| Modifier and Type | Class and Description |
|---|---|
class |
AminoAcid
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
|
class |
AtomContainer
Base class for all chemical objects that maintain a list of Atoms and
ElectronContainers.
|
class |
BioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
|
class |
Crystal
Class representing a molecular crystal.
|
class |
Monomer
A Monomer is an AtomContainer which stores additional monomer specific
informations for a group of Atoms.
|
class |
Polymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
|
class |
Ring
Class representing a ring structure in a molecule.
|
class |
Strand
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
|
| Modifier and Type | Field and Description |
|---|---|
protected IAtomContainer[] |
AtomContainerSet.atomContainers
Array of AtomContainers.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
AtomContainer.clone()
Clones this
IChemObject. |
IAtomContainer |
ConformerContainer.get(int i)
Get the conformer at a specified position.
|
IAtomContainer |
AtomContainerSet.getAtomContainer(int number)
Returns the AtomContainer at position
number in the
container. |
IAtomContainer |
Atom.getContainer()
Access the
IAtomContainer of which this atom is a member of. |
IAtomContainer |
Bond.getContainer() |
IAtomContainer |
BondRef.getContainer() |
IAtomContainer |
AtomRef.getContainer()
Access the
IAtomContainer of which this atom is a member of. |
IAtomContainer |
FragmentAtom.getFragment() |
IAtomContainer |
DefaultChemObjectBuilder.newAtomContainer()
Create a new atom container using the default constructor.
|
IAtomContainer |
ConformerContainer.remove(int i)
Removes the conformer at the specified position.
|
IAtomContainer |
ConformerContainer.set(int i,
IAtomContainer atomContainer) |
| Modifier and Type | Method and Description |
|---|---|
Iterable<IAtomContainer> |
AtomContainerSet.atomContainers()
Get an iterator for this AtomContainerSet.
|
Iterator<IAtomContainer> |
ConformerContainer.iterator()
Gets an iterator over the conformers.
|
ListIterator<IAtomContainer> |
ConformerContainer.listIterator() |
ListIterator<IAtomContainer> |
ConformerContainer.listIterator(int i) |
List<IAtomContainer> |
ConformerContainer.subList(int i,
int i1) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
ConformerContainer.add(IAtomContainer atomContainer)
Add a conformer to the end of the list.
|
void |
AtomContainer.add(IAtomContainer that)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
void |
ConformerContainer.add(int i,
IAtomContainer atomContainer) |
void |
Reaction.addAgent(IAtomContainer agent)
Adds an agent to this reaction.
|
void |
AtomContainerSet.addAtomContainer(IAtomContainer atomContainer)
Adds an atomContainer to this container.
|
void |
AtomContainerSet.addAtomContainer(IAtomContainer atomContainer,
double multiplier)
Adds an atomContainer to this container with the given
multiplier.
|
void |
Reaction.addProduct(IAtomContainer product)
Adds a product to this reaction.
|
void |
Reaction.addProduct(IAtomContainer product,
Double coefficient)
Adds a product to this reaction.
|
void |
Reaction.addReactant(IAtomContainer reactant)
Adds a reactant to this reaction.
|
void |
Reaction.addReactant(IAtomContainer reactant,
Double coefficient)
Adds a reactant to this reaction with a stoichiometry coefficient.
|
boolean |
RingSet.contains(IAtomContainer ring)
Checks for presence of a ring in this RingSet.
|
Double |
AtomContainerSet.getMultiplier(IAtomContainer container)
Returns the multiplier of the given AtomContainer.
|
Double |
Reaction.getProductCoefficient(IAtomContainer product)
Returns the stoichiometry coefficient of the given product.
|
Double |
Reaction.getReactantCoefficient(IAtomContainer reactant)
Returns the stoichiometry coefficient of the given reactant.
|
void |
AtomContainer.remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
AtomContainerSet.removeAtomContainer(IAtomContainer atomContainer)
Removes an AtomContainer from this container.
|
void |
AtomContainerSet.replaceAtomContainer(int position,
IAtomContainer container)
Replace the AtomContainer at a specific position (array has to be large enough).
|
IAtomContainer |
ConformerContainer.set(int i,
IAtomContainer atomContainer) |
void |
FragmentAtom.setFragment(IAtomContainer fragment) |
boolean |
AtomContainerSet.setMultiplier(IAtomContainer container,
Double multiplier)
Sets the coefficient of a AtomContainer to a given value.
|
boolean |
Reaction.setProductCoefficient(IAtomContainer product,
Double coefficient)
Sets the coefficient of a a product to a given value.
|
boolean |
Reaction.setReactantCoefficient(IAtomContainer reactant,
Double coefficient)
Sets the coefficient of a a reactant to a given value.
|
| Modifier and Type | Method and Description |
|---|---|
boolean |
ConformerContainer.addAll(Collection<? extends IAtomContainer> atomContainers) |
boolean |
ConformerContainer.addAll(int i,
Collection<? extends IAtomContainer> iAtomContainers) |
void |
AtomContainerSet.sortAtomContainers(Comparator<IAtomContainer> comparator)
Sort the AtomContainers and multipliers using a provided Comparator.
|
| Constructor and Description |
|---|
AtomContainer(IAtomContainer container)
Constructs an AtomContainer with a copy of the atoms and electronContainers
of another AtomContainer (A shallow copy, i.e., with the same objects as in
the original AtomContainer).
|
ConformerContainer(IAtomContainer atomContainer)
Create a ConformerContainer object from a single molecule object.
|
ConformerContainer(IAtomContainer[] atomContainers)
Create a ConformerContainer from an array of molecules.
|
Crystal(IAtomContainer container)
Constructs a new crystal with zero length cell axis
and adds the atoms in the AtomContainer as cell content.
|
Ring(IAtomContainer atomContainer)
Constructs a ring from the atoms in an IAtomContainer object.
|
| Modifier and Type | Method and Description |
|---|---|
boolean |
Aromaticity.apply(IAtomContainer molecule)
Apply this aromaticity model to a molecule.
|
static boolean |
CDKHueckelAromaticityDetector.detectAromaticity(IAtomContainer atomContainer)
Deprecated.
|
static boolean |
DoubleBondAcceptingAromaticityDetector.detectAromaticity(IAtomContainer atomContainer)
Deprecated.
|
Set<IBond> |
Aromaticity.findBonds(IAtomContainer molecule)
Find the bonds of a
molecule which this model determined were
aromatic. |
static boolean |
AromaticityCalculator.isAromatic(IRing ring,
IAtomContainer atomContainer)
Deprecated.
Tests the
ring in the molecule for aromaticity. |
static void |
Kekulization.kekulize(IAtomContainer ac)
Assign a Kekulé representation to the aromatic systems of a compound.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomType |
MMFF94AtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atomInterface)
Deprecated.
