
|
String[] |
WeightedPathDescriptor.getParameterNames()
Gets the parameterNames attribute of the WeightedPathDescriptor object.
|
String[] |
WeightDescriptor.getParameterNames()
Gets the parameterNames attribute of the WeightDescriptor object.
|
String[] |
VAdjMaDescriptor.getParameterNames()
Gets the parameterNames attribute of the VAdjMaDescriptor object
|
String[] |
VABCDescriptor.getParameterNames()
Returns the names of the parameters for this descriptor.
|
String[] |
TPSADescriptor.getParameterNames()
Gets the parameterNames attribute of the TPSADescriptor object.
|
String[] |
RuleOfFiveDescriptor.getParameterNames()
Gets the parameterNames attribute of the RuleOfFiveDescriptor object.
|
String[] |
RotatableBondsCountDescriptor.getParameterNames()
Gets the parameterNames attribute of the RotatableBondsCountDescriptor
object
|
String[] |
PetitjeanShapeIndexDescriptor.getParameterNames()
Gets the parameterNames attribute of the PetitjeanShapeIndexDescriptor object.
|
String[] |
PetitjeanNumberDescriptor.getParameterNames()
Gets the parameterNames attribute of the PetitjeanNumberDescriptor object
|
String[] |
MomentOfInertiaDescriptor.getParameterNames()
Gets the parameterNames attribute of the MomentOfInertiaDescriptor object.
|
String[] |
MDEDescriptor.getParameterNames()
Gets the parameterNames attribute of the WeightDescriptor object.
|
String[] |
MannholdLogPDescriptor.getParameterNames()
Gets the parameterNames attribute for this descriptor.
|
String[] |
LongestAliphaticChainDescriptor.getParameterNames()
Gets the parameterNames attribute of the LongestAliphaticChainDescriptor object.
|
String[] |
LengthOverBreadthDescriptor.getParameterNames()
Gets the parameterNames attribute of the PetitjeanNumberDescriptor object
|
String[] |
LargestPiSystemDescriptor.getParameterNames()
Gets the parameterNames attribute of the LargestPiSystemDescriptor object.
|
String[] |
LargestChainDescriptor.getParameterNames()
Gets the parameterNames attribute of the LargestPiSystemDescriptor object.
|
String[] |
KierHallSmartsDescriptor.getParameterNames()
Gets the parameterNames attribute of the descriptor.
|
String[] |
KappaShapeIndicesDescriptor.getParameterNames()
Gets the parameterNames attribute of the
KappaShapeIndicesDescriptor object
|
String[] |
IPMolecularLearningDescriptor.getParameterNames()
Gets the parameterNames attribute of the IPMolecularLearningDescriptor object
|
String[] |
HybridizationRatioDescriptor.getParameterNames()
Gets the parameterNames attribute of the HybridizationRatioDescriptor object.
|
String[] |
HBondDonorCountDescriptor.getParameterNames()
Gets the parameterNames of the HBondDonorCountDescriptor.
|
String[] |
HBondAcceptorCountDescriptor.getParameterNames()
Gets the parameterNames attribute of the HBondAcceptorCountDescriptor object.
|
String[] |
GravitationalIndexDescriptor.getParameterNames()
Gets the parameterNames attribute of the GravitationalIndexDescriptor object.
|
String[] |
FragmentComplexityDescriptor.getParameterNames()
Gets the parameterNames attribute of the FragmentComplexityDescriptor object.
|
String[] |
EccentricConnectivityIndexDescriptor.getParameterNames()
Gets the parameterNames attribute of the EccentricConnectivityIndexDescriptor object
|
String[] |
CPSADescriptor.getParameterNames()
Gets the parameterNames attribute of the CPSADescriptor object.
|
String[] |
ChiPathDescriptor.getParameterNames() |
String[] |
ChiPathClusterDescriptor.getParameterNames() |
String[] |
ChiClusterDescriptor.getParameterNames() |
String[] |
ChiChainDescriptor.getParameterNames() |
String[] |
CarbonTypesDescriptor.getParameterNames()
Gets the parameterNames attribute of the GravitationalIndexDescriptor object.
|
String[] |
BPolDescriptor.getParameterNames()
Gets the parameterNames attribute of the BPolDescriptor object
|
String[] |
BondCountDescriptor.getParameterNames()
Gets the parameterNames attribute of the BondCountDescriptor object
|
String[] |
BCUTDescriptor.getParameterNames()
Gets the parameterNames attribute of the BCUTDescriptor object.
|
String[] |
BasicGroupCountDescriptor.getParameterNames()
Returns the names of the parameters for this descriptor.
|
String[] |
AutocorrelationDescriptorPolarizability.getParameterNames() |
String[] |
AutocorrelationDescriptorMass.getParameterNames() |
String[] |
AutocorrelationDescriptorCharge.getParameterNames() |
String[] |
AtomCountDescriptor.getParameterNames()
Gets the parameterNames attribute of the AtomCountDescriptor object.
|
String[] |
AromaticBondsCountDescriptor.getParameterNames()
Gets the parameterNames attribute of the AromaticBondsCountDescriptor object.
|
String[] |
AromaticAtomsCountDescriptor.getParameterNames()
Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.
|
String[] |
APolDescriptor.getParameterNames()
Gets the parameterNames attribute of the APolDescriptor object.
|
String[] |
AminoAcidCountDescriptor.getParameterNames()
Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.
|
String[] |
ALOGPDescriptor.getParameterNames() |
String[] |
AcidicGroupCountDescriptor.getParameterNames()
Returns the names of the parameters for this descriptor.
|
Object[] |
ZagrebIndexDescriptor.getParameters()
Gets the parameters attribute of the ZagrebIndexDescriptor object.
|
Object[] |
XLogPDescriptor.getParameters()
Gets the parameters attribute of the XLogPDescriptor object.
|
Object[] |
WienerNumbersDescriptor.getParameters()
Gets the parameters attribute of the WienerNumbersDescriptor object.
|
Object[] |
WHIMDescriptor.getParameters()
Gets the parameters attribute of the WHIMDescriptor object.
|
Object[] |
WeightedPathDescriptor.getParameters()
Gets the parameters attribute of the WeightedPathDescriptor object.
|
Object[] |
WeightDescriptor.getParameters()
Gets the parameters attribute of the WeightDescriptor object.
|
Object[] |
VAdjMaDescriptor.getParameters()
Gets the parameters attribute of the VAdjMaDescriptor object
|
Object[] |
VABCDescriptor.getParameters()
Returns the current parameter values.
|
Object[] |
TPSADescriptor.getParameters()
Gets the parameters attribute of the TPSADescriptor object.
|
Object[] |
RuleOfFiveDescriptor.getParameters()
Gets the parameters attribute of the RuleOfFiveDescriptor object.
|
Object[] |
RotatableBondsCountDescriptor.getParameters()
Gets the parameters attribute of the RotatableBondsCountDescriptor object
|
Object[] |
PetitjeanShapeIndexDescriptor.getParameters()
Gets the parameters attribute of the PetitjeanShapeIndexDescriptor object.
|
Object[] |
PetitjeanNumberDescriptor.getParameters()
Gets the parameters attribute of the PetitjeanNumberDescriptor object
|
Object[] |
MomentOfInertiaDescriptor.getParameters()
Gets the parameters attribute of the MomentOfInertiaDescriptor object.
|
Object[] |
MDEDescriptor.getParameters()
Gets the parameters attribute of the WeightDescriptor object.
|
Object[] |
MannholdLogPDescriptor.getParameters()
Gets the parameters attribute of the MannholdLogPDescriptor object.
|
Object[] |
LongestAliphaticChainDescriptor.getParameters()
Gets the parameters attribute of the LongestAliphaticChainDescriptor object.
|
Object[] |
LengthOverBreadthDescriptor.getParameters()
Gets the parameters attribute of the PetitjeanNumberDescriptor object
|
Object[] |
LargestPiSystemDescriptor.getParameters()
Gets the parameters attribute of the LargestPiSystemDescriptor object.
|
Object[] |
LargestChainDescriptor.getParameters()
Gets the parameters attribute of the LargestChainDescriptor object.
|
Object[] |
KierHallSmartsDescriptor.getParameters()
Gets the parameters attribute of the descriptor.
|
Object[] |
KappaShapeIndicesDescriptor.getParameters()
Gets the parameters attribute of the
KappaShapeIndicesDescriptor object
|
Object[] |
IPMolecularLearningDescriptor.getParameters()
Gets the parameters attribute of the IPMolecularLearningDescriptor object
|
Object[] |
HybridizationRatioDescriptor.getParameters()
Gets the parameters attribute of the HybridizationRatioDescriptor object.
|
Object[] |
HBondDonorCountDescriptor.getParameters()
Gets the parameters of the HBondDonorCountDescriptor instance.
|
Object[] |
HBondAcceptorCountDescriptor.getParameters()
Gets the parameters attribute of the HBondAcceptorCountDescriptor object.
|
Object[] |
GravitationalIndexDescriptor.getParameters()
Gets the parameters attribute of the GravitationalIndexDescriptor object.
|
Object[] |
FragmentComplexityDescriptor.getParameters()
Gets the parameters attribute of the FragmentComplexityDescriptor object.
|
Object[] |
EccentricConnectivityIndexDescriptor.getParameters()
Gets the parameters attribute of the EccentricConnectivityIndexDescriptor object
|
Object[] |
CPSADescriptor.getParameters()
Gets the parameters attribute of the CPSADescriptor object.
|
Object[] |
ChiPathDescriptor.getParameters() |
Object[] |
ChiPathClusterDescriptor.getParameters() |
Object[] |
ChiClusterDescriptor.getParameters() |
Object[] |
ChiChainDescriptor.getParameters() |
Object[] |
CarbonTypesDescriptor.getParameters()
Gets the parameters attribute of the GravitationalIndexDescriptor object.
|
Object[] |
BPolDescriptor.getParameters()
Gets the parameters attribute of the BPolDescriptor object
|
Object[] |
BondCountDescriptor.getParameters()
Gets the parameters attribute of the BondCountDescriptor object
|
Object[] |
BCUTDescriptor.getParameters()
Gets the parameters attribute of the BCUTDescriptor object.
|
Object[] |
BasicGroupCountDescriptor.getParameters()
Returns the current parameter values.
|
Object[] |
AutocorrelationDescriptorPolarizability.getParameters() |
Object[] |
AutocorrelationDescriptorMass.getParameters() |
Object[] |
AutocorrelationDescriptorCharge.getParameters() |
Object[] |
AtomCountDescriptor.getParameters()
Gets the parameters attribute of the AtomCountDescriptor object.
|
Object[] |
AromaticBondsCountDescriptor.getParameters()
Gets the parameters attribute of the AromaticBondsCountDescriptor object.
|
Object[] |
AromaticAtomsCountDescriptor.getParameters()
Gets the parameters attribute of the AromaticAtomsCountDescriptor object.
|
Object[] |
APolDescriptor.getParameters()
Gets the parameters attribute of the APolDescriptor object.
|
Object[] |
AminoAcidCountDescriptor.getParameters()
Gets the parameters attribute of the AminoAcidsCountDescriptor object.
|
Object[] |
ALOGPDescriptor.getParameters() |
Object[] |
AcidicGroupCountDescriptor.getParameters()
Returns the current parameter values.
|
Object |
ZagrebIndexDescriptor.getParameterType(String name)
Gets the parameterType attribute of the ZagrebIndexDescriptor object.
|
Object |
XLogPDescriptor.getParameterType(String name)
Gets the parameterType attribute of the XLogPDescriptor object.
|
Object |
WienerNumbersDescriptor.getParameterType(String name)
Gets the parameterType attribute of the WienerNumbersDescriptor object.
|
Object |
WHIMDescriptor.getParameterType(String name)
Gets the parameterType attribute of the WHIMDescriptor object.
|
Object |
WeightedPathDescriptor.getParameterType(String name)
Gets the parameterType attribute of the WeightedPathDescriptor object.
|
Object |
WeightDescriptor.getParameterType(String name)
Gets the parameterType attribute of the WeightDescriptor object.
|
Object |
VAdjMaDescriptor.getParameterType(String name)
Gets the parameterType attribute of the VAdjMaDescriptor object
|
Object |
VABCDescriptor.getParameterType(String name)
Returns a class matching that of the parameter with the given name.
|
Object |
TPSADescriptor.getParameterType(String name)
Gets the parameterType attribute of the TPSADescriptor object.
|
Object |
RuleOfFiveDescriptor.getParameterType(String name)
Gets the parameterType attribute of the RuleOfFiveDescriptor object.
|
Object |
RotatableBondsCountDescriptor.getParameterType(String name)
Gets the parameterType attribute of the RotatableBondsCountDescriptor
object
|
Object |
PetitjeanShapeIndexDescriptor.getParameterType(String name)
Gets the parameterType attribute of the PetitjeanShapeIndexDescriptor object.
|
Object |
PetitjeanNumberDescriptor.getParameterType(String name)
Gets the parameterType attribute of the PetitjeanNumberDescriptor object
|
Object |
MomentOfInertiaDescriptor.getParameterType(String name)
Gets the parameterType attribute of the MomentOfInertiaDescriptor object.
|
Object |
MDEDescriptor.getParameterType(String name)
Gets the parameterType attribute of the WeightDescriptor object.
|
Object |
MannholdLogPDescriptor.getParameterType(String name)
Gets the parameterType attribute for a given parameter name.
|
Object |
LongestAliphaticChainDescriptor.getParameterType(String name)
Gets the parameterType attribute of the LongestAliphaticChainDescriptor object.
|
Object |
LengthOverBreadthDescriptor.getParameterType(String name)
Gets the parameterType attribute of the PetitjeanNumberDescriptor object
|
Object |
LargestPiSystemDescriptor.getParameterType(String name)
Gets the parameterType attribute of the LargestPiSystemDescriptor object.
|
Object |
LargestChainDescriptor.getParameterType(String name)
Gets the parameterType attribute of the LargestChainDescriptor object.
|
Object |
KierHallSmartsDescriptor.getParameterType(String name)
Gets the parameterType attribute of the descriptor.
|
Object |
KappaShapeIndicesDescriptor.getParameterType(String name)
Gets the parameterType attribute of the
KappaShapeIndicesDescriptor object
|
Object |
IPMolecularLearningDescriptor.getParameterType(String name)
Gets the parameterType attribute of the IPMolecularLearningDescriptor object
|
Object |
HybridizationRatioDescriptor.getParameterType(String name)
Gets the parameterType attribute of the HybridizationRatioDescriptor object.
|
Object |
HBondDonorCountDescriptor.getParameterType(String name)
Gets the parameterType of the HBondDonorCountDescriptor.
|
Object |
HBondAcceptorCountDescriptor.getParameterType(String name)
Gets the parameterType attribute of the HBondAcceptorCountDescriptor object.
|
Object |
GravitationalIndexDescriptor.getParameterType(String name)
Gets the parameterType attribute of the GravitationalIndexDescriptor object.
|
Object |
FragmentComplexityDescriptor.getParameterType(String name)
Gets the parameterType attribute of the FragmentComplexityDescriptor object.
|
Object |
EccentricConnectivityIndexDescriptor.getParameterType(String name)
Gets the parameterType attribute of the EccentricConnectivityIndexDescriptor object
|
Object |
CPSADescriptor.getParameterType(String name)
Gets the parameterType attribute of the CPSADescriptor object.
|
Object |
ChiPathDescriptor.getParameterType(String name) |
Object |
ChiPathClusterDescriptor.getParameterType(String name) |
Object |
ChiClusterDescriptor.getParameterType(String name) |
Object |
ChiChainDescriptor.getParameterType(String name) |
Object |
CarbonTypesDescriptor.getParameterType(String name)
Gets the parameterType attribute of the GravitationalIndexDescriptor object.
|
Object |
BPolDescriptor.getParameterType(String name)
Gets the parameterType attribute of the BPolDescriptor object
|
Object |
BondCountDescriptor.getParameterType(String name)
Gets the parameterType attribute of the BondCountDescriptor object
|
Object |
BCUTDescriptor.getParameterType(String name)
Gets the parameterType attribute of the BCUTDescriptor object.
|
Object |
BasicGroupCountDescriptor.getParameterType(String name)
Returns a class matching that of the parameter with the given name.
|
Object |
AutocorrelationDescriptorPolarizability.getParameterType(String name) |
Object |
AutocorrelationDescriptorMass.getParameterType(String name) |
Object |
AutocorrelationDescriptorCharge.getParameterType(String name) |
Object |
AtomCountDescriptor.getParameterType(String name)
Gets the parameterType attribute of the AtomCountDescriptor object.
|
Object |
AromaticBondsCountDescriptor.getParameterType(String name)
Gets the parameterType attribute of the AromaticBondsCountDescriptor object.
|
Object |
AromaticAtomsCountDescriptor.getParameterType(String name)
Gets the parameterType attribute of the AromaticAtomsCountDescriptor object.
|
Object |
APolDescriptor.getParameterType(String name)
Gets the parameterType attribute of the APolDescriptor object.
|
Object |
AminoAcidCountDescriptor.getParameterType(String name)
Gets the parameterType attribute of the AromaticAtomsCountDescriptor object.
|
Object |
ALOGPDescriptor.getParameterType(String name) |
Object |
AcidicGroupCountDescriptor.getParameterType(String name)
Returns a class matching that of the parameter with the given name.
|
DescriptorSpecification |
ZagrebIndexDescriptor.getSpecification()
Gets the specification attribute of the ZagrebIndexDescriptor object.
|
DescriptorSpecification |
XLogPDescriptor.getSpecification()
Gets the specification attribute of the XLogPDescriptor object.
|
DescriptorSpecification |
WienerNumbersDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
WHIMDescriptor.getSpecification() |
DescriptorSpecification |
WeightedPathDescriptor.getSpecification() |
DescriptorSpecification |
WeightDescriptor.getSpecification()
Returns a
Map which specifies which descriptor is implemented by this class. |
DescriptorSpecification |
VAdjMaDescriptor.getSpecification()
Gets the specification attribute of the VAdjMaDescriptor object
|
DescriptorSpecification |
VABCDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
TPSADescriptor.getSpecification()
Gets the specification attribute of the TPSADescriptor object.
|
DescriptorSpecification |
RuleOfFiveDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
RotatableBondsCountDescriptor.getSpecification()
Gets the specification attribute of the RotatableBondsCountDescriptor
object
|
DescriptorSpecification |
PetitjeanShapeIndexDescriptor.getSpecification() |
DescriptorSpecification |
PetitjeanNumberDescriptor.getSpecification()
Gets the specification attribute of the PetitjeanNumberDescriptor object
|
DescriptorSpecification |
MomentOfInertiaDescriptor.getSpecification() |
DescriptorSpecification |
MDEDescriptor.getSpecification()
Returns a
Map which specifies which descriptor is implemented by this class. |
DescriptorSpecification |
MannholdLogPDescriptor.getSpecification()
Gets the specification attribute of the MannholdLogPDescriptor object.
|
DescriptorSpecification |
LongestAliphaticChainDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
LengthOverBreadthDescriptor.getSpecification()
Gets the specification attribute of the PetitjeanNumberDescriptor object
|
DescriptorSpecification |
LargestPiSystemDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
LargestChainDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
KierHallSmartsDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
KappaShapeIndicesDescriptor.getSpecification()
Gets the specification attribute of the
KappaShapeIndicesDescriptor object
|
DescriptorSpecification |
IPMolecularLearningDescriptor.getSpecification()
Gets the specification attribute of the IPMolecularLearningDescriptor object
|
DescriptorSpecification |
HybridizationRatioDescriptor.getSpecification()
Returns a
DescriptorSpecification which specifies which descriptor is implemented by this class. |
DescriptorSpecification |
HBondDonorCountDescriptor.getSpecification()
Gets the specification attribute of the HBondDonorCountDescriptor
object
|
DescriptorSpecification |
HBondAcceptorCountDescriptor.getSpecification()
Gets the specification attribute of the HBondAcceptorCountDescriptor object.
|
DescriptorSpecification |
GravitationalIndexDescriptor.getSpecification() |
DescriptorSpecification |
FragmentComplexityDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
EccentricConnectivityIndexDescriptor.getSpecification() |
DescriptorSpecification |
CPSADescriptor.getSpecification() |
DescriptorSpecification |
ChiPathDescriptor.getSpecification() |
DescriptorSpecification |
ChiPathClusterDescriptor.getSpecification() |
DescriptorSpecification |
ChiClusterDescriptor.getSpecification() |
DescriptorSpecification |
ChiChainDescriptor.getSpecification() |
DescriptorSpecification |
CarbonTypesDescriptor.getSpecification() |
DescriptorSpecification |
BPolDescriptor.getSpecification() |
DescriptorSpecification |
BondCountDescriptor.getSpecification()
Gets the specification attribute of the BondCountDescriptor object
|
DescriptorSpecification |
BCUTDescriptor.getSpecification() |
DescriptorSpecification |
BasicGroupCountDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
AutocorrelationDescriptorPolarizability.getSpecification() |
DescriptorSpecification |
AutocorrelationDescriptorMass.getSpecification() |
DescriptorSpecification |
AutocorrelationDescriptorCharge.getSpecification() |
DescriptorSpecification |
AtomCountDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
AromaticBondsCountDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
AromaticAtomsCountDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
APolDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
AminoAcidCountDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
DescriptorSpecification |
ALOGPDescriptor.getSpecification() |
DescriptorSpecification |
AcidicGroupCountDescriptor.getSpecification()
Returns a
Map which specifies which descriptor
is implemented by this class. |
void |
ZagrebIndexDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the ZagrebIndexDescriptor object.
|
void |
XLogPDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the XLogPDescriptor object.
|
void |
WienerNumbersDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the WienerNumbersDescriptor object.
|
void |
WHIMDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the WHIMDescriptor object.
|
void |
WeightedPathDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the WeightedPathDescriptor object.
|
void |
WeightDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the WeightDescriptor object.
|
void |
VAdjMaDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the VAdjMaDescriptor object
|
void |
VABCDescriptor.setParameters(Object[] params)
Sets the parameters for this descriptor.
|
void |
TPSADescriptor.setParameters(Object[] params)
Sets the parameters attribute of the TPSADescriptor object.
|
void |
RuleOfFiveDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the RuleOfFiveDescriptor object.
|
void |
RotatableBondsCountDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the RotatableBondsCountDescriptor object
|
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 |
MomentOfInertiaDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the MomentOfInertiaDescriptor object.
|
void |
MDEDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the WeightDescriptor object.
|
void |
MannholdLogPDescriptor.setParameters(Object[] params)
This
IDescriptor does not have any parameters. |
void |
LongestAliphaticChainDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the LongestAliphaticChainDescriptor object.
|
void |
LengthOverBreadthDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the PetitjeanNumberDescriptor object
|
void |
LargestPiSystemDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the LargestPiSystemDescriptor object.
|
void |
LargestChainDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the LargestChain object.
|
void |
KierHallSmartsDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the descriptor.
|
void |
KappaShapeIndicesDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the
KappaShapeIndicesDescriptor object
|
void |
IPMolecularLearningDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the IPMolecularLearningDescriptor object
|
void |
HybridizationRatioDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the HybridizationRatioDescriptor object.
|
void |
HBondDonorCountDescriptor.setParameters(Object[] params)
Sets the parameter of this HBondDonorCountDescriptor instance.
|
void |
HBondAcceptorCountDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the HBondAcceptorCountDescriptor object.
|
void |
GravitationalIndexDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the GravitationalIndexDescriptor object.
|
void |
FragmentComplexityDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the FragmentComplexityDescriptor object.
|
void |
EccentricConnectivityIndexDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the EccentricConnectivityIndexDescriptor object
|
void |
CPSADescriptor.setParameters(Object[] params)
Sets the parameters attribute of the CPSADescriptor object.
|
void |
ChiPathDescriptor.setParameters(Object[] params) |
void |
ChiPathClusterDescriptor.setParameters(Object[] params) |
void |
ChiClusterDescriptor.setParameters(Object[] params) |
void |
ChiChainDescriptor.setParameters(Object[] params) |
void |
CarbonTypesDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the GravitationalIndexDescriptor object.
|
void |
BPolDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the BPolDescriptor object
|
void |
BondCountDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the BondCountDescriptor object
|
void |
BCUTDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the BCUTDescriptor object.
|
void |
BasicGroupCountDescriptor.setParameters(Object[] params)
Sets the parameters for this descriptor.
|
void |
AutocorrelationDescriptorPolarizability.setParameters(Object[] params) |
void |
AutocorrelationDescriptorMass.setParameters(Object[] params) |
void |
AutocorrelationDescriptorCharge.setParameters(Object[] params) |
void |
AtomCountDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the AtomCountDescriptor object.
|
void |
AromaticBondsCountDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the AromaticBondsCountDescriptor object.
|
void |
AromaticAtomsCountDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the AromaticAtomsCountDescriptor object.
|
void |
APolDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the APolDescriptor object.
|
void |
AminoAcidCountDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the AminoAcidsCountDescriptor object.
|
void |
ALOGPDescriptor.setParameters(Object[] params) |
void |
AcidicGroupCountDescriptor.setParameters(Object[] params)
Sets the parameters for this descriptor.
|
Constructor and Description |
---|
AcidicGroupCountDescriptor()
Creates a new
AcidicGroupCountDescriptor . |
BasicGroupCountDescriptor()
Creates a new
BasicGroupCountDescriptor . |
Modifier and Type | Method and Description |
---|---|
DescriptorValue |
TaeAminoAcidDescriptor.calculate(IAtomContainer container)
Calculates the 147 TAE descriptors for amino acids.
|
String[] |
TaeAminoAcidDescriptor.getDescriptorNames() |
IDescriptorResult |
TaeAminoAcidDescriptor.getDescriptorResultType()
Returns the specific type of the DescriptorResult object.
|
String[] |
TaeAminoAcidDescriptor.getParameterNames()
Gets the parameterNames attribute of the TaeAminOAcidDescriptor object.
|
Object[] |
TaeAminoAcidDescriptor.getParameters()
Gets the parameters attribute of the TaeAminoAcidDescriptor object.
|
Object |
TaeAminoAcidDescriptor.getParameterType(String name)
Gets the parameterType attribute of the TaeAminoAcidDescriptor object.
|
DescriptorSpecification |
TaeAminoAcidDescriptor.getSpecification() |
void |
TaeAminoAcidDescriptor.setParameters(Object[] params)
Sets the parameters attribute of the TaeAminoAcidDescriptor object.
|
Modifier and Type | Method and Description |
---|---|
void |
DoubleArrayResult.add(double value) |
void |
IntegerArrayResult.add(int value) |
boolean |
BooleanResult.booleanValue() |
double |
DoubleResult.doubleValue() |
int |
IntegerArrayResult.get(int index)
The first int is at index = 0;
|
double |
DoubleArrayResult.get(int index)
The first double is at index = 0;
|
int |
IntegerResult.intValue() |
int |
IntegerResultType.length() |
int |
IntegerResult.length() |
int |
IntegerArrayResultType.length() |
int |
IntegerArrayResult.length() |
int |
DoubleResultType.length() |
int |
DoubleResult.length() |
int |
DoubleArrayResultType.length() |
int |
DoubleArrayResult.length() |
int |
BooleanResultType.length() |
String |
IntegerResultType.toString() |
String |
IntegerResult.toString() |
String |
IntegerArrayResultType.toString() |
String |
IntegerArrayResult.toString() |
String |
DoubleResultType.toString() |
String |
DoubleResult.toString() |
String |
DoubleArrayResultType.toString() |
String |
DoubleArrayResult.toString() |
String |
BooleanResultType.toString() |
String |
BooleanResult.toString() |
Modifier and Type | Method and Description |
---|---|
void |
ReactionChain.addReaction(IReaction reaction,
int position)
Added a IReaction for this chain in position.
|
String |
ReactionSpecification.getImplementationIdentifier() |
String |
ReactionSpecification.getImplementationTitle() |
String |
ReactionSpecification.getImplementationVendor() |
IParameterReact |
ReactionEngine.getParameterClass(Class<?> paramClass)
Return the IParameterReact if it exists given the class.
|
List<IParameterReact> |
ReactionEngine.getParameterList()
Returns the current parameter values.
|
IReaction |
ReactionChain.getReaction(int position)
Get the reaction of this chain reaction object at the position.
|
int |
ReactionChain.getReactionStep(IReaction reaction)
Get the position of the reaction into this chain reaction object.
|
String |
ReactionSpecification.getSpecificationReference() |
void |
ReactionEngine.setParameterList(List<IParameterReact> params)
Returns the current parameter Map for this reaction.
|
Constructor and Description |
---|
ReactionSpecification(String specificationReference,
String implementationTitle,
String implementationIdentifier,
String implementationVendor)
Container for specifying the type of reaction.
|
Modifier and Type | Method and Description |
---|---|
IReaction |
TautomerizationMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
SharingElectronMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
RemovingSEofNBMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
RemovingSEofBMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
RearrangementChargeMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
RadicalSiteRearrangementMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
RadicalSiteIonizationMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
HomolyticCleavageMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
HeterolyticCleavageMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
AdductionPBMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
AdductionLPMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
Modifier and Type | Method and Description |
---|---|
ReactionSpecification |
TautomerizationReaction.getSpecification()
Gets the specification attribute of the TautomerizationReaction object.
|
ReactionSpecification |
SharingLonePairReaction.getSpecification()
Gets the specification attribute of the SharingLonePairReaction object.
|
ReactionSpecification |
SharingChargeSBReaction.getSpecification()
Gets the specification attribute of the SharingChargeSBReaction object
|
ReactionSpecification |
SharingChargeDBReaction.getSpecification()
Gets the specification attribute of the SharingChargeDBReaction object
|
ReactionSpecification |
SharingAnionReaction.getSpecification()
Gets the specification attribute of the SharingAnionReaction object.
|
ReactionSpecification |
RearrangementRadicalReaction.getSpecification()
Gets the specification attribute of the RearrangementRadicalReaction object
|
ReactionSpecification |
RearrangementLonePairReaction.getSpecification()
Gets the specification attribute of the RearrangementLonePairReaction object
|
ReactionSpecification |
RearrangementCationReaction.getSpecification()
Gets the specification attribute of the RearrangementCationReaction object
|
ReactionSpecification |
RearrangementAnionReaction.getSpecification()
Gets the specification attribute of the RearrangementAnionReaction object
|
ReactionSpecification |
RadicalSiteRrGammaReaction.getSpecification()
Gets the specification attribute of the RadicalSiteRrGammaReaction object
|
ReactionSpecification |
RadicalSiteRrDeltaReaction.getSpecification()
Gets the specification attribute of the RadicalSiteRrDeltaReaction object
|
ReactionSpecification |
RadicalSiteRrBetaReaction.getSpecification()
Gets the specification attribute of the RadicalSiteRrBetaReaction object
|
ReactionSpecification |
RadicalSiteRrAlphaReaction.getSpecification()
Gets the specification attribute of the RadicalSiteRrAlphaReaction object
|
ReactionSpecification |
RadicalSiteInitiationReaction.getSpecification()
Gets the specification attribute of the RadicalSiteInitiationReaction object
|
ReactionSpecification |
RadicalSiteInitiationHReaction.getSpecification()
Gets the specification attribute of the RadicalSiteInitiationHReaction object
|
ReactionSpecification |
RadicalSiteHrGammaReaction.getSpecification()
Gets the specification attribute of the RadicalSiteHrGammaReaction object
|
ReactionSpecification |
RadicalSiteHrDeltaReaction.getSpecification()
Gets the specification attribute of the RadicalSiteHrDeltaReaction object
|
ReactionSpecification |
RadicalSiteHrBetaReaction.getSpecification()
Gets the specification attribute of the RadicalSiteHrBetaReaction object
|
ReactionSpecification |
RadicalSiteHrAlphaReaction.getSpecification()
Gets the specification attribute of the RadicalSiteHrAlphaReaction object
|
ReactionSpecification |
RadicalChargeSiteInitiationReaction.getSpecification()
Gets the specification attribute of the RadicalChargeSiteInitiationReaction object
|
ReactionSpecification |
RadicalChargeSiteInitiationHReaction.getSpecification()
Gets the specification attribute of the RadicalChargeSiteInitiationHReaction object
|
ReactionSpecification |
PiBondingMovementReaction.getSpecification()
Gets the specification attribute of the PiBondingMovementReaction object
|
ReactionSpecification |
HyperconjugationReaction.getSpecification()
Gets the specification attribute of the HyperconjugationReaction object
|
ReactionSpecification |
HomolyticCleavageReaction.getSpecification()
Gets the specification attribute of the HomolyticCleavageReaction object.