Assign the mmff94 atom type to a given atom.
|
IAtomType |
MM2AtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atomInterface)
Deprecated.
Assign the mm2 atom type to a given atom.
|
IAtomType |
StructGenMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atom)
Finds the AtomType matching the Atom's element symbol, formal charge and
hybridization state.
|
IAtomType |
IAtomTypeMatcher.findMatchingAtomType(IAtomContainer container,
IAtom atom)
Method that assigns an atom type to a given atom belonging to an atom
container.
|
IAtomType |
CDKAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atom)
Method that assigns an atom type to a given atom belonging to an atom
container.
|
IAtomType |
EStateAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atom) |
IAtomType |
SybylAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atom)
Sybyl atom type perception for a single atom.
|
IAtomType[] |
MMFF94AtomTypeMatcher.findMatchingAtomTypes(IAtomContainer atomContainer)
Deprecated.
|
IAtomType[] |
MM2AtomTypeMatcher.findMatchingAtomTypes(IAtomContainer atomContainer)
Deprecated.
|
IAtomType[] |
StructGenMatcher.findMatchingAtomTypes(IAtomContainer atomContainer) |
IAtomType[] |
IAtomTypeMatcher.findMatchingAtomTypes(IAtomContainer container)
Method that assigns atom types to atoms in the given atom container.
|
IAtomType[] |
CDKAtomTypeMatcher.findMatchingAtomTypes(IAtomContainer atomContainer)
Method that assigns atom types to atoms in the given atom container.
|
IAtomType[] |
EStateAtomTypeMatcher.findMatchingAtomTypes(IAtomContainer atomContainer) |
IAtomType[] |
SybylAtomTypeMatcher.findMatchingAtomTypes(IAtomContainer atomContainer)
Method that assigns atom types to atoms in the given atom container.
|
static boolean |
EStateAtomTypeMatcher.inSameAromaticRing(IAtomContainer m,
IAtom atom1,
IAtom atom2,
IRingSet rs) |
List<IAtomType> |
StructGenAtomTypeGuesser.possibleAtomTypes(IAtomContainer atomContainer,
IAtom atom)
Finds the AtomType matching the Atom's element symbol, formal charge and
hybridization state.
|
List<IAtomType> |
IAtomTypeGuesser.possibleAtomTypes(IAtomContainer container,
IAtom atom)
Method that returns an iterator with a suitable list of atom types
given the provided atom.
|
| Modifier and Type | Method and Description |
|---|---|
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.
|
IAtomContainer |
InductivePartialCharges.assignInductivePartialCharges(IAtomContainer ac)
Main method, set charge as atom properties.
|
IAtomContainer |
MMFF94PartialCharges.assignMMFF94PartialCharges(IAtomContainer ac)
Main method which assigns MMFF94 partial charges
|
IAtomContainer |
AtomTypeCharges.setCharges(IAtomContainer atomContainer)
Sets initial charges for atom types.
|
| 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.
|
IAtomContainer |
MMFF94PartialCharges.assignMMFF94PartialCharges(IAtomContainer ac)
Main method which assigns MMFF94 partial charges
|
double |
Polarizability.calculateBondPolarizability(IAtomContainer atomContainer,
IBond bond)
calculate bond polarizability.
|
void |
MMFF94PartialCharges.calculateCharges(IAtomContainer container) |
void |
IElectronicPropertyCalculator.calculateCharges(IAtomContainer container) |
void |
GasteigerPEPEPartialCharges.calculateCharges(IAtomContainer container) |
void |
AtomTypeCharges.calculateCharges(IAtomContainer container) |
void |
GasteigerMarsiliPartialCharges.calculateCharges(IAtomContainer container) |
void |
InductivePartialCharges.calculateCharges(IAtomContainer container) |
double |
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[] |
InductivePartialCharges.getPaulingElectronegativities(IAtomContainer ac,
boolean modified)
Gets the paulingElectronegativities attribute of the
InductivePartialCharges object.
|
double |
Polarizability.getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer,
IAtom atom)
Gets the polarizabilitiyFactorForAtom.
|
IAtomContainer |
AtomTypeCharges.setCharges(IAtomContainer atomContainer)
Sets initial charges for atom types.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
Isotopes.clearMajorIsotopes(IAtomContainer mol)
Clear the isotope information from atoms that are major isotopes (e.g.
|
void |
IsotopeFactory.configureAtoms(IAtomContainer container)
Configures atoms in an AtomContainer to
carry all the correct data according to their element type.
|
| Modifier and Type | Class and Description |
|---|---|
class |
DebugAminoAcid
Debugging data class.
|
class |
DebugAtomContainer
Debugging data class.
|
class |
DebugBioPolymer
Debugging data class.
|
class |
DebugCrystal
Debugging data class.
|
class |
DebugMonomer
Debugging data class.
|
class |
DebugPDBMonomer
Debugging data class.
|
class |
DebugPDBPolymer
Debugging data class.
|
class |
DebugPolymer
Debugging data class.
|
class |
DebugRing
Debugging data class.
|
class |
DebugStrand
Debugging data class.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
DebugAtomContainer.clone()
Clones this
IChemObject. |
IAtomContainer |
DebugAtomContainerSet.getAtomContainer(int number)
Returns the AtomContainer at position
number in the
container. |
IAtomContainer |
DebugSubstance.getAtomContainer(int number)
Returns the AtomContainer at position
number in the
container. |
IAtomContainer |
DebugAtom.getContainer()
Access the
IAtomContainer of which this atom is a member of. |
IAtomContainer |
DebugFragmentAtom.getFragment()
Returns the fully expended form of the IFragmentAtom.
|
IAtomContainer |
DebugChemObjectBuilder.newAtomContainer()
Create a new atom container using the default constructor.
|
| Modifier and Type | Method and Description |
|---|---|
Iterable<IAtomContainer> |
DebugAtomContainerSet.atomContainers()
Get an iterator for this AtomContainerSet.
|
Iterable<IAtomContainer> |
DebugSubstance.atomContainers()
Get an iterator for this AtomContainerSet.
|
| Modifier and Type | Method and Description |
|---|---|
void |
DebugStrand.add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
void |
DebugRing.add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
void |
DebugCrystal.add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
void |
DebugAminoAcid.add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
void |
DebugPolymer.add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
void |
DebugBioPolymer.add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
void |
DebugMonomer.add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
void |
DebugAtomContainer.add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
void |
DebugReaction.addAgent(IAtomContainer agent)
Adds an agent to this reaction.
|
void |
DebugAtomContainerSet.addAtomContainer(IAtomContainer atomContainer)
Adds an atomContainer to this container.
|
void |
DebugSubstance.addAtomContainer(IAtomContainer atomContainer)
Adds an atomContainer to this container.
|
void |
DebugAtomContainerSet.addAtomContainer(IAtomContainer atomContainer,
double multiplier)
Adds an atomContainer to this container with the given
multiplier.