|
ReactionSpecification |
HeterolyticCleavageSBReaction.getSpecification()
Gets the specification attribute of the HeterolyticCleavageSBReaction object.
|
ReactionSpecification |
HeterolyticCleavagePBReaction.getSpecification()
Gets the specification attribute of the HeterolyticCleavagePBReaction object.
|
ReactionSpecification |
ElectronImpactSDBReaction.getSpecification()
Gets the specification attribute of the ElectronImpactSDBReaction object.
|
ReactionSpecification |
ElectronImpactPDBReaction.getSpecification()
Gets the specification attribute of the ElectronImpactPDBReaction object.
|
ReactionSpecification |
ElectronImpactNBEReaction.getSpecification()
Gets the specification attribute of the ElectronImpactNBEReaction object.
|
ReactionSpecification |
CarbonylEliminationReaction.getSpecification()
Gets the specification attribute of the CarbonylEliminationReaction object.
|
ReactionSpecification |
AdductionSodiumLPReaction.getSpecification()
Gets the specification attribute of the AdductionSodiumLPReaction object.
|
ReactionSpecification |
AdductionProtonPBReaction.getSpecification()
Gets the specification attribute of the AdductionProtonPBReaction object.
|
ReactionSpecification |
AdductionProtonLPReaction.getSpecification()
Gets the specification attribute of the AdductionProtonLPReaction object.
|
IReactionSet |
TautomerizationReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
SharingLonePairReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
SharingChargeSBReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
SharingChargeDBReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
SharingAnionReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RearrangementRadicalReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RearrangementLonePairReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RearrangementCationReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RearrangementAnionReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteRrGammaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteRrDeltaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteRrBetaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteRrAlphaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteInitiationReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteInitiationHReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteHrGammaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteHrDeltaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteHrBetaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteHrAlphaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalChargeSiteInitiationReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalChargeSiteInitiationHReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
PiBondingMovementReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
HyperconjugationReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
HomolyticCleavageReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
HeterolyticCleavageSBReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
HeterolyticCleavagePBReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
ElectronImpactSDBReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
ElectronImpactPDBReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
ElectronImpactNBEReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
CarbonylEliminationReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
AdductionSodiumLPReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
AdductionProtonPBReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
AdductionProtonLPReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
Modifier and Type | Method and Description |
---|---|
Object |
ParameterReact.getValue()
Get the value of the parameter.
|
boolean |
ParameterReact.isSetParameter()
Get if this parameter needs to take account.
|
void |
ParameterReact.setParameter(boolean set)
Set the parameter to take account.
|
void |
ParameterReact.setValue(Object value)
Set the value of the parameter.
|
Modifier and Type | Method and Description |
---|---|
void |
RendererModel.addCDKChangeListener(ICDKChangeListener listener)
Adds a change listener to the list of listeners
|
static Rectangle2D |
BoundsCalculator.calculateBounds(IAtomContainer atomContainer)
Calculate the bounding rectangle for an atom container.
|
static Rectangle2D |
BoundsCalculator.calculateBounds(IChemModel chemModel)
Calculate the bounding rectangle for a chem model.
|
static Rectangle2D |
BoundsCalculator.calculateBounds(IMoleculeSet moleculeSet)
Calculate the bounding rectangle for a molecule set.
|
static Rectangle2D |
BoundsCalculator.calculateBounds(IReaction reaction)
Calculate the bounding rectangle for a reaction.
|
static Rectangle2D |
BoundsCalculator.calculateBounds(IReactionSet reactionSet)
Calculate the bounding rectangle for a reaction set.
|
void |
RendererModel.fireChange()
Notifies registered listeners of certain changes that have occurred in
this model.
|
<T extends IGeneratorParameter<S>,S> |
RendererModel.get(Class<T> paramType)
Returns the
IGeneratorParameter for the active IRenderer . |
IAtomContainer |
RendererModel.getClipboardContent()
Returns the atoms and bonds on the Renderer2D clipboard.
|
<T extends IGeneratorParameter<S>,S> |
RendererModel.getDefault(Class<T> param)
Returns the default value for the
IGeneratorParameter for the
active IRenderer . |
IAtomContainer |
RendererModel.getExternalSelectedPart()
Get externally selected atoms.
|
IAtom |
RendererModel.getHighlightedAtom()
Returns the atom currently highlighted.
|
IBond |
RendererModel.getHighlightedBond()
Returns the Bond currently highlighted.
|
Map<IAtom,IAtom> |
RendererModel.getMerge()
This is the central facility for handling "merges" of atoms.
|
boolean |
RendererModel.getNotification()
Determines if the model sends around change notifications.
|
<T extends IGeneratorParameter<?>> |
RendererModel.getParameter(Class<T> param)
Returns the
IGeneratorParameter for the active IRenderer . |
List<IGeneratorParameter<?>> |
RendererModel.getRenderingParameters()
Returns all
IGeneratorParameter s for the current
RendererModel . |
IChemObjectSelection |
RendererModel.getSelection()
Returns an
IChemObjectSelection with the currently selected
IChemObject s. |
String |
RendererModel.getToolTipText(IAtom atom)
Gets the toolTipText for atom certain atom.
|
Map<IAtom,String> |
RendererModel.getToolTipTextMap()
Gets the toolTipTextMap.
|
<T extends IGeneratorParameter<?>> |
RendererModel.hasParameter(Class<T> param)
Returns true if the passed
IGeneratorParameter s has been
registered. |
void |
RendererModel.registerParameters(IGenerator<? extends IChemObject> generator)
Registers rendering parameters from
IGenerator s
with this model. |
void |
RendererModel.removeCDKChangeListener(ICDKChangeListener listener)
Removes a change listener from the list of listeners
|
<T extends IGeneratorParameter<S>,S> |
RendererModel.set(Class<T> paramType,
S value)
Sets the
IGeneratorParameter for the active IRenderer . |
void |
RendererModel.setClipboardContent(IAtomContainer content)
Sets the atoms and bonds on the Renderer2D clipboard.
|
void |
RendererModel.setExternalSelectedPart(IAtomContainer externalSelectedPart)
Set externally selected atoms.
|
void |
RendererModel.setHighlightedAtom(IAtom highlightedAtom)
Sets the atom currently highlighted.
|
void |
RendererModel.setHighlightedBond(IBond highlightedBond)
Sets the Bond currently highlighted.
|
void |
RendererModel.setNotification(boolean notification)
Dis- or enables sending around change notifications.
|
void |
RendererModel.setSelection(IChemObjectSelection selection)
Set the selected
IChemObject s. |
void |
RendererModel.setToolTipTextMap(Map<IAtom,String> map)
Sets the toolTipTextMap.
|
Constructor and Description |
---|
ChemModelRenderer(List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager)
A renderer that generates diagrams using the specified
generators and manages fonts with the supplied font manager.
|
MoleculeSetRenderer(List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager)
A renderer that generates diagrams using the specified
generators and manages fonts with the supplied font manager.
|
ReactionRenderer(List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager)
A renderer that generates diagrams using the specified
generators and manages fonts with the supplied font manager.
|
ReactionSetRenderer(List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager)
A renderer that generates diagrams using the specified
generators and manages fonts with the supplied font manager.
|
Modifier and Type | Method and Description |
---|---|
Color |
RasmolColors.getAtomColor(IAtom atom)
Returns the Rasmol color for the given atom's element.
|
Color |
PartialAtomicChargeColors.getAtomColor(IAtom atom)
Returns the a color reflecting the given atom's partial charge.
|
Color |
CPKAtomColors.getAtomColor(IAtom atom)
Returns the font color for atom given atom.
|
Color |
CDKAtomColors.getAtomColor(IAtom atom)
Returns the CDK scheme color for the given atom's element.
|
Color |
CDK2DAtomColors.getAtomColor(IAtom atom)
Returns the CDK 2D color for the given atom's element.
|
Color |
RasmolColors.getAtomColor(IAtom atom,
Color defaultColor)
Returns the Rasmol color for the given atom's element, or
defaults to the given color if no color is defined.
|
Color |
PartialAtomicChargeColors.getAtomColor(IAtom atom,
Color defaultColor)
Returns the a color reflecting the given atom's partial charge, or
defaults to the given color if no color is defined.
|
Color |
CPKAtomColors.getAtomColor(IAtom atom,
Color defaultColor)
Returns the font color for atom given atom.
|
Color |
CDKAtomColors.getAtomColor(IAtom atom,
Color defaultColor)
Returns the CDK scheme color for the given atom's element, or
defaults to the given color if no color is defined.
|
Color |
CDK2DAtomColors.getAtomColor(IAtom atom,
Color defaultColor)
Returns the CDK 2D color for the given atom's element, or
defaults to the given color if no color is defined.
|
Modifier and Type | Method and Description |
---|---|
void |
WedgeLineElement.accept(IRenderingVisitor v)
Converts this
TextElement into widget specific objects. |
void |
TextGroupElement.accept(IRenderingVisitor v)
Converts this
TextElement into widget specific objects. |
void |
TextElement.accept(IRenderingVisitor visotor)
Converts this
TextElement into widget specific objects. |
void |
RingElement.accept(IRenderingVisitor v)
Converts this
TextElement into widget specific objects. |
void |
RectangleElement.accept(IRenderingVisitor visitor)
Converts this
TextElement into widget specific objects. |
void |
PathElement.accept(IRenderingVisitor v)
Converts this
TextElement into widget specific objects. |
void |
OvalElement.accept(IRenderingVisitor visitor)
Converts this
TextElement into widget specific objects. |
void |
LineElement.accept(IRenderingVisitor visitor)
Converts this
TextElement into widget specific objects. |
void |
GeneralPath.accept(IRenderingVisitor v)
Converts this
TextElement into widget specific objects. |
void |
ElementGroup.accept(IRenderingVisitor v)
Converts this
TextElement into widget specific objects. |
void |
AtomSymbolElement.accept(IRenderingVisitor v)
Converts this
TextElement into widget specific objects. |
void |
ArrowElement.accept(IRenderingVisitor v)
Converts this
TextElement into widget specific objects. |
Constructor and Description |
---|
AtomSymbolElement(double x,
double y,
String symbol,
Integer formalCharge,
Integer hydrogenCount,
int alignment,
Color color) |
GeneralPath(List<PathElement> elements,
Color color)
Make a path from a list of path elements.
|
LineElement(double firstPointX,
double firstPointY,
double secondPointX,
double secondPointY,
double width,
Color color)
Make a line element.
|
OvalElement(double xCoord,
double yCoord,
Color color)
Make an oval with a default radius of 10.
|
PathElement(List<javax.vecmath.Point2d> points,
Color color)
Make a path from the list of points.
|
RectangleElement(double xCoord1,
double yCoord1,
double xCoord2,
double yCoord2,
Color color)
Make a rectangle from two opposite corners (x1, y1) and (x2, y2).
|
RingElement(double x,
double y,
double radius,
Color color)
Make a ring element centered on (x, y) with radius and color given.
|
TextElement(double xCoord,
double yCoord,
String text,
Color color)
Constructs a new TextElement with the content
text to be
drawn at position (x,y) in the color color . |
TextGroupElement(double x,
double y,
String text,
Color color)
Make a text group at (x, y) with the text and color given.
|
WedgeLineElement(double x1,
double y1,
double x2,
double y2,
double width,
boolean dashed,
WedgeLineElement.Direction direction,
Color color)
Make a wedge between the points (x1, y1) and (x2, y2) with a certain
width, direction, dash, and color.
|
WedgeLineElement(LineElement element,
boolean dashed,
WedgeLineElement.Direction direction,
Color color)
Make a wedge along the given line element.
|
Modifier and Type | Method and Description |
---|---|
float[] |
QuadTo.points()
Get the points in the path.
|
float[] |
MoveTo.points()
Get the points in the path.
|
float[] |
LineTo.points()
Get the points in the path.
|
float[] |
CubicTo.points()
Get the points in the path.
|
Constructor and Description |
---|
CubicTo(javax.vecmath.Point2d cp1,
javax.vecmath.Point2d cp2,
javax.vecmath.Point2d ep)
Make a cubic curve path element.
|
LineTo(javax.vecmath.Point2d point)
Make a line to this point.
|
MoveTo(javax.vecmath.Point2d point)
Make a move to path element.
|
QuadTo(javax.vecmath.Point2d cp,
javax.vecmath.Point2d ep)
Make a quad curve.
|
Constructor and Description |
---|
AWTFontManager()
Make a manager for fonts in AWT, with a minimum font size of 9.
|
Modifier and Type | Method and Description |
---|---|
IRenderingElement |
ExtendedAtomGenerator.generate(IAtomContainer container,
IAtom atom,
RendererModel model)
Generate the rendering element(s) for a particular atom.
|
IRenderingElement |
BasicAtomGenerator.generate(IAtomContainer atomContainer,
IAtom atom,
RendererModel model)
Generate the rendering element(s) for a particular atom.
|
IRenderingElement |
RadicalGenerator.generate(IAtomContainer container,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
LonePairGenerator.generate(IAtomContainer container,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
BasicAtomGenerator.generate(IAtomContainer container,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
AtomNumberGenerator.generate(IAtomContainer container,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
AtomContainerBoundsGenerator.generate(IAtomContainer container,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
ReactionSceneGenerator.generate(IReaction reaction,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
ReactionPlusGenerator.generate(IReaction reaction,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
ReactionBoxGenerator.generate(IReaction reaction,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
ReactionArrowGenerator.generate(IReaction reaction,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
ReactantsBoxGenerator.generate(IReaction reaction,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
ProductsBoxGenerator.generate(IReaction reaction,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
MappingGenerator.generate(IReaction reaction,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
BoundsGenerator.generate(IReaction reaction,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
BasicAtomGenerator.generateCompactElement(IAtom atom,
RendererModel model)
Generate a compact element for an atom, such as a circle or a square,
rather than text element.
|
AtomSymbolElement |
BasicAtomGenerator.generateElement(IAtom atom,
int alignment,
RendererModel model)
Generate an atom symbol element.
|
List<IGeneratorParameter<?>> |
RingGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
ReactionSceneGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
ReactionPlusGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
ReactionBoxGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
ReactionArrowGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
ReactantsBoxGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
RadicalGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
ProductsBoxGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
MappingGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
LonePairGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
ExtendedAtomGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
BoundsGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
BasicSceneGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
BasicGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
BasicBondGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
BasicAtomGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
AtomNumberGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
List<IGeneratorParameter<?>> |
AtomContainerBoundsGenerator.getParameters()
Returns the list of
IGeneratorParameter for this particular
generator. |
boolean |
AtomMassGenerator.showCarbon(IAtom atom,
IAtomContainer container,
RendererModel model)
Returns true if the mass number of this element is set and not
equal the mass number of the most abundant isotope of this element.
|
Modifier and Type | Method and Description |
---|---|
T |
AbstractGeneratorParameter.getValue()
Gets the value for this parameter.
|
void |
AbstractGeneratorParameter.setValue(T value)
Sets the value for this parameter.
|
Modifier and Type | Method and Description |
---|---|
Graphics2D |
AWTDrawVisitor.getGraphics()
Returns the
Graphics2D for for this visitor. |
RendererModel |
AWTDrawVisitor.getRendererModel()
Returns the current
RendererModel . |
Map<Integer,BasicStroke> |
AWTDrawVisitor.getStrokeMap()
Returns the current stroke map.
|
void |
AWTDrawVisitor.setFontManager(IFontManager fontManager)
The font manager must be set by any renderer that uses this class!
This manager is needed to keep track of fonts of the right size.
|
void |
AWTDrawVisitor.setRendererModel(RendererModel rendererModel)
Sets the
RendererModel this IDrawVisitor should use. |
void |
AbstractAWTDrawVisitor.setTransform(AffineTransform transform)
Sets a new affine transformation to convert world coordinates into
screen coordinates.
|
int[] |
AbstractAWTDrawVisitor.transformPoint(double xCoord,
double yCoord)
Transforms a point according to the current affine transformation,
converting a world coordinate into a screen coordinate.
|
void |
AWTDrawVisitor.visit(IRenderingElement element)
Translates a
IRenderingElement into a widget toolkit specific
rendering element. |
Constructor and Description |
---|
AWTDrawVisitor(Graphics2D graphics)
Constructs a new
IDrawVisitor using the AWT widget toolkit,
taking a Graphics2D object to which the chemical content
is drawn. |
Modifier and Type | Method and Description |
---|---|
void |
AllRingsFinderMod.checkTimeout()
Checks if the timeout has been reached and throws an
exception if so.
|
void |
AllRingsFinder.checkTimeout()
Checks if the timeout has been reached and throws an
exception if so.
|
static IAtomContainer |
RingPartitioner.convertToAtomContainer(IRingSet ringSet)
Converts a RingSet to an AtomContainer.
|
IRingSet |
AllRingsFinderMod.findAllRings(IAtomContainer atomContainer)
Returns a ringset containing all rings in the given AtomContainer
Calls
AllRingsFinderMod.findAllRings(org.openscience.cdk.interfaces.IAtomContainer, Integer) with max ring size argument set to null (=unlimited ring sizes) |
IRingSet |
AllRingsFinder.findAllRings(IAtomContainer atomContainer)
Returns a ringset containing all rings in the given AtomContainer
Calls
AllRingsFinder.findAllRings(IAtomContainer, Integer) with max ring size argument set to null (=unlimited ring sizes) |
IRingSet |
SSSRFinder.findSSSR()
Finds a Smallest Set of Smallest Rings.
|
int |
Path.getIntersectionSize(Path other) |
long |
AllRingsFinderMod.getTimeout()
Gets the timeout values in milliseconds of the AllRingsFinder object
|
long |
AllRingsFinder.getTimeout()
Gets the timeout values in milliseconds of the AllRingsFinder object
|
static Path |
Path.join(Path path1,
Path path2,
IAtom atom)
Joins two paths.
|
static List<IRingSet> |
RingPartitioner.partitionRings(IRingSet ringSet)
Partitions a RingSet into RingSets of connected rings.
|
Object |
Queue.pop()
Returns an Object from the queue
|
void |
Queue.push(Object o)
Places an Object into the queue
|
AllRingsFinderMod |
AllRingsFinderMod.setTimeout(long timeout)
Sets the timeout value in milliseconds of the AllRingsFinder object
This is used to prevent this AllRingsFinder
to run for ages in certain rare cases with ring systems of
large size or special topology
|
AllRingsFinder |
AllRingsFinder.setTimeout(long timeout)
Sets the timeout value in milliseconds of the AllRingsFinder object
This is used to prevent this AllRingsFinder
to run for ages in certain rare cases with ring systems of
large size or special topology
|
Modifier and Type | Method and Description |
---|---|
Collection |
CycleBasis.cycles()
Returns the cycles that form the cycle basis.
|
List |
CycleBasis.equivalenceClasses()
Returns the connected components of this cycle basis, in regard to matroid theory.
|
Collection |
CycleBasis.essentialCycles()
Returns the essential cycles of this cycle basis.
|
Map |
CycleBasis.relevantCycles()
Returns the essential cycles of this cycle basis.
|
int[] |
CycleBasis.weightVector() |
Modifier and Type | Method and Description |
---|---|
void |
Orbit.addAtom(int atomIndex)
Adds an atom index to the orbit.
|
List<Orbit> |
MoleculeSignature.calculateOrbits()
Calculates the orbits of the atoms of the molecule.
|
Object |
Orbit.clone() |
boolean |
Orbit.contains(int atomIndex)
Checks to see if the orbit contains this atom index.
|
static IAtomContainer |
MoleculeSignature.fromSignatureString(String signatureString,
IChemObjectBuilder coBuilder)
Builder for molecules (rather, for atom containers) from signature
strings.
|
IAtomContainer |
MoleculeFromSignatureBuilder.getAtomContainer()
Gets the atom container.
|
List<Integer> |
Orbit.getAtomIndices()
Gets all the atom indices as a list.
|
int |
Orbit.getFirstAtom()
Gets the first atom index of the orbit.
|
int |
Orbit.getHeight()
Gets the height of the signature label.
|
String |
Orbit.getLabel()
Gets the label of the orbit.
|
boolean |
Orbit.hasLabel(String otherLabel)
Checks to see if the orbit has this string as a label.
|
boolean |
SignatureQuotientGraph.isConnected(int index1,
int index2) |
boolean |
Orbit.isEmpty()
Checks to see if the orbit is empty.
|
Iterator<Integer> |
Orbit.iterator() |
void |
MoleculeFromSignatureBuilder.makeEdge(int vertexIndex1,
int vertexIndex2,
String vertexSymbol1,
String vertexSymbol2,
String edgeLabel) |
void |
MoleculeFromSignatureBuilder.makeGraph() |
void |
MoleculeFromSignatureBuilder.makeVertex(String label) |
void |
Orbit.remove(int atomIndex)
Removes an atom index from the orbit.
|
signature.AbstractVertexSignature |
MoleculeSignature.signatureForVertex(int vertexIndex) |
String |
MoleculeSignature.signatureStringForVertex(int vertexIndex) |
String |
MoleculeSignature.signatureStringForVertex(int vertexIndex,
int height) |
void |
Orbit.sort()
Sorts the atom indices in this orbit
|
String |
MoleculeSignature.toCanonicalSignatureString(int height)
Make a canonical signature string of a given height.
|
String |
Orbit.toString() |
Modifier and Type | Method and Description |
---|---|
IMolecularFormula |
MolecularFormula.add(IMolecularFormula formula)
Adds an molecularFormula to this MolecularFormula.
|
void |
MolecularFormulaSet.add(IMolecularFormulaSet formulaSet)
Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
|
void |
AdductFormula.add(IMolecularFormulaSet formulaSet)
Adds all molecularFormulas in the AdductFormula to this chemObject.
|
void |
ReactionScheme.add(IReactionScheme scheme)
Add a Scheme of Reactions.
|
IMolecularFormula |
MolecularFormula.addIsotope(IIsotope isotope)
Adds an Isotope to this MolecularFormula one time.
|
IMolecularFormula |
MolecularFormula.addIsotope(IIsotope isotope,
int count)
Adds an Isotope to this MolecularFormula in a number of occurrences.
|
void |
MolecularFormulaSet.addMolecularFormula(IMolecularFormula formula)
Adds an molecularFormula to this chemObject.
|
void |
AdductFormula.addMolecularFormula(IMolecularFormula formula)
Adds an molecularFormula to this chemObject.
|
Object |
ReactionScheme.clone()
Clones this ReactionScheme object and its content.
|
Object |
MolecularFormulaSet.clone()
Clones this MolecularFormulaSet object and its content.
|
Object |
MolecularFormula.clone()
Clones this MolecularFormula object and its content.
|
Object |
AdductFormula.clone()
Clones this AdductFormula object and its content.
|
boolean |
MolecularFormula.contains(IIsotope isotope)
True, if the MolecularFormula contains the given IIsotope object and not
the instance.
|
boolean |
AdductFormula.contains(IIsotope isotope)
True, if the AdductFormula contains the given IIsotope object and not
the instance.
|
boolean |
MolecularFormulaSet.contains(IMolecularFormula formula)
True, if the MolecularFormulaSet contains the given IMolecularFormula object.
|
boolean |
AdductFormula.contains(IMolecularFormula formula)
True, if the AdductFormula contains the given IMolecularFormula object.
|
Integer |
MolecularFormula.getCharge()
Returns the partial charge of this IMolecularFormula.
|
Integer |
AdductFormula.getCharge()
Returns the partial charge of this Adduct.
|
int |
MolecularFormula.getIsotopeCount()
Checks a set of Nodes for the number of different isotopes in the
IMolecularFormula.
|
int |
AdductFormula.getIsotopeCount()
Checks a set of Nodes for the number of different isotopes in the
adduct formula.
|
int |
MolecularFormula.getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the
IMolecularFormula from a particular isotope.
|
int |
AdductFormula.getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the
adduct formula from a particular isotope.
|
IMolecularFormula |
MolecularFormulaSet.getMolecularFormula(int position)
Returns the MolecularFormula at position
number in the
chemObject. |
IMolecularFormula |
AdductFormula.getMolecularFormula(int position)
Returns the MolecularFormula at position
number in the
chemObject. |
Map<Object,Object> |
MolecularFormula.getProperties()
Returns a Map with the IChemObject's properties.I should
integrate into ChemObject.
|
Object |
MolecularFormula.getProperty(Object description)
Returns a property for the IChemObject.
|
int |
ReactionScheme.getReactionSchemeCount()
Returns the number of ReactionScheme in this Scheme.
|
boolean |
ReactionSet.isEmpty() |
boolean |
ChemModel.isEmpty() |
boolean |
AtomContainerSet.isEmpty() |
boolean |
AtomContainer.isEmpty() |
Iterable<IIsotope> |
MolecularFormula.isotopes()
Returns an Iterator for looping over all isotopes in this IMolecularFormula.
|
Iterable<IIsotope> |
AdductFormula.isotopes()
Returns an Iterator for looping over all isotopes in this adduct formula.
|
Iterator<IMolecularFormula> |
MolecularFormulaSet.iterator()
Returns an Iterator for looping over all IMolecularFormula
in this MolecularFormulaSet.
|
Iterator<IMolecularFormula> |
AdductFormula.iterator()
Returns an Iterator for looping over all IMolecularFormula
in this adduct formula.
|
IAtomParity |
AtomParity.map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds) |
Iterable<IMolecularFormula> |
MolecularFormulaSet.molecularFormulas()
Returns an Iterable for looping over all IMolecularFormula
in this MolecularFormulaSet.
|
Iterable<IMolecularFormula> |
AdductFormula.molecularFormulas()
Returns an Iterable for looping over all IMolecularFormula
in this adduct formula.
|
Iterable<IReactionScheme> |
ReactionScheme.reactionSchemes()
Returns an Iterable for looping over all IMolecularScheme
in this ReactionScheme.
|
void |
MolecularFormula.removeAllIsotopes()
Removes all isotopes of this molecular formula.
|
void |
MolecularFormulaSet.removeAllMolecularFormulas()
Removes all IMolecularFormula from this chemObject.
|
void |
AdductFormula.removeAllMolecularFormulas()
Removes all IMolecularFormula from this chemObject.
|
void |
ReactionScheme.removeAllReactionSchemes()
Removes all IReactionScheme from this chemObject.
|
void |
MolecularFormula.removeIsotope(IIsotope isotope)
Removes the given isotope from the MolecularFormula.
|
void |
MolecularFormulaSet.removeMolecularFormula(IMolecularFormula formula)
Removes an IMolecularFormula from this chemObject.
|
void |
AdductFormula.removeMolecularFormula(IMolecularFormula formula)
Removes an IMolecularFormula from this chemObject.
|
void |
MolecularFormulaSet.removeMolecularFormula(int position)
Removes an MolecularFormula from this chemObject.
|
void |
AdductFormula.removeMolecularFormula(int position)
Removes an MolecularFormula from this chemObject.
|
void |
MolecularFormula.removeProperty(Object description)
Removes a property for a IChemObject.
|
void |
ReactionScheme.removeReactionScheme(IReactionScheme scheme)
Removes an IReactionScheme from this chemObject.
|
void |
MolecularFormula.setCharge(Integer charge)
Sets the partial charge of this IMolecularFormula.
|
void |
AdductFormula.setCharge(Integer charge)
Deprecated.
|
void |
MolecularFormula.setProperties(Map<Object,Object> properties)
Sets the properties of this object.
|
void |
MolecularFormula.setProperty(Object description,
Object property)
Sets a property for a IChemObject.
|
int |
MolecularFormulaSet.size()
Returns the number of MolecularFormulas in this MolecularFormulaSet.
|
int |
AdductFormula.size()
Returns the number of MolecularFormulas in this AdductFormula.
|
void |
AtomContainerSet.sortAtomContainers(Comparator<IAtomContainer> comparator)
Sort the AtomContainers and multipliers using a provided Comparator
|
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 |
---|---|
void |
InvPair.commit() |
String |
SmilesGenerator.createChiralSMILES(IAtomContainer molecule,
boolean[] doubleBondConfiguration)
Generate canonical and chiral SMILES from the
molecule . |
String |
SmilesGenerator.createSMILES(IAtomContainer molecule)
Generate canonical SMILES from the
molecule . |
String |
SmilesGenerator.createSMILESWithoutCheckForMultipleMolecules(IAtomContainer molecule,
boolean chiral,
boolean[] doubleBondConfiguration)
Generate canonical SMILES from the
molecule . |
boolean |
InvPair.equals(Object object)
Check whether this instance equals another instance.
|
IMolecule |
DeduceBondSystemTool.fixAromaticBondOrders(IMolecule molecule)
Added missing bond orders based on atom type information.
|
IAtom |
InvPair.getAtom() |
long |
InvPair.getCurr()
Get the current seed.
|
long |
InvPair.getLast() |
int |
InvPair.getPrime()
Get the current prime number.
|
boolean |
FixBondOrdersTool.isInterrupted()
Returns if the next or running calculation should be interrupted.
|
boolean |
DeduceBondSystemTool.isInterrupted()
Returns if the next or running calculation should be interrupted.
|
boolean |
DeduceBondSystemTool.isOK(IMolecule m)
Determines if, according to the algorithms implemented in this class, the given
molecule has properly distributed double bonds.
|
IMolecule |
FixBondOrdersTool.kekuliseAromaticRings(IMolecule molecule)
kekuliseAromaticRings - function to add double/single bond order information for molecules having rings containing all atoms marked SP2 or Planar3 hybridisation.
|
IReaction |
SmilesParser.parseReactionSmiles(String smiles)
Parse a reaction SMILES.
|
IMolecule |
SmilesParser.parseSmiles(String smiles)
Parses a SMILES string and returns a Molecule object.
|
void |
InvPair.setAtom(IAtom newAtom) |
void |
InvPair.setCurr(long newCurr)
Set the value of the seed.
|
void |
FixBondOrdersTool.setInterrupted(boolean interrupted)
Sets if the calculation should be interrupted.
|
void |
DeduceBondSystemTool.setInterrupted(boolean interrupted)
Sets if the calculation should be interrupted.
|
void |
InvPair.setLast(long newLast) |
void |
InvPair.setPrime()
Sets the prime number based on the current seed.
|
void |
SmilesGenerator.setUseAromaticityFlag(boolean useAromaticityFlag)
Indicates whether output should be an aromatic SMILES.
|
String |
InvPair.toString()
String representation.
|
Constructor and Description |
---|
DeduceBondSystemTool()
Constructor for the DeduceBondSystemTool object.
|
DeduceBondSystemTool(AllRingsFinder ringFinder)
Constructor for the DeduceBondSystemTool object accepting a custom
AllRingsFinder . |
Modifier and Type | Method and Description |
---|---|
int |
SMARTSQueryTool.countMatches()
Returns the number of times the pattern was found in the target molecule.