|
void |
DebugSubstance.addAtomContainer(IAtomContainer atomContainer,
double multiplier)
Adds an atomContainer to this container with the given
multiplier.
|
void |
DebugReaction.addProduct(IAtomContainer product)
Adds a product to this reaction.
|
void |
DebugReaction.addProduct(IAtomContainer product,
Double coefficient)
Adds a product to this reaction.
|
void |
DebugReaction.addReactant(IAtomContainer reactant)
Adds a reactant to this reaction.
|
void |
DebugReaction.addReactant(IAtomContainer reactant,
Double coefficient)
Adds a reactant to this reaction with a stoichiometry coefficient.
|
Double |
DebugAtomContainerSet.getMultiplier(IAtomContainer container)
Returns the multiplier of the given AtomContainer.
|
Double |
DebugSubstance.getMultiplier(IAtomContainer container)
Returns the multiplier of the given AtomContainer.
|
Double |
DebugReaction.getProductCoefficient(IAtomContainer product)
Returns the stoichiometry coefficient of the given product.
|
Double |
DebugReaction.getReactantCoefficient(IAtomContainer reactant)
Returns the stoichiometry coefficient of the given reactant.
|
void |
DebugStrand.remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
DebugRing.remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
DebugCrystal.remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
DebugAminoAcid.remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
DebugPolymer.remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
DebugBioPolymer.remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
DebugMonomer.remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
DebugAtomContainer.remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
DebugAtomContainerSet.removeAtomContainer(IAtomContainer atomContainer)
Removes an AtomContainer from this container.
|
void |
DebugSubstance.removeAtomContainer(IAtomContainer atomContainer)
Removes an AtomContainer from this container.
|
void |
DebugAtomContainerSet.replaceAtomContainer(int position,
IAtomContainer container)
Replace the AtomContainer at a specific position (array has to be large enough).
|
void |
DebugSubstance.replaceAtomContainer(int position,
IAtomContainer container)
Replace the AtomContainer at a specific position (array has to be large enough).
|
void |
DebugFragmentAtom.setFragment(IAtomContainer fragment)
Sets the fully expended form of the IFragmentAtom.
|
boolean |
DebugAtomContainerSet.setMultiplier(IAtomContainer container,
Double multiplier)
Sets the coefficient of a AtomContainer to a given value.
|
boolean |
DebugSubstance.setMultiplier(IAtomContainer container,
Double multiplier)
Sets the coefficient of a AtomContainer to a given value.
|
boolean |
DebugReaction.setProductCoefficient(IAtomContainer product,
Double coefficient)
Sets the coefficient of a a product to a given value.
|
boolean |
DebugReaction.setReactantCoefficient(IAtomContainer reactant,
Double coefficient)
Sets the coefficient of a a reactant to a given value.
|
| Constructor and Description |
|---|
DebugAtomContainer(IAtomContainer container) |
DebugCrystal(IAtomContainer container) |
DebugRing(IAtomContainer container) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
Abbreviations.add(IAtomContainer mol,
String label)
Add an abbreviation to the factory.
|
int |
Abbreviations.apply(IAtomContainer mol)
Generates and assigns abbreviations to a molecule.
|
Depiction |
DepictionGenerator.depict(IAtomContainer mol)
Depict a single molecule.
|
List<Sgroup> |
Abbreviations.generate(IAtomContainer mol)
Find all enabled abbreviations in the provided molecule.
|
| Modifier and Type | Method and Description |
|---|---|
Depiction |
DepictionGenerator.depict(Iterable<IAtomContainer> mols)
Depict a set of molecules, they will be depicted in a grid.
|
Depiction |
DepictionGenerator.depict(Iterable<IAtomContainer> mols,
int nrow,
int ncol)
Depict a set of molecules, they will be depicted in a grid with the
specified number of rows and columns.
|
| Modifier and Type | Method and Description |
|---|---|
void |
CircularFingerprinter.calculate(IAtomContainer mol)
Calculates the fingerprints for the given
IAtomContainer, and stores them for subsequent retrieval. |
Collection<IAtom> |
SimpleAtomCanonicalizer.canonicalizeAtoms(IAtomContainer container) |
protected void |
Fingerprinter.encodePaths(IAtomContainer mol,
int depth,
BitSet fp,
int size) |
protected int[] |
Fingerprinter.findPathes(IAtomContainer container,
int searchDepth)
Deprecated.
|
IBitFingerprint |
LingoFingerprinter.getBitFingerprint(IAtomContainer iAtomContainer) |
IBitFingerprint |
SignatureFingerprinter.getBitFingerprint(IAtomContainer atomContainer) |
IBitFingerprint |
SubstructureFingerprinter.getBitFingerprint(IAtomContainer atomContainer)
Returns the bit fingerprint for the given
IAtomContainer. |
IBitFingerprint |
CircularFingerprinter.getBitFingerprint(IAtomContainer mol)
Calculates the circular fingerprint for the given
IAtomContainer, and folds the result into a single bitset
(see getSize()). |
IBitFingerprint |
ExtendedFingerprinter.getBitFingerprint(IAtomContainer container)
Generates a fingerprint of the default size for the given
AtomContainer, using path and ring metrics.
|
IBitFingerprint |
MACCSFingerprinter.getBitFingerprint(IAtomContainer container)
Returns the bit fingerprint for the given
IAtomContainer. |
IBitFingerprint |
ShortestPathFingerprinter.getBitFingerprint(IAtomContainer ac)
Generates a shortest path based BitSet fingerprint for the given AtomContainer.
|
IBitFingerprint |
EStateFingerprinter.getBitFingerprint(IAtomContainer atomContainer)
Returns the bit fingerprint for the given
IAtomContainer. |
IBitFingerprint |
AtomPairs2DFingerprinter.getBitFingerprint(IAtomContainer container) |
IBitFingerprint |
PubchemFingerprinter.getBitFingerprint(IAtomContainer atomContainer)
Calculate 881 bit Pubchem fingerprint for a molecule.
|
IBitFingerprint |
Fingerprinter.getBitFingerprint(IAtomContainer container)
Generates a fingerprint of the default size for the given AtomContainer.
|
IBitFingerprint |
IFingerprinter.getBitFingerprint(IAtomContainer container)
Returns the bit fingerprint for the given
IAtomContainer. |
IBitFingerprint |
Fingerprinter.getBitFingerprint(IAtomContainer container,
AllRingsFinder ringFinder)
Generates a fingerprint of the default size for the given AtomContainer.
|
BitSet |
GraphOnlyFingerprinter.getBitFingerprint(IAtomContainer container,
int size) |
IBitFingerprint |
ExtendedFingerprinter.getBitFingerprint(IAtomContainer atomContainer,
IRingSet ringSet,
List<IRingSet> rslist)
Generates a fingerprint of the default size for the given
AtomContainer, using path and ring metrics.