|
List<List<Integer>> |
SMARTSQueryTool.getMatchingAtoms()
Get the atoms in the target molecule that match the query pattern.
|
String |
SMARTSQueryTool.getSmarts()
Returns the current SMARTS pattern being used.
|
List<List<Integer>> |
SMARTSQueryTool.getUniqueMatchingAtoms()
Get the atoms in the target molecule that match the query pattern.
|
boolean |
SMARTSQueryTool.matches(IAtomContainer atomContainer,
boolean forceInitialization)
Perform a SMARTS match and check whether the query is present in the target molecule.
|
void |
SMARTSQueryTool.setSmarts(String smarts)
Set a new SMARTS pattern.
|
Modifier and Type | Method and Description |
---|---|
List<Map<IAtom,IAtom>> |
Isomorphism.getAllAtomMapping()
Returns all plausible mappings between query and target molecules
Each map in the list has atom-atom equivalence of the mappings
between query and target molecule i.e.
|
List<Map<Integer,Integer>> |
Isomorphism.getAllMapping()
Returns all plausible mappings between query and target molecules
Each map in the list has atom-atom equivalence index of the mappings
between query and target molecule i.e.
|
Double |
Isomorphism.getEnergyScore(int Key)
Returns summation energy score of the disorder if the MCS is removed
from the target and query graph.
|
double |
Isomorphism.getEuclideanDistance()
Returns Euclidean Distance between query and target molecule.
|
Map<IAtom,IAtom> |
Isomorphism.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
Map<Integer,Integer> |
Isomorphism.getFirstMapping()
Returns one of the best matches with atom indexes mapped.
|
Integer |
Isomorphism.getFragmentSize(int Key)
Returns number of fragment generated in the solution space,
if the MCS is removed from the target and query graph.
|
IAtomContainer |
Isomorphism.getProductMolecule()
Returns modified target molecule on which mapping was
performed.
|
IAtomContainer |
Isomorphism.getReactantMolecule()
Returns modified query molecule on which mapping was
performed.
|
Integer |
Isomorphism.getStereoScore(int Key)
Returns a number which denotes the quality of the mcs.
|
double |
Isomorphism.getTanimotoSimilarity()
Returns Tanimoto similarity between query and target molecules
(Score is between 0-min and 1-max).
|
void |
Isomorphism.init(IAtomContainer reactant,
IAtomContainer product,
boolean removeHydrogen,
boolean cleanAndConfigureMolecule)
initialize query and target molecules.
|
void |
Isomorphism.init(IMolecule reactant,
IMolecule product,
boolean removeHydrogen,
boolean cleanAndConfigureMolecule)
initialize query and target molecules.
|
void |
Isomorphism.init(String sourceMolFileName,
String targetMolFileName,
boolean removeHydrogen,
boolean cleanAndConfigureMolecule)
Initialize the query and targetAtomCount mol via mol files
|
boolean |
Isomorphism.isStereoMisMatch()
Returns true if mols have different stereo
chemistry else false if no stereo mismatch.
|
boolean |
Isomorphism.isSubgraph()
Checks if query is a subgraph of the target.
|
void |
Isomorphism.setChemFilters(boolean stereoFilter,
boolean fragmentFilter,
boolean energyFilter)
initialize query and target molecules.
|
Constructor and Description |
---|
Isomorphism(Algorithm algorithmType,
boolean bondTypeFlag)
This is the algorithm factory and entry port for all the MCS algorithm in the Isomorphism
supported algorithm
Algorithm types:
|
Modifier and Type | Method and Description |
---|---|
List<Map<IAtom,IAtom>> |
MCSPlusHandler.getAllAtomMapping()
Returns all plausible mappings between query and target molecules.
|
List<Map<Integer,Integer>> |
MCSPlusHandler.getAllMapping()
Returns all plausible mappings between query and target molecules.
|
Map<IAtom,IAtom> |
MCSPlusHandler.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
Map<Integer,Integer> |
MCSPlusHandler.getFirstMapping()
Returns one of the best matches with atom indexes mapped.
|
void |
MCSPlusHandler.searchMCS(boolean shouldMatchBonds)
Initialise the MCS search algorithm.
|
void |
MCSPlusHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Initialise the query and target molecule.
|
void |
MCSPlusHandler.set(MolHandler source,
MolHandler target)
Initialise the query and target molecule.
|
Modifier and Type | Method and Description |
---|---|
List<Map<IAtom,IAtom>> |
CDKSubGraphHandler.getAllAtomMapping()
Returns all plausible mappings between query and target molecules.
|
List<Map<IAtom,IAtom>> |
CDKMCSHandler.getAllAtomMapping()
Returns all plausible mappings between query and target molecules.
|
List<Map<Integer,Integer>> |
CDKSubGraphHandler.getAllMapping()
Returns all plausible mappings between query and target molecules.
|
List<Map<Integer,Integer>> |
CDKMCSHandler.getAllMapping()
Returns all plausible mappings between query and target molecules.
|
Map<IAtom,IAtom> |
CDKSubGraphHandler.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
Map<IAtom,IAtom> |
CDKMCSHandler.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
Map<Integer,Integer> |
CDKSubGraphHandler.getFirstMapping()
Returns one of the best matches with atom indexes mapped.
|
Map<Integer,Integer> |
CDKMCSHandler.getFirstMapping()
Returns one of the best matches with atom indexes mapped.
|
boolean |
CDKSubGraphHandler.isSubgraph(boolean shouldMatchBonds)
Initialise the Subgraph search algorithm.
|
void |
CDKMCSHandler.searchMCS(boolean shouldMatchBonds)
Initialise the MCS search algorithm.
|
void |
CDKSubGraphHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Initialise the query and target molecule.
|
void |
CDKMCSHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Initialise the query and target molecule.
|
void |
CDKSubGraphHandler.set(MolHandler source,
MolHandler target)
Initialise the query and target molecule.
|
void |
CDKMCSHandler.set(MolHandler source,
MolHandler target)
Initialise the query and target molecule.
|
Modifier and Type | Method and Description |
---|---|
List<Map<IAtom,IAtom>> |
SingleMappingHandler.getAllAtomMapping()
Returns all plausible mappings between query and target molecules.
|
List<Map<Integer,Integer>> |
SingleMappingHandler.getAllMapping()
Returns all plausible mappings between query and target molecules.
|
Map<IAtom,IAtom> |
SingleMappingHandler.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
Map<Integer,Integer> |
SingleMappingHandler.getFirstMapping()
Returns one of the best matches with atom indexes mapped.
|
void |
SingleMappingHandler.searchMCS(boolean bondTypeMatch)
Initialise the MCS search algorithm.
|
void |
SingleMappingHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Initialise the query and target molecule.
|
void |
SingleMappingHandler.set(MolHandler source,
MolHandler target)
Initialise the query and target molecule.
|
Constructor and Description |
---|
SingleMappingHandler(boolean removeH) |
Modifier and Type | Method and Description |
---|---|
List<Map<IAtom,IAtom>> |
VFlibTurboHandler.getAllAtomMapping()
Returns all plausible mappings between query and target molecules.
|
List<Map<IAtom,IAtom>> |
VFlibSubStructureHandler.getAllAtomMapping()
Returns all plausible mappings between query and target molecules.
|
List<Map<IAtom,IAtom>> |
VFlibMCSHandler.getAllAtomMapping()
Returns all plausible mappings between query and target molecules.
|
List<Map<Integer,Integer>> |
VFlibTurboHandler.getAllMapping()
Returns all plausible mappings between query and target molecules.
|
List<Map<Integer,Integer>> |
VFlibSubStructureHandler.getAllMapping()
Returns all plausible mappings between query and target molecules.
|
List<Map<Integer,Integer>> |
VFlibMCSHandler.getAllMapping()
Returns all plausible mappings between query and target molecules.
|
Map<IAtom,IAtom> |
VFlibTurboHandler.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
Map<IAtom,IAtom> |
VFlibSubStructureHandler.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
Map<IAtom,IAtom> |
VFlibMCSHandler.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
Map<Integer,Integer> |
VFlibTurboHandler.getFirstMapping()
Returns one of the best matches with atom indexes mapped.
|
Map<Integer,Integer> |
VFlibSubStructureHandler.getFirstMapping()
Returns one of the best matches with atom indexes mapped.
|
Map<Integer,Integer> |
VFlibMCSHandler.getFirstMapping()
Returns one of the best matches with atom indexes mapped.
|
void |
VFlibMCSHandler.searchMCS(boolean bondTypeMatch)
Initialise the MCS search algorithm.
|
void |
VFlibTurboHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Initialise the query and target molecule.
|
void |
VFlibSubStructureHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Initialise the query and target molecule.
|
void |
VFlibMCSHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Initialise the query and target molecule.
|
void |
VFlibTurboHandler.set(MolHandler reactant,
MolHandler product)
Initialise the query and target molecule.
|
void |
VFlibSubStructureHandler.set(MolHandler reactant,
MolHandler product)
Initialise the query and target molecule.
|
void |
VFlibMCSHandler.set(MolHandler reactant,
MolHandler product)
Initialise the query and target molecule.
|
Constructor and Description |
---|
VFlibMCSHandler()
Constructor for an extended VF Algorithm for the MCS search
|
VFlibSubStructureHandler()
Constructor for an extended VF Algorithm for the MCS search
|
VFlibTurboHandler()
Constructor for an extended VF Algorithm for the MCS search
|
Modifier and Type | Method and Description |
---|---|
static List<Map<Integer,Integer>> |
PostFilter.filter(List<List<Integer>> mappings)
Creates a new instance of Post Filter and removes
redundant mapping(s).
|
List<Double> |
ChemicalFilters.getSortedEnergy()
Return sorted energy in ascending order.
|
List<Integer> |
ChemicalFilters.getSortedFragment()
Return sorted fragment in ascending order of the size.
|
List<Double> |
ChemicalFilters.getStereoMatches()
Return Stereo matches in descending order.
|
void |
ChemicalFilters.sortResultsByEnergies()
Sort MCS solution by bond breaking energy.
|
void |
ChemicalFilters.sortResultsByFragments()
Sort solution by ascending order of the fragment count.
|
void |
ChemicalFilters.sortResultsByStereoAndBondMatch()
Sort MCS solution by stereo and bond type matches.
|
Constructor and Description |
---|
ChemicalFilters(List<Map<Integer,Integer>> allMCS,
List<Map<IAtom,IAtom>> allAtomMCS,
Map<Integer,Integer> firstSolution,
Map<IAtom,IAtom> firstAtomMCS,
IAtomContainer sourceMol,
IAtomContainer targetMol)
This class has all the three chemical filters supported by the SMSD.
|
Modifier and Type | Method and Description |
---|---|
static TimeOut |
TimeOut.getInstance()
Get Instance of the timeout.
|
double |
TimeOut.getTimeOut()
Return cutoff value for time out.
|
boolean |
TimeOut.isTimeOutFlag()
Return true if its a timeout else return false.
|
void |
TimeOut.setTimeOut(double timeout)
set cutoff value for time out eg.
|
void |
TimeOut.setTimeOutFlag(boolean timeOut)
Set true if timeout occures else false
|
Modifier and Type | Method and Description |
---|---|
void |
FinalMappings.add(Map<Integer,Integer> mapping)
Adds mapping to the mapping list
|
void |
LabelContainer.addLabel(String label)
Add label if its not present
|
void |
FinalMappings.clear()
clear the mapping
|
IBond.Order |
BondEnergy.getBondOrder()
Returns the bond order for this bond type energy.
|
int |
BondEnergy.getEnergy()
Returns the energy for this bond type.
|
BinaryTree |
BinaryTree.getEqual()
Returns equal node
|
List<Map<Integer,Integer>> |
FinalMappings.getFinalMapping()
Returns the stored mappings
|
static LabelContainer |
LabelContainer.getInstance()
Create ids from atom labels
|
static FinalMappings |
FinalMappings.getInstance()
Stores mapping solutions
|
Iterator<Map<Integer,Integer>> |
FinalMappings.getIterator()
Returns a mapping Iterator
|
String |
LabelContainer.getLabel(Integer labelID)
Returns Label of a given ID
|
Integer |
LabelContainer.getLabelID(String label)
Returns label ID
|
BinaryTree |
BinaryTree.getNotEqual()
Returns not equal node
|
int |
LabelContainer.getSize()
Returns label count
|
int |
FinalMappings.getSize()
Returns number of stored mappings
|
String |
BondEnergy.getSymbolFirstAtom()
Returns the element symbol of the first atom.
|
String |
BondEnergy.getSymbolSecondAtom()
Returns the element symbol of the second atom.
|
int |
BinaryTree.getValue()
Return value of the node
|
void |
FinalMappings.set(List<Map<Integer,Integer>> list)
Sets mapping list
|
void |
BinaryTree.setEqual(BinaryTree equal)
Set equal node
|
void |
BinaryTree.setNotEqual(BinaryTree notEqual)
Set not equal node
|
Constructor and Description |
---|
BinaryTree(int value)
Creates a new instance of BinaryTree.
|
BondEnergy(String symbol1,
String symbol2,
IBond.Order order,
int energy)
Creates a new bond energy for the given elements and
bond order.
|
Modifier and Type | Method and Description |
---|---|
static void |
ExtAtomContainerManipulator.aromatizeMolecule(IAtomContainer mol)
This function finds rings and uses aromaticity detection code to
aromatize the molecule.
|
static IAtomContainer |
MoleculeSanityCheck.checkAndCleanMolecule(IAtomContainer molecule)
Modules for cleaning a molecule
|
static void |
MoleculeSanityCheck.configure(IAtomContainer mol)
Fixes Aromaticity of the molecule
i.e.
|
static IAtomContainer |
ExtAtomContainerManipulator.convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
Returns IAtomContainer without Hydrogen.
|
double |
TimeManager.getElapsedTimeInHours()
Returns Elapsed Time In Hours
|
double |
TimeManager.getElapsedTimeInMilliSeconds()
Returns Elapsed Time In Mill Seconds
|
double |
TimeManager.getElapsedTimeInMinutes()
Returns Elapsed Time In Minutes
|
double |
TimeManager.getElapsedTimeInSeconds()
Return Elapsed Time In Seconds
|
int |
BondEnergies.getEnergies(IAtom sourceAtom,
IAtom targetAtom,
IBond.Order bondOrder)
Returns bond energy for a bond type, given atoms and bond type
|
int |
BondEnergies.getEnergies(IBond bond)
Returns bond energy for a bond type, given atoms and bond type
|
int |
BondEnergies.getEnergies(String sourceAtom,
String targetAtom,
IBond.Order bondOrder)
Returns bond energy for a bond type, given atoms and bond type
|
static int |
ExtAtomContainerManipulator.getExplicitHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
Returns The number of explicit hydrogens for a given IAtom.
|
static int |
ExtAtomContainerManipulator.getHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
The summed implicit + explicit hydrogens of the given IAtom.
|
static int |
ExtAtomContainerManipulator.getImplicitHydrogenCount(IAtom atom)
Returns The number of Implicit Hydrogen Count for a given IAtom.
|
static BondEnergies |
BondEnergies.getInstance()
Returns Singleton pattern instance for the Bond Energy class
|
IAtomContainer |
MolHandler.getMolecule()
Returns the modified container
|
boolean |
MolHandler.getRemoveHydrogenFlag()
Returns true if hydrogens were made implicit else return false
|
static IAtomContainer |
ExtAtomContainerManipulator.makeDeepCopy(IAtomContainer container)
Retrurns deep copy of the molecule
|
static IMolecule |
ExtAtomContainerManipulator.makeDeepCopy(IMolecule container)
Retrurns deep copy of the molecule
|
static void |
ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Convenience method to perceive atom types for all
IAtom s in the
IAtomContainer , using the CDKAtomTypeMatcher . |
static IMolecule |
ExtAtomContainerManipulator.removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer atomContainer)
Returns IAtomContainer without Hydrogen.