|
ICountFingerprint |
LingoFingerprinter.getCountFingerprint(IAtomContainer container) |
ICountFingerprint |
SignatureFingerprinter.getCountFingerprint(IAtomContainer container) |
ICountFingerprint |
SubstructureFingerprinter.getCountFingerprint(IAtomContainer atomContainer)
Returns the count fingerprint for the given
IAtomContainer. |
ICountFingerprint |
CircularFingerprinter.getCountFingerprint(IAtomContainer mol)
Calculates the circular fingerprint for the given
IAtomContainer, and returns a datastructure that enumerates all
of the fingerprints, and their counts (i.e. |
ICountFingerprint |
ExtendedFingerprinter.getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the given
IAtomContainer. |
ICountFingerprint |
MACCSFingerprinter.getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the given
IAtomContainer. |
ICountFingerprint |
ShortestPathFingerprinter.getCountFingerprint(IAtomContainer iac) |
ICountFingerprint |
EStateFingerprinter.getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the given
IAtomContainer. |
ICountFingerprint |
AtomPairs2DFingerprinter.getCountFingerprint(IAtomContainer mol) |
ICountFingerprint |
PubchemFingerprinter.getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the given
IAtomContainer. |
ICountFingerprint |
Fingerprinter.getCountFingerprint(IAtomContainer container) |
ICountFingerprint |
IFingerprinter.getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the given
IAtomContainer. |
BitSet |
ExtendedFingerprinter.getFingerprint(IAtomContainer mol) |
BitSet |
AbstractFingerprinter.getFingerprint(IAtomContainer mol)
Generate a binary fingerprint as a bit.
|
BitSet |
IFingerprinter.getFingerprint(IAtomContainer mol)
Generate a binary fingerprint as a bit.
|
Map<String,Integer> |
LingoFingerprinter.getRawFingerprint(IAtomContainer atomContainer) |
Map<String,Integer> |
SignatureFingerprinter.getRawFingerprint(IAtomContainer atomContainer) |
Map<String,Integer> |
SubstructureFingerprinter.getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.
|
Map<String,Integer> |
CircularFingerprinter.getRawFingerprint(IAtomContainer mol)
Invalid: it is not appropriate to convert the integer hash codes into strings.
|
Map<String,Integer> |
ExtendedFingerprinter.getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.
|
Map<String,Integer> |
MACCSFingerprinter.getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.
|
Map<String,Integer> |
ShortestPathFingerprinter.getRawFingerprint(IAtomContainer ac)
Returns the raw representation of the fingerprint for the given IAtomContainer.
|
Map<String,Integer> |
EStateFingerprinter.getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.
|
Map<String,Integer> |
AtomPairs2DFingerprinter.getRawFingerprint(IAtomContainer mol) |
Map<String,Integer> |
PubchemFingerprinter.getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.
|
Map<String,Integer> |
Fingerprinter.getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.
|
Map<String,Integer> |
IFingerprinter.getRawFingerprint(IAtomContainer container)
Returns the raw representation of the fingerprint for the given IAtomContainer.
|
| Constructor and Description |
|---|
ShortestPathWalker(IAtomContainer container)
Create a new shortest path walker for a given container.
|
| Modifier and Type | Method and Description |
|---|---|
void |
Bayesian.addMolecule(IAtomContainer mol,
boolean active)
Appends a new row to the model source data, which consists of a molecule and whether or not it
is considered active.
|
double |
Bayesian.predict(IAtomContainer mol)
For a given molecule, determines its fingerprints and uses them to calculate a Bayesian prediction.
|
| Modifier and Type | Method and Description |
|---|---|
boolean |
Mmff.assignAtomTypes(IAtomContainer mol)
Assign MMFF Symbolic atom types.
|
void |
Mmff.clearProps(IAtomContainer mol)
Clear all transient properties assigned by this class.
|
boolean |
Mmff.effectiveCharges(IAtomContainer mol)
Assign the effective formal charges used by MMFF in calculating the
final partial charge values.
|
boolean |
Mmff.partialCharges(IAtomContainer mol)
Assign the partial charges, all existing charges are cleared.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer[] |
ExhaustiveFragmenter.getFragmentsAsContainers()
Get the fragments generated as
IAtomContainer objects.. |
IAtomContainer[] |
IFragmenter.getFragmentsAsContainers()
Get fragments generated as
IAtomContainer objects. |
IAtomContainer[] |
MurckoFragmenter.getFragmentsAsContainers()
Get all frameworks and ring systems as
IAtomContainer objects. |
IAtomContainer[] |
MurckoFragmenter.getFrameworksAsContainers()
Get frameworks as
IAtomContainer as objects. |
IAtomContainer[] |
MurckoFragmenter.getRingSystemsAsContainers()
Get rings systems as
IAtomContainer objects. |
protected static IAtomContainer |
FragmentUtils.makeAtomContainer(IAtom atom,
List<IBond> parts,
IAtom excludedAtom) |
static IAtomContainer |
MurckoFragmenter.scaffold(IAtomContainer mol)
Computes the Murcko Scaffold for the provided molecule in linear time.
|
| Modifier and Type | Method and Description |
|---|---|
protected static List<IAtomContainer> |
FragmentUtils.splitMolecule(IAtomContainer atomContainer,
IBond bond)
Non destructively split a molecule into two parts at the specified bond.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ExhaustiveFragmenter.generateFragments(IAtomContainer atomContainer)
Generate fragments for the input molecule.
|
void |
IFragmenter.generateFragments(IAtomContainer atomContainer)
Generate fragments for the input molecule.
|
void |
MurckoFragmenter.generateFragments(IAtomContainer atomContainer)
Perform the fragmentation procedure.
|
static IAtomContainer |
MurckoFragmenter.scaffold(IAtomContainer mol)
Computes the Murcko Scaffold for the provided molecule in linear time.
|
protected static List<IAtomContainer> |
FragmentUtils.splitMolecule(IAtomContainer atomContainer,
IBond bond)
Non destructively split a molecule into two parts at the specified bond.
|
protected static List<IBond> |
FragmentUtils.traverse(IAtomContainer atomContainer,
IAtom atom,
List<IBond> bondList) |
| Modifier and Type | Method and Description |
|---|---|
static void |
AtomTools.add3DCoordinates1(IAtomContainer atomContainer)
Generate coordinates for all atoms which are singly bonded and have
no coordinates.
|
double[] |
RDFCalculator.calculate(IAtomContainer container,
IAtom atom)
Calculates a RDF for
Atom atom in the environment
of the atoms in the AtomContainer. |
static javax.vecmath.Point3d[] |
AtomTools.calculate3DCoordinatesForLigands(IAtomContainer atomContainer,
IAtom refAtom,
int nwanted,
double length,
double angle)
Adds 3D coordinates for singly-bonded ligands of a reference atom (A).
|
static void |
GeometryTools.center(IAtomContainer atomCon,
Dimension areaDim)
Deprecated.