|
Constructor and Description |
---|
MolHandler(IAtomContainer container,
boolean removeHydrogen,
boolean cleanMolecule)
Creates a new instance of MolHandler
|
MolHandler(String MolFile,
boolean removeHydrogen,
boolean cleanMolecule)
Creates a new instance of MolHandler
|
TimeManager()
Constructor for storing execution time
|
Modifier and Type | Method and Description |
---|---|
static boolean |
StereoTool.allCoplanar(javax.vecmath.Vector3d planeNormal,
javax.vecmath.Point3d pointInPlane,
javax.vecmath.Point3d... points)
Check that all the points in the list are coplanar (in the same plane)
as the plane defined by the planeNormal and the pointInPlane.
|
IBond[] |
DoubleBondStereochemistry.getBonds()
Returns an array of ligand bonds around the double bond.
|
IChemObjectBuilder |
TetrahedralChirality.getBuilder()
Returns a
IChemObjectBuilder for the data classes that extend
this class. |
IChemObjectBuilder |
DoubleBondStereochemistry.getBuilder()
Returns a
IChemObjectBuilder for the data classes that extend
this class. |
IAtom |
TetrahedralChirality.getChiralAtom()
Atom that is the chirality center.
|
static StereoTool.TetrahedralSign |
StereoTool.getHandedness(IAtom baseAtomA,
IAtom baseAtomB,
IAtom baseAtomC,
IAtom apexAtom)
Gets the tetrahedral handedness of four atoms - three of which form the
'base' of the tetrahedron, and the other the apex.
|
IAtom[] |
TetrahedralChirality.getLigands()
Returns an array of ligand atoms around the chiral atom.
|
static javax.vecmath.Vector3d |
StereoTool.getNormal(javax.vecmath.Point3d ptA,
javax.vecmath.Point3d ptB,
javax.vecmath.Point3d ptC)
Given three points (A, B, C), makes the vectors A-B and A-C, and makes
the cross product of these two vectors; this has the effect of making a
third vector at right angles to AB and AC.
|
static StereoTool.SquarePlanarShape |
StereoTool.getSquarePlanarShape(IAtom atomA,
IAtom atomB,
IAtom atomC,
IAtom atomD)
Given four atoms (assumed to be in the same plane), returns the
arrangement of those atoms in that plane.
|
ITetrahedralChirality.Stereo |
TetrahedralChirality.getStereo()
Defines the stereochemistry around the chiral atom.
|
IDoubleBondStereochemistry.Conformation |
DoubleBondStereochemistry.getStereo()
Defines the stereochemistry around the double bond.
|
static ITetrahedralChirality.Stereo |
StereoTool.getStereo(IAtom atom1,
IAtom atom2,
IAtom atom3,
IAtom atom4)
Take four atoms, and return Stereo.CLOCKWISE or Stereo.ANTI_CLOCKWISE.
|
IBond |
DoubleBondStereochemistry.getStereoBond()
IBond that is the stereo center. |
static boolean |
StereoTool.isColinear(javax.vecmath.Point3d ptA,
javax.vecmath.Point3d ptB,
javax.vecmath.Point3d ptC)
Checks the three supplied points to see if they fall on the same line.
|
static boolean |
StereoTool.isOctahedral(IAtom atomA,
IAtom atomB,
IAtom atomC,
IAtom atomD,
IAtom atomE,
IAtom atomF,
IAtom atomG)
Checks these 7 atoms to see if they are at the points of an octahedron.
|
static boolean |
StereoTool.isSquarePlanar(IAtom atomA,
IAtom atomB,
IAtom atomC,
IAtom atomD)
Checks these four atoms for square planarity.
|
static boolean |
StereoTool.isTrigonalBipyramidal(IAtom atomA,
IAtom atomB,
IAtom atomC,
IAtom atomD,
IAtom atomE,
IAtom atomF)
Checks these 6 atoms to see if they form a trigonal-bipyramidal shape.
|
ITetrahedralChirality |
TetrahedralChirality.map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds) |
IDoubleBondStereochemistry |
DoubleBondStereochemistry.map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds) |
void |
TetrahedralChirality.setBuilder(IChemObjectBuilder builder)
Sets a new
IChemObjectBuilder . |
void |
DoubleBondStereochemistry.setBuilder(IChemObjectBuilder builder)
Sets a new
IChemObjectBuilder . |
static double |
StereoTool.signedDistanceToPlane(javax.vecmath.Vector3d planeNormal,
javax.vecmath.Point3d pointInPlane,
javax.vecmath.Point3d point)
Given a normalized normal for a plane, any point in that plane, and
a point, will return the distance between the plane and that point.
|
String |
TetrahedralChirality.toString()
Returns a
String representation of this chiral element. |
Constructor and Description |
---|
TetrahedralChirality(IAtom chiralAtom,
IAtom[] ligandAtoms,
ITetrahedralChirality.Stereo chirality)
Constructor to create a new
ITetrahedralChirality implementation instance. |
Modifier and Type | Method and Description |
---|---|
List<IAtomContainer> |
InChITautomerGenerator.getTautomers(IAtomContainer molecule)
Public method to get tautomers for an input molecule, based on the InChI which will be calculated by jniinchi.
|
List<IAtomContainer> |
InChITautomerGenerator.getTautomers(IAtomContainer inputMolecule,
String inchi)
Overloaded
InChITautomerGenerator.getTautomers(IAtomContainer) to get tautomers for an input molecule with the InChI already
provided as input argument. |
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.
|
int |
ElementComparator.compare(Object o1,
Object o2)
Returns a negative if o1 comes before o2 in a molecular formula,
returns zero if they are identical, and positive if o1 comes
after o2 in the formula.
|
static void |
LoggingTool.configureLog4j()
Forces the
LoggingTool to configurate the Log4J toolkit. |
static ILoggingTool |
SystemOutLoggingTool.create(Class<?> sourceClass)
Creates a new
SystemOutLoggingTool for the given class. |
static ILoggingTool |
LoggingTool.create(Class<?> sourceClass)
Creates a new
LoggingTool for the given class. |
static void |
IDCreator.createIDs(IChemObject chemObject)
Labels the Atom's and Bond's in the AtomContainer using the a1, a2, b1, b2
scheme often used in CML.
|
static ILoggingTool |
LoggingToolFactory.createLoggingTool(Class<?> sourceClass)
Dynamically create a
ILoggingTool for the given
sourceClass . |
static boolean |
DeAromatizationTool.deAromatize(IRing ring)
Methods that takes a ring of which all bonds are aromatic, and assigns single
and double bonds.
|
void |
SystemOutLoggingTool.debug(Object object)
Shows DEBUG output for the Object.
|
void |
LoggingTool.debug(Object object)
Shows DEBUG output for the Object.
|
void |
SystemOutLoggingTool.debug(Object object,
Object... objects)
Shows DEBUG output for the given Object's.
|
void |
LoggingTool.debug(Object object,
Object... objects)
Shows DEBUG output for the given Object's.
|
void |
SystemOutLoggingTool.dumpClasspath()
Outputs the system property for java.class.path.
|
void |
LoggingTool.dumpClasspath()
Outputs the system property for java.class.path.
|
void |
SystemOutLoggingTool.dumpSystemProperties()
Outputs system properties for the operating system and the java
version.
|
void |
LoggingTool.dumpSystemProperties()
Outputs system properties for the operating system and the java
version.
|
void |
SystemOutLoggingTool.error(Object object)
Shows ERROR output for the Object.
|
void |
LoggingTool.error(Object object)
Shows ERROR output for the Object.
|
void |
SystemOutLoggingTool.error(Object object,
Object... objects)
Shows ERROR output for the given Object's.
|
void |
LoggingTool.error(Object object,
Object... objects)
Shows ERROR output for the given Object's.
|
void |
SystemOutLoggingTool.fatal(Object object)
Shows FATAL output for the Object.
|
void |
LoggingTool.fatal(Object object)
Shows FATAL output for the Object.
|
FormatStringBuffer |
FormatStringBuffer.format(char ch)
Format a char.
|
FormatStringBuffer |
FormatStringBuffer.format(double dbl)
Format a double.
|
FormatStringBuffer |
FormatStringBuffer.format(float flt)
Format a float.
|
FormatStringBuffer |
FormatStringBuffer.format(int i)
Format a float.
|
FormatStringBuffer |
FormatStringBuffer.format(long l)
Format a float.
|
FormatStringBuffer |
FormatStringBuffer.format(String str)
Format a String.
|
IAtomContainer |
StructureResonanceGenerator.getContainer(IMolecule molecule,
IAtom atom)
Get the container which the atom is found on resonance from a IMolecule.
|
IAtomContainer |
StructureResonanceGenerator.getContainer(IMolecule molecule,
IBond bond)
Get the container which the bond is found on resonance from a IMolecule.
|
IAtomContainerSet |
StructureResonanceGenerator.getContainers(IMolecule molecule)
Get the container which is found resonance from a IMolecule.
|
double |
AtomicProperties.getElectronegativity(String symbol) |
String |
HOSECodeGenerator.getHOSECode(IAtomContainer ac,
IAtom root,
int noOfSpheres)
|
static AtomicProperties |
AtomicProperties.getInstance() |
static CDKValencyChecker |
CDKValencyChecker.getInstance(IChemObjectBuilder builder) |
static CDKHydrogenAdder |
CDKHydrogenAdder.getInstance(IChemObjectBuilder builder) |
static Class<? extends ILoggingTool> |
LoggingToolFactory.getLoggingToolClass()
Gets the currently used
ILoggingTool implementation. |
double |
AtomicProperties.getMass(String symbol) |
int |
StructureResonanceGenerator.getMaximalStructures()
Get the number maximal of resonance structures to be found.
|
double |
AtomicProperties.getNormalizedElectronegativity(String symbol) |
double |
AtomicProperties.getNormalizedMass(String symbol) |
double |
AtomicProperties.getNormalizedPolarizability(String symbol) |
double |
AtomicProperties.getNormalizedVdWVolume(String symbol) |
double |
AtomicProperties.getPolarizability(String symbol) |
List<IReactionProcess> |
StructureResonanceGenerator.getReactions()
Get the reactions that must be presents in the generation of the resonance.
|
IMoleculeSet |
StructureResonanceGenerator.getStructures(IMolecule molecule)
Get the resonance structures from an IMolecule.
|
double |
AtomicProperties.getVdWVolume(String symbol) |
void |
SystemOutLoggingTool.info(Object object)
Shows INFO output for the Object.
|
void |
LoggingTool.info(Object object)
Shows INFO output for the Object.
|
void |
SystemOutLoggingTool.info(Object object,
Object... objects)
Shows INFO output for the given Object's.
|
void |
LoggingTool.info(Object object,
Object... objects)
Shows INFO output for the given Object's.
|
boolean |
SystemOutLoggingTool.isDebugEnabled()
Use this method for computational demanding debug info.
|
boolean |
LoggingTool.isDebugEnabled()
Use this method for computational demanding debug info.
|
boolean |
CDKValencyChecker.isSaturated(IAtomContainer atomContainer) |
boolean |
CDKValencyChecker.isSaturated(IAtom atom,
IAtomContainer container) |
String |
HOSECodeGenerator.makeBremserCompliant(String code) |
FormatStringBuffer |
FormatStringBuffer.reset()
Reset this FormatStringBuffer with the format string
given in the constructor or last call to reset(String).
|
FormatStringBuffer |
FormatStringBuffer.reset(String format)
Reset this FormatStringBuffer.
|
void |
StructureResonanceGenerator.setDefaultReactions()
Set the default reactions that must be presents to generate the resonance.
|
static void |
LoggingToolFactory.setLoggingToolClass(Class<? extends ILoggingTool> loggingTool)
Sets the
ILoggingTool implementation to be used. |
void |
StructureResonanceGenerator.setMaximalStructures(int maxStruct)
Set the number maximal of resonance structures to be found.
|
void |
StructureResonanceGenerator.setReactions(List<IReactionProcess> newReactionsList)
Set the reactions that must be used in the generation of the resonance.
|
void |
SystemOutLoggingTool.setStackLength(int length)
Sets the number of StackTraceElements to be printed in DEBUG mode when
calling
debug(Throwable) . |
void |
LoggingTool.setStackLength(int length)
Sets the number of StackTraceElements to be printed in DEBUG mode when
calling
debug(Throwable) . |
String |
FormatStringBuffer.toString()
Get the result of the formatting.
|
void |
SystemOutLoggingTool.warn(Object object)
Shows WARN output for the Object.
|
void |
LoggingTool.warn(Object object)
Shows WARN output for the Object.
|
void |
SystemOutLoggingTool.warn(Object object,
Object... objects)
Shows WARN output for the given Object's.
|
void |
LoggingTool.warn(Object object,
Object... objects)
Shows WARN output for the given Object's.
|
Constructor and Description |
---|
HOSECodeGenerator()
Constructor for the HOSECodeGenerator.
|
LoggingTool()
Constructs a LoggingTool which produces log lines without any special
indication which class the message originates from.
|
LoggingTool(Class<?> classInst)
Constructs a LoggingTool which produces log lines indicating them to be
for the given Class.
|
LoggingTool(Object object)
Constructs a LoggingTool which produces log lines indicating them to be
for the Class of the
Object . |
SystemOutLoggingTool(Class<?> classInst)
Constructs a ILoggingTool which produces log lines indicating them to be
for the given Class.
|
Modifier and Type | Method and Description |
---|---|
static String |
SingleElectronDiff.diff(IChemObject first,
IChemObject second) |
static String |
LonePairDiff.diff(IChemObject first,
IChemObject second) |
static String |
IsotopeDiff.diff(IChemObject first,
IChemObject second) |
static String |
ElementDiff.diff(IChemObject first,
IChemObject second) |
static String |
ElectronContainerDiff.diff(IChemObject first,
IChemObject second) |
static String |
ChemObjectDiff.diff(IChemObject first,
IChemObject second) |
static String |
BondDiff.diff(IChemObject first,
IChemObject second) |
static String |
AtomTypeDiff.diff(IChemObject first,
IChemObject second) |
static String |
AtomDiff.diff(IChemObject first,
IChemObject second) |
static String |
AtomContainerDiff.diff(IChemObject first,
IChemObject second) |
static IDifference |
SingleElectronDiff.difference(IChemObject first,
IChemObject second) |
static IDifference |
LonePairDiff.difference(IChemObject first,
IChemObject second) |
static IDifference |
IsotopeDiff.difference(IChemObject first,
IChemObject second) |
static IDifference |
ElementDiff.difference(IChemObject first,
IChemObject second) |
static IDifference |
ElectronContainerDiff.difference(IChemObject first,
IChemObject second) |
static IDifference |
ChemObjectDiff.difference(IChemObject first,
IChemObject second) |
static IDifference |
BondDiff.difference(IChemObject first,
IChemObject second) |
static IDifference |
AtomTypeDiff.difference(IChemObject first,
IChemObject second) |
static IDifference |
AtomDiff.difference(IChemObject first,
IChemObject second) |
static IDifference |
AtomContainerDiff.difference(IChemObject first,
IChemObject second) |
Modifier and Type | Method and Description |
---|---|
void |
AbstractDifferenceList.addChild(IDifference childDiff) |
void |
AbstractDifferenceList.addChildren(List<IDifference> children) |
int |
AbstractDifferenceList.childCount() |
static IDifference |
BooleanArrayDifference.construct(String name,
boolean[] first,
boolean[] second) |
static IDifference |
BooleanDifference.construct(String name,
Boolean first,
Boolean second) |
static IDifference |
DoubleDifference.construct(String name,
Double first,
Double second) |
static IDifference |
AtomTypeHybridizationDifference.construct(String name,
IAtomType.Hybridization first,
IAtomType.Hybridization second) |
static IDifference |
BondOrderDifference.construct(String name,
IBond.Order first,
IBond.Order second) |
static IDifference |
IntegerDifference.construct(String name,
Integer first,
Integer second) |
static IDifference |
Point2dDifference.construct(String name,
javax.vecmath.Point2d first,
javax.vecmath.Point2d second) |
static IDifference |
Point3dDifference.construct(String name,
javax.vecmath.Point3d first,
javax.vecmath.Point3d second) |
static IDifference |
StringDifference.construct(String name,
String first,
String second) |
Iterable<IDifference> |
AbstractDifferenceList.getChildren() |
String |
StringDifference.toString() |
String |
Point3dDifference.toString() |
String |
Point2dDifference.toString() |
String |
IntegerDifference.toString() |
String |
DoubleDifference.toString() |
String |
ChemObjectDifference.toString() |
String |
BooleanDifference.toString() |
String |
BooleanArrayDifference.toString() |
String |
BondOrderDifference.toString() |
String |
AtomTypeHybridizationDifference.toString() |
Constructor and Description |
---|
ChemObjectDifference(String name) |
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 void |
AtomContainerManipulator.clearAtomConfigurations(IAtomContainer container)
This method will reset all atom configuration to UNSET.