Centers the molecule in the given area.
|
static void |
GeometryUtil.center(IAtomContainer atomCon,
double[] areaDim)
Centers the molecule in the given area.
|
static List<IAtom> |
GeometryTools.findClosestInSpace(IAtomContainer container,
IAtom startAtom,
int max)
Deprecated.
Returns the atoms which are closes to an atom in an AtomContainer by
distance in 3d.
|
static List<IAtom> |
GeometryUtil.findClosestInSpace(IAtomContainer container,
IAtom startAtom,
int max)
Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.
|
static javax.vecmath.Point2d |
GeometryTools.get2DCenter(IAtomContainer container)
Deprecated.
Returns the geometric center of all the atoms in the atomContainer.
|
static javax.vecmath.Point2d |
GeometryUtil.get2DCenter(IAtomContainer container)
Returns the geometric center of all the atoms in the atomContainer.
|
static javax.vecmath.Point2d |
GeometryTools.get2DCentreOfMass(IAtomContainer ac)
Deprecated.
Calculates the center of mass for the
Atoms in the
AtomContainer for the 2D coordinates. |
static javax.vecmath.Point2d |
GeometryUtil.get2DCentreOfMass(IAtomContainer ac)
Calculates the center of mass for the
Atoms in the AtomContainer for the 2D
coordinates. |
static GeometryTools.CoordinateCoverage |
GeometryTools.get2DCoordinateCoverage(IAtomContainer container)
Deprecated.
Determines the coverage of this
IAtomContainer's 2D coordinates. |
static GeometryUtil.CoordinateCoverage |
GeometryUtil.get2DCoordinateCoverage(IAtomContainer container)
Determines the coverage of this
IAtomContainer's 2D
coordinates. |
static Dimension |
GeometryTools.get2DDimension(IAtomContainer atomCon)
Deprecated.
Returns the java.awt.Dimension of a molecule.
|
static double[] |
GeometryUtil.get2DDimension(IAtomContainer atomCon)
Returns the dimension of a molecule (width/height).
|
static javax.vecmath.Point3d |
GeometryTools.get3DCenter(IAtomContainer ac)
Deprecated.
Returns the geometric center of all the atoms in this atomContainer.
|
static javax.vecmath.Point3d |
GeometryUtil.get3DCenter(IAtomContainer ac)
Returns the geometric center of all the atoms in this atomContainer.
|
static javax.vecmath.Point3d |
GeometryTools.get3DCentreOfMass(IAtomContainer ac)
Deprecated.
Calculates the center of mass for the
Atoms in the
AtomContainer for the 2D coordinates. |
static javax.vecmath.Point3d |
GeometryUtil.get3DCentreOfMass(IAtomContainer ac)
Calculates the center of mass for the
Atoms in the AtomContainer. |
static GeometryTools.CoordinateCoverage |
GeometryTools.get3DCoordinateCoverage(IAtomContainer container)
Deprecated.
Determines the coverage of this
IAtomContainer's 3D coordinates. |
static GeometryUtil.CoordinateCoverage |
GeometryUtil.get3DCoordinateCoverage(IAtomContainer container)
Determines the coverage of this
IAtomContainer's 3D
coordinates. |
static double |
GeometryTools.getAllAtomRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms,
boolean Coords3d)
Deprecated.
Return the RMSD between the 2 aligned molecules.
|
static double |
GeometryUtil.getAllAtomRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms,
boolean Coords3d)
Return the RMSD between the 2 aligned molecules.
|
static double |
GeometryTools.getAngleRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms)
Deprecated.
Return the variation of each angle value between the 2 aligned molecules.
|
static double |
GeometryUtil.getAngleRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms)
Return the variation of each angle value between the 2 aligned molecules.
|
static int |
GeometryTools.getBestAlignmentForLabel(IAtomContainer container,
IAtom atom)
Deprecated.
Determines the best alignment for the label of an atom in 2D space.
|
static int |
GeometryUtil.getBestAlignmentForLabel(IAtomContainer container,
IAtom atom)
Determines the best alignment for the label of an atom in 2D space.
|
static int |
GeometryTools.getBestAlignmentForLabelXY(IAtomContainer container,
IAtom atom)
Deprecated.
Determines the best alignment for the label of an atom in 2D space.
|
static int |
GeometryUtil.getBestAlignmentForLabelXY(IAtomContainer container,
IAtom atom)
Determines the best alignment for the label of an atom in 2D space.
|
static double |
GeometryTools.getBondLengthAverage(IAtomContainer container)
Deprecated.
An average of all 2D bond length values is produced.
|
static double |
GeometryUtil.getBondLengthAverage(IAtomContainer container)
An average of all 2D bond length values is produced.
|
static double |
GeometryTools.getBondLengthAverage3D(IAtomContainer container)
Deprecated.
An average of all 3D bond length values is produced, using point3ds in atoms.
|
static double |
GeometryUtil.getBondLengthAverage3D(IAtomContainer container)
An average of all 3D bond length values is produced, using point3ds in atoms.
|
static double |
GeometryTools.getBondLengthMedian(IAtomContainer container)
Deprecated.
Calculate the median bond length of an atom container.
|
static double |
GeometryUtil.getBondLengthMedian(IAtomContainer container)
Calculate the median bond length of an atom container.
|
static double |
GeometryTools.getBondLengthRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms,
boolean Coords3d)
Deprecated.
Return the RMSD of bonds length between the 2 aligned molecules.
|
static double |
GeometryUtil.getBondLengthRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms,
boolean Coords3d)
Return the RMSD of bonds length between the 2 aligned molecules.
|
static IAtom |
GeometryTools.getClosestAtom(double xPosition,
double yPosition,
IAtomContainer atomCon)
Deprecated.
Returns the atom of the given molecule that is closest to the given
coordinates.
|
static IAtom |
GeometryUtil.getClosestAtom(double xPosition,
double yPosition,
IAtomContainer atomCon)
Returns the atom of the given molecule that is closest to the given coordinates.
|
static IAtom |
GeometryTools.getClosestAtom(double xPosition,
double yPosition,
IAtomContainer atomCon,
IAtom toignore)
Deprecated.
Returns the atom of the given molecule that is closest to the given
coordinates and is not the atom.
|
static IAtom |
GeometryUtil.getClosestAtom(double xPosition,
double yPosition,
IAtomContainer atomCon,
IAtom toignore)
Returns the atom of the given molecule that is closest to the given coordinates and is not
the atom.
|
static IAtom |
GeometryTools.getClosestAtom(IAtomContainer atomCon,
IAtom atom)
Deprecated.
Returns the atom of the given molecule that is closest to the given atom
(excluding itself).
|
static IAtom |
GeometryUtil.getClosestAtom(IAtomContainer atomCon,
IAtom atom)
Returns the atom of the given molecule that is closest to the given atom (excluding itself).
|
static IAtom |
GeometryTools.getClosestAtom(int xPosition,
int yPosition,
IAtomContainer atomCon)
Deprecated.
Returns the atom of the given molecule that is closest to the given
coordinates.
|
static IAtom |
GeometryUtil.getClosestAtom(int xPosition,
int yPosition,
IAtomContainer atomCon)
Returns the atom of the given molecule that is closest to the given coordinates.
|
static IBond |
GeometryTools.getClosestBond(double xPosition,
double yPosition,
IAtomContainer atomCon)
Deprecated.
Returns the bond of the given molecule that is closest to the given
coordinates.
|
static IBond |
GeometryUtil.getClosestBond(double xPosition,
double yPosition,
IAtomContainer atomCon)
Returns the bond of the given molecule that is closest to the given coordinates.
|
static IBond |
GeometryTools.getClosestBond(int xPosition,
int yPosition,
IAtomContainer atomCon)
Deprecated.
Returns the bond of the given molecule that is closest to the given
coordinates.
|
static IBond |
GeometryUtil.getClosestBond(int xPosition,
int yPosition,
IAtomContainer atomCon)
Returns the bond of the given molecule that is closest to the given coordinates.
|
static double |
GeometryTools.getHeavyAtomRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms,
boolean hetAtomOnly,
boolean Coords3d)
Deprecated.
Return the RMSD of the heavy atoms between the 2 aligned molecules.
|
static double |
GeometryUtil.getHeavyAtomRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms,
boolean hetAtomOnly,
boolean Coords3d)
Return the RMSD of the heavy atoms between the 2 aligned molecules.
|
static double[] |
GeometryTools.getMinMax(IAtomContainer container)
Deprecated.
Returns the minimum and maximum X and Y coordinates of the atoms in the
AtomContainer.
|
static double[] |
GeometryUtil.getMinMax(IAtomContainer container)
Returns the minimum and maximum X and Y coordinates of the atoms in the
AtomContainer.
|
static double |
GeometryTools.getNormalizationFactor(IAtomContainer container)
Deprecated.
Calculates the normalization factor in order to get an average bond length
of 1.5.
|
static double |
GeometryUtil.getNormalizationFactor(IAtomContainer container)
Calculates the normalization factor in order to get an average bond length of 1.5.
|
static Rectangle2D |
GeometryTools.getRectangle2D(IAtomContainer container)
Deprecated.
Returns the 2D rectangle spanning the space occupied by the atom
container.
|
static double |
GeometryTools.getScaleFactor(IAtomContainer container,
double bondLength)
Deprecated.
Determines the scale factor for displaying a structure loaded from disk in
a frame.
|
static double |
GeometryUtil.getScaleFactor(IAtomContainer container,
double bondLength)
Determines the scale factor for displaying a structure loaded from disk in a frame.
|
static boolean |
GeometryTools.has2DCoordinates(IAtomContainer container)
Deprecated.
Determines if all this
IAtomContainer's atoms contain 2D coordinates. |
static boolean |
GeometryUtil.has2DCoordinates(IAtomContainer container)
Determines if all this
IAtomContainer's atoms contain
2D coordinates. |
static int |
GeometryTools.has2DCoordinatesNew(IAtomContainer container)
Deprecated.
use
GeometryTools.get2DCoordinateCoverage(org.openscience.cdk.interfaces.IAtomContainer) for determining
partial coordinates |
static int |
GeometryUtil.has2DCoordinatesNew(IAtomContainer container)
Deprecated.
use
GeometryUtil.get2DCoordinateCoverage(org.openscience.cdk.interfaces.IAtomContainer)
for determining partial coordinates |
static boolean |
GeometryTools.has3DCoordinates(IAtomContainer container)
Deprecated.
Determines if all this
IAtomContainer's atoms contain 3D coordinates. |
static boolean |
GeometryUtil.has3DCoordinates(IAtomContainer container)
Determines if all this
IAtomContainer's atoms contain
3D coordinates. |
static boolean |
CrystalGeometryTools.hasCrystalCoordinates(IAtomContainer container)
Determines if this model contains fractional (crystal) coordinates.
|
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.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 Map<Integer,Integer> |
GeometryTools.mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
double searchRadius,
Map<Integer,Integer> mappedAtoms)
Deprecated.
Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest
AtomContainer) atomcontainer.
|
static Map<Integer,Integer> |
GeometryUtil.mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
double searchRadius,
Map<Integer,Integer> mappedAtoms)
Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest
AtomContainer) atomcontainer.
|
static void |
Projector.project2D(IAtomContainer container) |
static void |
Projector.project2D(IAtomContainer container,
HashMap<IAtom,javax.vecmath.Point2d> renderingCoordinates) |
static void |
GeometryTools.rotate(IAtomContainer atomCon,
javax.vecmath.Point2d center,
double angle)
Deprecated.
Rotates a molecule around a given center by a given angle.
|
static void |
GeometryUtil.rotate(IAtomContainer atomCon,
javax.vecmath.Point2d center,
double angle)
Rotates a molecule around a given center by a given angle.
|
static void |
GeometryTools.scaleMolecule(IAtomContainer atomCon,
Dimension areaDim,
double fillFactor)
Deprecated.
Scales a molecule such that it fills a given percentage of a given
dimension.
|
static void |
GeometryTools.scaleMolecule(IAtomContainer atomCon,
double scaleFactor)
Deprecated.
Multiplies all the coordinates of the atoms of the given molecule with the
scalefactor.
|
static void |
GeometryUtil.scaleMolecule(IAtomContainer atomCon,
double scaleFactor)
Multiplies all the coordinates of the atoms of the given molecule with the scalefactor.
|
static void |
GeometryUtil.scaleMolecule(IAtomContainer atomCon,
double[] areaDim,
double fillFactor)
Scales a molecule such that it fills a given percentage of a given dimension.
|
static double[] |
GeometryUtil.shiftContainer(IAtomContainer container,
double[] bounds,
double[] last,
double gap)
Shift the container horizontally to the right to make its bounds not overlap with the other
bounds.
|
static Rectangle2D |
GeometryTools.shiftContainer(IAtomContainer container,
Rectangle2D bounds,
Rectangle2D last,
double gap)
Deprecated.
Shift the container horizontally to the right to make its bounds not
overlap with the other bounds.
|
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.
|
static void |
GeometryTools.translate2D(IAtomContainer atomCon,
double transX,
double transY)
Deprecated.
Translates the given molecule by the given Vector.
|
static void |
GeometryUtil.translate2D(IAtomContainer atomCon,
double transX,
double transY)
Translates the given molecule by the given Vector.
|
static void |
GeometryTools.translate2D(IAtomContainer atomCon,
javax.vecmath.Vector2d vector)
Deprecated.