|
int |
AtomContainerComparator.compare(IAtomContainer o1,
IAtomContainer o2) |
static boolean |
MolecularFormulaManipulator.compare(IMolecularFormula formula1,
IMolecularFormula formula2)
Compare two IMolecularFormula looking at type and number of IIsotope and
charge of the formula.
|
int |
RingSizeComparator.compare(IRing object1,
IRing object2) |
static void |
AtomTypeManipulator.configure(IAtom atom,
IAtomType atomType)
Method that assign properties to an atom given a particular atomType.
|
static void |
AtomTypeManipulator.configureUnsetProperties(IAtom atom,
IAtomType atomType)
Method that assign properties to an atom given a particular atomType.
|
static boolean |
MolecularFormulaSetManipulator.contains(IMolecularFormulaSet formulaSet,
IMolecularFormula formula)
True, if the IMolecularFormulaSet contains the given IMolecularFormula but not
as object.
|
static boolean |
AtomContainerSetManipulator.containsByID(IAtomContainerSet atomContainerSet,
String id)
Tells if an AtomContainerSet contains at least one AtomContainer with the
same ID as atomContainer.
|
static boolean |
MolecularFormulaManipulator.containsElement(IMolecularFormula formula,
IElement element)
True, if the MolecularFormula contains the given element as IIsotope object.
|
static void |
AtomContainerManipulator.convertImplicitToExplicitHydrogens(IAtomContainer atomContainer)
Adds explicit hydrogens (without coordinates) to the IAtomContainer,
equaling the number of set implicit hydrogens.
|
static int |
AtomContainerManipulator.countExplicitHydrogens(IAtomContainer atomContainer,
IAtom atom)
Count explicit hydrogens.
|
static int |
AtomContainerManipulator.countHydrogens(IAtomContainer atomContainer,
IAtom atom) |
static IBond.Order |
BondManipulator.createBondOrder(double bondOrder)
Convenience method to convert a double into an IBond.Order.
|
static IAtomContainer |
ChemModelManipulator.createNewMolecule(IChemModel chemModel)
Adds a new Molecule to the MoleculeSet inside a given ChemModel.
|
static IReactionScheme |
ReactionSchemeManipulator.createReactionScheme(IReactionSet reactionSet)
Create a IReactionScheme give a IReactionSet object.
|
static IBond.Order |
BondManipulator.decreaseBondOrder(IBond.Order oldOrder)
Returns the IBond.Order one lower.
|
static void |
BondManipulator.decreaseBondOrder(IBond bond)
Decrease the order of a bond.
|
static double |
BondManipulator.destroyBondOrder(IBond.Order bondOrder)
Convert a
IBond.Order to a numeric value. |
static List<IElement> |
MolecularFormulaManipulator.elements(IMolecularFormula formula)
Get a list of all Elements which are contained
molecular.
|
static IAtomContainer |
AtomContainerManipulator.extractSubstructure(IAtomContainer atomContainer,
int... atomIndices)
Extract a substructure from an atom container, in the form of a new
cloned atom container with only the atoms with indices in atomIndices and
bonds that connect these atoms.
|
static IReactionSet |
ReactionSchemeManipulator.extractTopReactions(IReactionScheme reactionScheme)
Extract a set of Reactions which are in top of a IReactionScheme.
|
static List<IAtomContainer> |
AtomContainerSetManipulator.getAllAtomContainers(IAtomContainerSet set)
Returns all the AtomContainer's of a MoleculeSet.
|
static List<IAtomContainer> |
ChemFileManipulator.getAllAtomContainers(IChemFile file)
Returns all the AtomContainer's of a ChemFile.
|
static List<IAtomContainer> |
ChemModelManipulator.getAllAtomContainers(IChemModel chemModel)
Returns all the AtomContainer's of a ChemModel.
|
static List<IAtomContainer> |
ChemSequenceManipulator.getAllAtomContainers(IChemSequence sequence)
Returns all the AtomContainer's of a ChemSequence.
|
static List<IAtomContainer> |
MoleculeSetManipulator.getAllAtomContainers(IMoleculeSet set)
Returns all the AtomContainer's of a MoleculeSet.
|
static List<IAtomContainer> |
ReactionManipulator.getAllAtomContainers(IReaction reaction)
Returns all the AtomContainer's of a Reaction.
|
static List<IAtomContainer> |
ReactionSetManipulator.getAllAtomContainers(IReactionSet set)
Returns all the AtomContainer's of a Reaction.
|
static List<IAtomContainer> |
RingSetManipulator.getAllAtomContainers(IRingSet set)
Returns all the AtomContainer's in a RingSet.
|
static List<IChemModel> |
ChemFileManipulator.getAllChemModels(IChemFile file)
Get a list of all ChemModels inside an IChemFile.
|
static List<IChemObject> |
AtomContainerSetManipulator.getAllChemObjects(IAtomContainerSet set)
Does not recursively return the contents of the AtomContainer.
|
static List<IChemObject> |
ChemFileManipulator.getAllChemObjects(IChemFile file)
Returns a List of all IChemObject inside a ChemFile.
|
static List<IChemObject> |
ChemModelManipulator.getAllChemObjects(IChemModel chemModel)
Retrieve a List of all ChemObject objects within an IChemModel.
|
static List<IChemObject> |
ChemSequenceManipulator.getAllChemObjects(IChemSequence sequence)
Returns a List of all IChemObject inside a ChemSequence.
|
static List<IChemObject> |
MoleculeSetManipulator.getAllChemObjects(IMoleculeSet set) |
static List<IChemObject> |
ReactionManipulator.getAllChemObjects(IReaction reaction) |
static List<IChemObject> |
ReactionSetManipulator.getAllChemObjects(IReactionSet set) |
static List<String> |
AtomContainerManipulator.getAllIDs(IAtomContainer mol) |
static List<String> |
AtomContainerSetManipulator.getAllIDs(IAtomContainerSet set) |
static List<String> |
ChemFileManipulator.getAllIDs(IChemFile file) |
static List<String> |
ChemModelManipulator.getAllIDs(IChemModel chemModel) |
static List<String> |
ChemSequenceManipulator.getAllIDs(IChemSequence sequence) |
static List<String> |
MoleculeSetManipulator.getAllIDs(IMoleculeSet set) |
static List<String> |
ReactionManipulator.getAllIDs(IReaction reaction) |
static List<String> |
ReactionSchemeManipulator.getAllIDs(IReactionScheme scheme)
Get all ID of this IReactionSet.
|
static List<String> |
ReactionSetManipulator.getAllIDs(IReactionSet set) |
static IAtomContainer |
RingSetManipulator.getAllInOneContainer(IRingSet ringSet)
Puts all rings of a ringSet in a single atomContainer
|
static IMoleculeSet |
ReactionManipulator.getAllMolecules(IReaction reaction)
get all molecule of a IReaction.
|
static IMoleculeSet |
ReactionSchemeManipulator.getAllMolecules(IReactionScheme scheme)
get all Molecules object from a set of Reactions.
|
static IMoleculeSet |
ReactionSchemeManipulator.getAllMolecules(IReactionScheme scheme,
IMoleculeSet molSet)
Get all Molecules object from a set of Reactions given a IMoleculeSet to add.
|
static IMoleculeSet |
ReactionSetManipulator.getAllMolecules(IReactionSet set)
get all Molecules object from a set of Reactions.
|
static IMoleculeSet |
ReactionManipulator.getAllProducts(IReaction reaction)
get all products of a IReaction
|
static IMoleculeSet |
ReactionManipulator.getAllReactants(IReaction reaction)
get all reactants of a IReaction
|
static List<IReaction> |
ChemFileManipulator.getAllReactions(IChemFile file)
Get a list of all IReaction inside an IChemFile.
|
static IReactionSet |
ReactionSchemeManipulator.getAllReactions(IReactionScheme scheme)
Get all IReaction's object from a given IReactionScheme.
|
static IAtom[] |
AtomContainerManipulator.getAtomArray(IAtomContainer container)
Constructs an array of Atom objects from an AtomContainer.
|
static IAtom[] |
BondManipulator.getAtomArray(IBond container)
Constructs an array of Atom objects from Bond.
|
static IAtom[] |
AtomContainerManipulator.getAtomArray(List<IAtom> list)
Constructs an array of Atom objects from a List of Atom objects.
|
static IAtom |
AtomContainerManipulator.getAtomById(IAtomContainer ac,
String id)
Returna an atom in an atomcontainer identified by id
|
static IAtomContainer |
MolecularFormulaManipulator.getAtomContainer(IMolecularFormula formula)
Method that actually does the work of convert the IMolecularFormula
to IAtomContainer.
|
static IAtomContainer |
MolecularFormulaManipulator.getAtomContainer(IMolecularFormula formula,
IAtomContainer atomContainer)
Method that actually does the work of convert the IMolecularFormula
to IAtomContainer given a IAtomContainer.
|
static int |
MoleculeSetManipulator.getAtomCount(IAtomContainerSet set) |
static int |
AtomContainerSetManipulator.getAtomCount(IAtomContainerSet set) |
static int |
ChemFileManipulator.getAtomCount(IChemFile file)
Get the total number of atoms inside an IChemFile.
|
static int |
ChemModelManipulator.getAtomCount(IChemModel chemModel)
Get the total number of atoms inside an IChemModel.
|
static int |
ChemSequenceManipulator.getAtomCount(IChemSequence sequence)
Get the total number of atoms inside an IChemSequence.
|
static int |
MolecularFormulaManipulator.getAtomCount(IMolecularFormula formula)
Checks a set of Nodes for the occurrence of each isotopes
instance in the molecular formula.
|
static int |
ReactionManipulator.getAtomCount(IReaction reaction) |
static int |
ReactionSetManipulator.getAtomCount(IReactionSet set) |
static int |
RingSetManipulator.getAtomCount(IRingSet set)
Return the total number of atoms over all the rings in the colllection.
|
static IAtomParity |
AtomContainerManipulator.getAtomParity(IAtomContainer container,
IAtom atom)
Helper methods that works through the stereo elements of the given atom container
and returns if the atom parity for the given atom, if one is defined.
|
static IBond[] |
AtomContainerManipulator.getBondArray(IAtomContainer container)
Constructs an array of Bond objects from an AtomContainer.
|
static IBond[] |
AtomContainerManipulator.getBondArray(List<IBond> list)
Constructs an array of Atom objects from a List of Atom objects.
|
static int |
MoleculeSetManipulator.getBondCount(IAtomContainerSet set) |
static int |
AtomContainerSetManipulator.getBondCount(IAtomContainerSet set) |
static int |
ChemFileManipulator.getBondCount(IChemFile file)
Get the total number of bonds inside an IChemFile.
|
static int |
ChemModelManipulator.getBondCount(IChemModel chemModel)
Get the total number of bonds inside an IChemModel.
|
static int |
ChemSequenceManipulator.getBondCount(IChemSequence sequence)
Get the total number of bonds inside an IChemSequence.
|
static int |
ReactionManipulator.getBondCount(IReaction reaction) |
static int |
ReactionSetManipulator.getBondCount(IReactionSet set) |
static int |
RingSetManipulator.getBondCount(IRingSet set)
Return the total number of bonds over all the rings in the colllection.
|
static double |
AtomContainerManipulator.getBondOrderSum(IAtomContainer container,
IAtom atom)
Returns the sum of the bond order equivalents for a given IAtom.
|
static double |
MolecularFormulaManipulator.getDBE(IMolecularFormula formula)
Returns the number of double bond equivalents in this molecule.
|
static int |
MolecularFormulaManipulator.getElementCount(IMolecularFormula formula,
IElement element)
Checks a set of Nodes for the occurrence of the isotopes in the
molecular formula from a particular IElement.
|
static IRing |
RingSetManipulator.getHeaviestRing(IRingSet ringSet,
IBond bond)
We define the heaviest ring as the one with the highest number of double bonds.
|
static List<IAtom> |
AtomContainerManipulator.getHeavyAtoms(IAtomContainer container)
Returns a set of nodes excluding all the hydrogens.
|
static List<IElement> |
MolecularFormulaManipulator.getHeavyElements(IMolecularFormula formula)
Returns a set of nodes excluding all the hydrogens
|
static String |
MolecularFormulaManipulator.getHillString(IMolecularFormula formula) |
static String |
MolecularFormulaManipulator.getHTML(IMolecularFormula formula)
Returns the string representation of the molecule formula based on Hill
System with numbers wrapped in <sub></sub> tags.
|
static String |
MolecularFormulaManipulator.getHTML(IMolecularFormula formula,
boolean chargeB,
boolean isotopeB)
Returns the string representation of the molecule formula based on Hill
System with numbers wrapped in <sub></sub> tags and the
isotope of each Element in <sup></sup> tags and the total
charge of IMolecularFormula in <sup></sup> tags.
|
static IAtomContainer |
AtomContainerManipulator.getIntersection(IAtomContainer container1,
IAtomContainer container2)
Compares this AtomContainer with another given AtomContainer and returns
the Intersection between them.
|
static List<IIsotope> |
MolecularFormulaManipulator.getIsotopes(IMolecularFormula formula,
IElement element)
Get a list of IIsotope from a given IElement which is contained
molecular.
|
static IRingSet |
RingSetManipulator.getLargestRingSet(List<IRingSet> ringSystems)
Returns the largest (number of atoms) ring set in a molecule
|
static double |
MolecularFormulaManipulator.getMajorIsotopeMass(IMolecularFormula formula)
Get the summed major isotopic mass of all elements from an MolecularFormula.
|
static IMolecularFormula |
MolecularFormulaManipulator.getMajorIsotopeMolecularFormula(String stringMF,
IChemObjectBuilder builder)
Construct an instance of IMolecularFormula, initialized with a molecular
formula string.
|
static IChemObject |
ReactionManipulator.getMappedChemObject(IReaction reaction,
IChemObject chemObject)
get the IAtom which is mapped
|
static IMolecularFormula |
MolecularFormulaRangeManipulator.getMaximalFormula(MolecularFormulaRange mfRange,
IChemObjectBuilder builder)
Returns the maximal occurrence of the IIsotope into IMolecularFormula
from this MolelecularFormulaRange.
|
static IBond.Order |
AtomContainerManipulator.getMaximumBondOrder(IAtomContainer container) |
static IBond.Order |
BondManipulator.getMaximumBondOrder(Iterator<IBond> bonds)
Returns the maximum bond order for a List of bonds, given an iterator to the list.
|
static IBond.Order |
BondManipulator.getMaximumBondOrder(List<IBond> bonds)
Returns the maximum bond order for a List of bonds.
|
static IMolecularFormula |
MolecularFormulaSetManipulator.getMaxOccurrenceElements(IMolecularFormulaSet mfSet)
Extract from a set of MolecularFormula the maximum occurrence of each element found and
put the element and occurrence in a new IMolecularFormula.
|
static IMolecularFormula |
MolecularFormulaRangeManipulator.getMinimalFormula(MolecularFormulaRange mfRange,
IChemObjectBuilder builder)
Returns the minimal occurrence of the IIsotope into IMolecularFormula
from this MolelecularFormulaRange.
|
static IBond.Order |
BondManipulator.getMinimumBondOrder(Iterator<IBond> bonds)
Returns the minimum bond order for a List of bonds, given an iterator
to the list.
|
static IBond.Order |
BondManipulator.getMinimumBondOrder(List<IBond> bonds)
Returns the minimum bond order for a List of bonds.
|
static IMolecularFormula |
MolecularFormulaSetManipulator.getMinOccurrenceElements(IMolecularFormulaSet mfSet)
Extract from a set of MolecularFormula the minimal occurrence of each element found and
put the element and occurrence in a new IMolecularFormula.
|
static IMolecularFormula |
MolecularFormulaManipulator.getMolecularFormula(IAtomContainer atomContainer)
Method that actually does the work of convert the atomContainer
to IMolecularFormula.
|
static IMolecularFormula |
MolecularFormulaManipulator.getMolecularFormula(IAtomContainer atomContainer,
IMolecularFormula formula)
Method that actually does the work of convert the atomContainer
to IMolecularFormula given a IMolecularFormula.
|
static IMolecularFormula |
MolecularFormulaManipulator.getMolecularFormula(String stringMF,
IChemObjectBuilder builder)
Construct an instance of IMolecularFormula, initialized with a molecular
formula string.
|
static IMolecularFormula |
MolecularFormulaManipulator.getMolecularFormula(String stringMF,
IMolecularFormula formula)
add in a instance of IMolecularFormula the elements extracts form
molecular formula string.
|
static ArrayList<IMoleculeSet> |
ReactionSchemeManipulator.getMoleculeSet(IMolecule origenMol,
IMolecule finalMol,
IReactionScheme reactionScheme)
Extract the list of molecules taking part in the IReactionScheme to originate a
product given a reactant.
|
static IRing |
RingSetManipulator.getMostComplexRing(IRingSet ringSet)
Returns the ring with the highest numbers of other rings attached to it.
|
static double |
AtomContainerManipulator.getNaturalExactMass(IAtomContainer atomContainer)
Returns the molecular mass of the IAtomContainer.
|
static double |
MolecularFormulaManipulator.getNaturalExactMass(IMolecularFormula formula)
Get the summed natural mass of all elements from an MolecularFormula.
|
static MolecularFormulaRange |
MolecularFormulaRangeManipulator.getRange(IMolecularFormulaSet mfSet)
Extract from a set of MolecularFormula the range of each each element found and
put the element and occurrence in a new MolecularFormulaRange.
|
static IReaction |
ReactionSetManipulator.getReactionByAtomContainerID(IReactionSet reactionSet,
String id)
Gets a reaction from a ReactionSet by ID of any product or reactant.
|
static IReaction |
ReactionSetManipulator.getReactionByReactionID(IReactionSet reactionSet,
String id)
Gets a reaction from a ReactionSet by ID.
|
static IAtomContainer |
AtomContainerSetManipulator.getRelevantAtomContainer(IAtomContainerSet containerSet,
IAtom atom) |
static IAtomContainer |
AtomContainerSetManipulator.getRelevantAtomContainer(IAtomContainerSet containerSet,
IBond bond) |
static IAtomContainer |
ChemModelManipulator.getRelevantAtomContainer(IChemModel chemModel,
IAtom atom)
This badly named methods tries to determine which AtomContainer in the
ChemModel is best suited to contain added Atom's and Bond's.
|
static IAtomContainer |
ChemModelManipulator.getRelevantAtomContainer(IChemModel chemModel,
IBond bond)
Retrieves the first IAtomContainer containing a given IBond from an
IChemModel.
|
static IAtomContainer |
MoleculeSetManipulator.getRelevantAtomContainer(IMoleculeSet moleculeSet,
IAtom atom) |
static IAtomContainer |
MoleculeSetManipulator.getRelevantAtomContainer(IMoleculeSet moleculeSet,
IBond bond) |
static IAtomContainer |
ReactionManipulator.getRelevantAtomContainer(IReaction reaction,
IAtom atom) |
static IAtomContainer |
ReactionManipulator.getRelevantAtomContainer(IReaction reaction,
IBond bond) |
static IAtomContainer |
ReactionSetManipulator.getRelevantAtomContainer(IReactionSet set,
IAtom atom) |
static IAtomContainer |
ReactionSetManipulator.getRelevantAtomContainer(IReactionSet set,
IBond bond) |
static IReaction |
ChemModelManipulator.getRelevantReaction(IChemModel chemModel,
IAtom atom)
Retrieves the first IReaction containing a given IAtom from an
IChemModel.
|
static IReaction |
ReactionSetManipulator.getRelevantReaction(IReactionSet set,
IAtom atom) |
static IReaction |
ReactionSetManipulator.getRelevantReaction(IReactionSet set,
IBond bond) |
static IReactionSet |
ReactionSetManipulator.getRelevantReactions(IReactionSet reactSet,
IAtomContainer molecule)
Get all Reactions object containing a Molecule from a set of Reactions.
|
static IReactionSet |
ReactionSetManipulator.getRelevantReactionsAsProduct(IReactionSet reactSet,
IAtomContainer molecule)
Get all Reactions object containing a Molecule as a Product from a set of
Reactions.
|
static IReactionSet |
ReactionSetManipulator.getRelevantReactionsAsReactant(IReactionSet reactSet,
IAtomContainer molecule)
Get all Reactions object containing a Molecule as a Reactant from a set
of Reactions.
|
static int |
AtomContainerManipulator.getSingleBondEquivalentSum(IAtomContainer container)
Returns the sum of bond orders, where a single bond counts as one
single bond equivalent, a double as two, etc.
|
static int |
BondManipulator.getSingleBondEquivalentSum(Iterator<IBond> bonds)
Get the single bond equivalent (SBE) of a list of bonds, given an iterator to the list.
|
static int |
BondManipulator.getSingleBondEquivalentSum(List<IBond> bonds)
Get the single bond equivalent (SBE) of a list of bonds.
|
static String |
MolecularFormulaManipulator.getString(IMolecularFormula formula)
Returns the string representation of the molecule formula.
|
static String |
MolecularFormulaManipulator.getString(IMolecularFormula formula,
boolean setOne)
Returns the string representation of the molecule formula.
|
static String |
MolecularFormulaManipulator.getString(IMolecularFormula formula,
String[] orderElements,
boolean setOne)
Returns the string representation of the molecule formula.
|
static double |
AtomContainerManipulator.getTotalCharge(IAtomContainer atomContainer)
Get the summed charge of all atoms in an AtomContainer
|
static double |
AtomContainerSetManipulator.getTotalCharge(IAtomContainerSet set) |
static double |
MoleculeSetManipulator.getTotalCharge(IMoleculeSet set) |
static double |
AtomContainerManipulator.getTotalExactMass(IAtomContainer atomContainer)
Get the summed exact mass of all atoms in an AtomContainer.
|
static double |
MolecularFormulaManipulator.getTotalExactMass(IMolecularFormula formula)
Get the summed exact mass of all isotopes from an MolecularFormula.
|
static int |
AtomContainerManipulator.getTotalFormalCharge(IAtomContainer atomContainer)
Get the total formal charge on a molecule.
|
static double |
AtomContainerSetManipulator.getTotalFormalCharge(IAtomContainerSet set) |
static double |
MoleculeSetManipulator.getTotalFormalCharge(IMoleculeSet set) |
static int |
AtomContainerManipulator.getTotalHydrogenCount(IAtomContainer atomContainer)
Count the total number of hydrogens (implicit and explicit).
|
static int |
AtomContainerSetManipulator.getTotalHydrogenCount(IAtomContainerSet set) |
static int |
MoleculeSetManipulator.getTotalHydrogenCount(IMoleculeSet set) |
static double |
MolecularFormulaManipulator.getTotalMassNumber(IMolecularFormula formula)
Get the summed mass number of all isotopes from an MolecularFormula.
|
static double |
AtomContainerManipulator.getTotalNaturalAbundance(IAtomContainer atomContainer)
Get the summed natural abundance of all atoms in an AtomContainer
|
static double |
MolecularFormulaManipulator.getTotalNaturalAbundance(IMolecularFormula formula)
Get the summed natural abundance of all isotopes from an MolecularFormula.
|
static int |
AtomContainerManipulator.getTotalNegativeFormalCharge(IAtomContainer atomContainer)
Get the total formal negative charge on a molecule.
|
static int |
AtomContainerManipulator.getTotalPositiveFormalCharge(IAtomContainer atomContainer)
Get the total positive formal charge on a molecule.
|
static IBond.Order |
BondManipulator.increaseBondOrder(IBond.Order oldOrder)
Returns the IBond.Order one higher.
|
static void |
BondManipulator.increaseBondOrder(IBond bond)
Increment the bond order of this bond.
|
static boolean |
BondManipulator.isHigherOrder(IBond.Order first,
IBond.Order second)
Returns true if the first bond has a higher bond order than the second bond.
|
static boolean |
BondManipulator.isLowerOrder(IBond.Order first,
IBond.Order second)
Returns true if the first bond has a lower bond order than the second bond.
|
static boolean |
RingSetManipulator.isSameRing(IRingSet ringSet,
IAtom atom1,
IAtom atom2)
Checks if
atom1 and atom2 share membership in the same ring or ring system. |
static void |
RingManipulator.markAromaticRings(IRing ring)
Marks the ring aromatic if all atoms and all bonds are aromatic.
|
static void |
RingSetManipulator.markAromaticRings(IRingSet ringset)
Iterates over the rings in the ring set, and marks the ring
aromatic if all atoms and all bonds are aromatic.
|
static IChemModel |
ChemModelManipulator.newChemModel(IAtomContainer atomContainer)
Create a new ChemModel containing an IAtomContainer.
|
static void |
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Convenience method to perceive atom types for all
IAtom s in the
IAtomContainer , using the CDKAtomTypeMatcher . |
static void |
AtomContainerManipulator.percieveAtomTypesAndConfigureUnsetProperties(IAtomContainer container)
Convenience method to perceive atom types for all
IAtom s in the
IAtomContainer , using the CDKAtomTypeMatcher . |
static IMolecularFormulaSet |
MolecularFormulaSetManipulator.remove(IMolecularFormulaSet formulaSet,
IMolecularFormula formulaMin,
IMolecularFormula formulaMax)
Remove all those IMolecularFormula which are not fit theirs IElement
occurrence into a limits.
|
static IMolecularFormulaSet |
MolecularFormulaSetManipulator.remove(IMolecularFormulaSet formulaSet,
MolecularFormulaRange formulaRange)
Remove all those IMolecularFormula which are not fit theirs IElement
occurrence into a limits.
|
static void |
AminoAcidManipulator.removeAcidicOxygen(IAminoAcid acid)
Removes the singly bonded oxygen from the acid group of the AminoAcid.
|
static void |
AtomContainerSetManipulator.removeAtomAndConnectedElectronContainers(IAtomContainerSet set,
IAtom atom) |
static void |
ChemModelManipulator.removeAtomAndConnectedElectronContainers(IChemModel chemModel,
IAtom atom)
Remove an Atom and the connected ElectronContainers from all AtomContainers
inside an IChemModel.
|
static void |
MoleculeSetManipulator.removeAtomAndConnectedElectronContainers(IMoleculeSet set,
IAtom atom) |
static void |
ReactionManipulator.removeAtomAndConnectedElectronContainers(IReaction reaction,
IAtom atom) |
static void |
ReactionSetManipulator.removeAtomAndConnectedElectronContainers(IReactionSet set,
IAtom atom) |
static void |
AtomContainerSetManipulator.removeElectronContainer(IAtomContainerSet set,
IElectronContainer electrons) |
static void |
ChemModelManipulator.removeElectronContainer(IChemModel chemModel,
IElectronContainer electrons)
Remove an ElectronContainer from all AtomContainers
inside an IChemModel.
|
static void |
MoleculeSetManipulator.removeElectronContainer(IMoleculeSet set,
IElectronContainer electrons) |
static void |
ReactionManipulator.removeElectronContainer(IReaction reaction,
IElectronContainer electrons) |
static void |
ReactionSetManipulator.removeElectronContainer(IReactionSet set,
IElectronContainer electrons) |
static IMolecularFormula |
MolecularFormulaManipulator.removeElement(IMolecularFormula formula,
IElement element)
Removes all isotopes from a given element in the MolecularFormula.
|
static IAtomContainer |
AtomContainerManipulator.removeHydrogens(IAtomContainer atomContainer)
Produces an AtomContainer without explicit Hs but with H count from one with Hs.
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static IAtomContainer |
AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded(IAtomContainer ac)
Produces an AtomContainer without explicit Hs but with H count from one with Hs.
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static boolean |
AtomContainerManipulator.replaceAtomByAtom(IAtomContainer container,
IAtom atom,
IAtom newAtom) |
static IReaction |
ReactionManipulator.reverse(IReaction reaction)
Returns a new Reaction object which is the reverse of the given
Reaction.
|
static boolean |
RingSetManipulator.ringAlreadyInSet(IRing newRing,
IRingSet ringSet)
Checks - and returns 'true' - if a certain ring is already
stored in the ringset.
|
static void |
AtomContainerSetManipulator.setAtomProperties(IAtomContainerSet set,
Object propKey,
Object propVal) |
static void |
ChemModelManipulator.setAtomProperties(IChemModel chemModel,
Object propKey,
Object propVal)
Sets the AtomProperties of all Atoms inside an IChemModel.
|
static void |
MoleculeSetManipulator.setAtomProperties(IMoleculeSet set,
Object propKey,
Object propVal) |
static void |
ReactionManipulator.setAtomProperties(IReaction reaction,
Object propKey,
Object propVal) |
static void |
ReactionSetManipulator.setAtomProperties(IReactionSet set,
Object propKey,
Object propVal) |
static String |
MolecularFormulaManipulator.simplifyMolecularFormula(String formula)
Simplify the molecular formula.
|
static void |
AtomContainerSetManipulator.sort(IAtomContainerSet atomContainerSet)
Sorts the IAtomContainers in the given IAtomContainerSet by the following
criteria with decreasing priority:
|
static void |
RingSetManipulator.sort(IRingSet ringSet)
Sorts the rings in the set by size.
|
Modifier and Type | Method and Description |
---|---|
static Integer |
PeriodicTable.getAtomicNumber(String symbol)
Get the atomic number of the element.
|
static String |
PeriodicTable.getCASId(String symbol)
Get the CAS ID for an element.
|
static String |
PeriodicTable.getChemicalSeries(String symbol)
Get the chemical series for an element.
|
static Double |
PeriodicTable.getCovalentRadius(String symbol)
Get the covalent radius for an element.
|
static int |
PeriodicTable.getElementCount()
Return the number of elements currently considered in the periodic table.
|
static Integer |
PeriodicTable.getGroup(String symbol)
Get the group of the element.
|
static String |
PeriodicTable.getName(String symbol)
Get the name of the element.
|
static Double |
PeriodicTable.getPaulingElectronegativity(String symbol)
Get the Pauling electronegativity of an element.
|
static Integer |
PeriodicTable.getPeriod(String symbol)
Get the period of the element.
|
static String |
PeriodicTable.getPhase(String symbol)
Get the phase of the element.
|
static String |
PeriodicTable.getSymbol(int atomicNumber) |
static Double |
PeriodicTable.getVdwRadius(String symbol)
Get the Van der Waals radius for the element in question.
|
Modifier and Type | Method and Description |
---|---|
static void |
ProblemMarker.markWithError(IChemObject object) |
static void |
ProblemMarker.markWithWarning(IChemObject object) |
static void |
ProblemMarker.unmark(IChemObject object) |
static void |
ProblemMarker.unmarkWithError(IChemObject object) |
static void |
ProblemMarker.unmarkWithWarning(IChemObject object) |