Translates a molecule from the origin to a new point denoted by a vector.
|
static void |
GeometryUtil.translate2D(IAtomContainer atomCon,
javax.vecmath.Vector2d vector)
Translates a molecule from the origin to a new point denoted by a vector.
|
static void |
GeometryTools.translate2DCenterTo(IAtomContainer container,
javax.vecmath.Point2d p)
Deprecated.
Translates the geometric 2DCenter of the given
AtomContainer container to the specified Point2d p.
|
static void |
GeometryUtil.translate2DCenterTo(IAtomContainer container,
javax.vecmath.Point2d p)
Translates the geometric 2DCenter of the given AtomContainer container to the specified
Point2d p.
|
static void |
GeometryTools.translate2DCentreOfMassTo(IAtomContainer atomCon,
javax.vecmath.Point2d p)
Deprecated.
Translates a molecule from the origin to a new point denoted by a vector.
|
static void |
GeometryUtil.translate2DCentreOfMassTo(IAtomContainer atomCon,
javax.vecmath.Point2d p)
Translates a molecule from the origin to a new point denoted by a vector.
|
static void |
GeometryTools.translateAllPositive(IAtomContainer atomCon)
Deprecated.
Adds an automatically calculated offset to the coordinates of all atoms
such that all coordinates are positive and the smallest x or y coordinate
is exactly zero.
|
static void |
GeometryUtil.translateAllPositive(IAtomContainer atomCon)
Adds an automatically calculated offset to the coordinates of all atoms such that all
coordinates are positive and the smallest x or y coordinate is exactly zero.
|
| Modifier and Type | Method and Description |
|---|---|
void |
KabschAlignment.rotateAtomContainer(IAtomContainer ac)
Rotates the
IAtomContainer coordinates by the rotation matrix. |
| Constructor and Description |
|---|
KabschAlignment(IAtomContainer ac1,
IAtomContainer ac2)
Sets up variables for the alignment algorithm.
|
KabschAlignment(IAtomContainer ac1,
IAtomContainer ac2,
double[] wts)
Sets up variables for the alignment algorithm.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
Ligand.getAtomContainer()
IAtomContainer of which this ligand is part. |
IAtomContainer |
ILigand.getAtomContainer()
IAtomContainer of which this ligand is part. |
| Modifier and Type | Method and Description |
|---|---|
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 for 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. |
static CIPTool.CIP_CHIRALITY |
CIPTool.getCIPChirality(IAtomContainer container,
IDoubleBondStereochemistry stereoCenter) |
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 void |
CIPTool.label(IAtomContainer container)
Convenience method for labelling all stereo elements.
|
| Constructor and Description |
|---|
ImplicitHydrogenLigand(IAtomContainer container,
VisitedAtoms visitedAtoms,
IAtom centralAtom) |
Ligand(IAtomContainer container,
VisitedAtoms visitedAtoms,
IAtom centralAtom,
IAtom ligandAtom) |
| Constructor and Description |
|---|
NumericalSurface(IAtomContainer atomContainer)
Constructor to initialize the surface calculation with default values.
|
NumericalSurface(IAtomContainer atomContainer,
double solventRadius,
int tesslevel)
Constructor to initialize the surface calculation with user specified values.
|
| Modifier and Type | Method and Description |
|---|---|
static double |
VABCVolume.calculate(IAtomContainer molecule)
Calculates the volume for the given
IAtomContainer. |
| Modifier and Type | Field and Description |
|---|---|
protected IAtomContainer |
AtomContainerPermutor.atomContainer
The atom container that is permuted at each step.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
AtomContainerBondPermutor.containerFromPermutation(int[] permutation) |
abstract IAtomContainer |
AtomContainerPermutor.containerFromPermutation(int[] permutation)
Convert a permutation (expressed as a list of numbers) into a permuted
atom container.
|
IAtomContainer |
AtomContainerAtomPermutor.containerFromPermutation(int[] permutation)
Generate the atom container with this permutation of the atoms.
|
IAtomContainer |
SpanningTree.getCyclicFragmentsContainer()
Returns an IAtomContainer which contains all the atoms and bonds which
are involved in ring systems.
|
IAtomContainer |
SpanningTree.getPath(IAtomContainer spt,
IAtom atom1,
IAtom atom2)
Find a path connected a1 and a2 in the tree.
|
IAtomContainer |
SpanningTree.getSpanningTree()
Access the computed spanning tree of the input molecule.
|
IAtomContainer |
AtomContainerPermutor.next() |
IAtomContainer |
AtomContainerPermutor.randomNext()
Get a new container, but randomly skip forwards in the list of possible
permutations to generate it.
|
| Modifier and Type | Method and Description |
|---|---|
static Cycles |
Cycles.all(IAtomContainer container)
Find all simple cycles in a molecule.
|
static Cycles |
Cycles.all(IAtomContainer container,
int length)
All cycles of smaller than or equal to the specified length.
|
static void |
PathTools.breadthFirstSearch(IAtomContainer atomContainer,
List<IAtom> sphere,
IAtomContainer 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,
IAtomContainer 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 boolean |
PathTools.depthFirstTargetSearch(IAtomContainer molecule,
IAtom root,
IAtom target,
IAtomContainer path)
Recursively performs 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 Cycles |
Cycles.edgeShort(IAtomContainer container)
Find the edge short cycles of a molecule.
|
static Cycles |
Cycles.essential(IAtomContainer container)
Find the essential cycles of a molecule.
|
Cycles |
CycleFinder.find(IAtomContainer molecule)
Find the cycles of the provided molecule.
|
Cycles |
CycleFinder.find(IAtomContainer molecule,
int length)
Find the cycles of the provided molecule.
|
Cycles |
CycleFinder.find(IAtomContainer molecule,
int[][] graph,
int length)
Find the cycles of the provided molecule when an adjacent relation
(graph) is already available.
|
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<List<IAtom>> |
PathTools.getAllPaths(IAtomContainer atomContainer,
IAtom start,
IAtom end)
Get a list of all the paths between two atoms.
|
static List<List<IAtom>> |
PathTools.getLimitedPathsOfLengthUpto(IAtomContainer atomContainer,
IAtom start,
int length,
int limit)
Get all the paths starting from an atom of length 0 up to the specified
length.
|
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)
Deprecated.
Creates a molecule graph for use with jgrapht.
|
IAtomContainer |
SpanningTree.getPath(IAtomContainer spt,
IAtom atom1,
IAtom atom2)
Find a path connected a1 and a2 in the tree.
|
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)
Deprecated.
This implementation recalculates all shortest paths from the start atom
for each method call and does not indicate if there are equally short paths
from the start to the end. Replaced by
ShortestPaths.atomsTo(IAtom) |
static int |
PathTools.getVertexCountAtDistance(IAtomContainer atomContainer,
int distance)
Returns the number of vertices that are a distance 'd' apart.
|
static boolean |
ConnectivityChecker.isConnected(IAtomContainer atomContainer)
Check whether a set of atoms in an
IAtomContainer is connected. |
static int |
Cycles.markRingAtomsAndBonds(IAtomContainer mol)
Find and mark all cyclic atoms and bonds in the provided molecule.
|
static int |
Cycles.markRingAtomsAndBonds(IAtomContainer mol,
int[][] adjList,
GraphUtil.EdgeToBondMap bondMap)
Find and mark all cyclic atoms and bonds in the provided molecule.
|
static Cycles |
Cycles.mcb(IAtomContainer container)
Find the minimum cycle basis (MCB) of a molecule.
|
static IAtomContainerSet |
ConnectivityChecker.partitionIntoMolecules(IAtomContainer container)
Partitions the atoms in an AtomContainer into covalently connected components.
|
static IAtomContainerSet |
ConnectivityChecker.partitionIntoMolecules(IAtomContainer container,
int[] components) |
static Cycles |
Cycles.relevant(IAtomContainer container)
Find the relevant cycles of a molecule.
|
protected static void |
PathTools.resetFlags(IAtomContainer atomContainer) |
static Cycles |
Cycles.sssr(IAtomContainer container)
Find the smallest set of smallest rings (SSSR) - aka minimum cycle basis
(MCB) of a molecule.
|
static int[][] |
GraphUtil.toAdjList(IAtomContainer container)
Create an adjacent list representation of the container.
|
static int[][] |
GraphUtil.toAdjList(IAtomContainer container,
GraphUtil.EdgeToBondMap bondMap)
Create an adjacent list representation of the
container and
fill in the bondMap for quick lookup. |
static int[][] |
GraphUtil.toAdjListSubgraph(IAtomContainer container,
Set<IBond> include)
Create an adjacent list representation of the container that only
includes bonds that are in the set provided as an argument.
|
static Cycles |
Cycles.tripletShort(IAtomContainer container)
Find the triplet short cycles of a molecule.
|
static Cycles |
Cycles.vertexShort(IAtomContainer container)
Find the vertex short cycles of a molecule.
|
static GraphUtil.EdgeToBondMap |
GraphUtil.EdgeToBondMap.withSpaceFor(IAtomContainer container)
Create a map with enough space for all the bonds in the molecule,
container. |
| Constructor and Description |
|---|
AllPairsShortestPaths(IAtomContainer container)
Create a new all shortest paths utility for an
IAtomContainer. |
AtomContainerAtomPermutor(IAtomContainer atomContainer)
A permutor wraps the original atom container, and produces cloned
(and permuted!) copies on demand.
|
AtomContainerBondPermutor(IAtomContainer atomContainer)
A permutor wraps the original atom container, and produces cloned
(and permuted!) copies on demand.
|
AtomContainerPermutor(int size,
IAtomContainer atomContainer)
Start the permutor off with an initial atom container, and the size of
the permutation.
|
ShortestPaths(IAtomContainer container,
IAtom start)
Create a new shortest paths tool for a single start atom.
|
SpanningTree(IAtomContainer atomContainer)
Create a new spanning tree for the provided molecule.
|
| Modifier and Type | Method and Description |
|---|---|
static long[] |
Canon.basicInvariants(IAtomContainer container,
int[][] graph)
|
static long[] |
Canon.basicInvariants(IAtomContainer container,
int[][] graph,
int flav)
Generate the initial invariants for each atom in the
container. |
void |
CanonicalLabeler.canonLabel(IAtomContainer atomContainer)
Deprecated.
Canonically label the fragment.
|
static IAtomContainerSet |
ConjugatedPiSystemsDetector.detect(IAtomContainer ac)
Detect all conjugated pi systems in an AtomContainer.
|
static double[] |
HuLuIndexTool.getAtomWeights(IAtomContainer atomContainer) |
static double |
HuLuIndexTool.getEAIDNumber(IAtomContainer atomContainer)
Calculates the extended adjacency matrix index.
|
static double[][] |
HuLuIndexTool.getExtendedAdjacenyMatrix(IAtomContainer atomContainer) |
static long[] |
MorganNumbersTools.getMorganNumbers(IAtomContainer molecule)
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.
|
int[] |
EquivalentClassPartitioner.getTopoEquivClassbyHuXu(IAtomContainer atomContainer)
Get the topological equivalent class of the molecule.
|
static long[] |
InChINumbersTools.getUSmilesNumbers(IAtomContainer container)
Obtain the InChI numbers for the input container to be used to order
atoms in Universal SMILES (O'Boyle, Noel. Journal of Cheminformatics. 2012. 4).
|
static long[] |
Canon.label(IAtomContainer container,
int[][] g)
Compute the canonical labels for the provided structure.
|
static long[] |
Canon.label(IAtomContainer container,
int[][] g,
Comparator<IAtom> cmp)
Compute the canonical labels for the provided structure.
|
static long[] |
Canon.label(IAtomContainer container,
int[][] g,
int opts)
Compute the canonical labels for the provided structure.
|
static long[] |
Canon.label(IAtomContainer container,
int[][] g,
long[] initial)
Compute the canonical labels for the provided structure.
|
double[] |
EquivalentClassPartitioner.prepareNode(IAtomContainer atomContainer)
Prepare the node identifier.
|
static long[] |
Canon.symmetry(IAtomContainer container,
int[][] g)
Compute the symmetry classes for the provided structure.
|
static long[] |
Canon.symmetry(IAtomContainer container,
int[][] g,
int opts)
Compute the symmetry classes for the provided structure.
|
| Constructor and Description |
|---|
EquivalentClassPartitioner(IAtomContainer atomContainer)
Constructor for the TopologicalEquivalentClass object.
|
| Modifier and Type | Method and Description |
|---|---|
static int[][] |
TopologicalMatrix.getMatrix(IAtomContainer container)
Returns the topological matrix for the given AtomContainer.
|
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 |
|---|---|
void |
RebondTool.rebond(IAtomContainer container)
Rebonding using a Binary Space Partition Tree.
|
| Modifier and Type | Method and Description |
|---|---|
PermutationGroup |
AtomContainerDiscretePartitionRefiner.getAutomorphismGroup(IAtomContainer atomContainer)
Gets the automorphism group of the atom container.
|
PermutationGroup |
AtomContainerDiscretePartitionRefiner.getAutomorphismGroup(IAtomContainer atomContainer,
Partition initialPartition)
Get the automorphism group of the molecule given an initial partition.
|
PermutationGroup |
AtomContainerDiscretePartitionRefiner.getAutomorphismGroup(IAtomContainer atomContainer,
PermutationGroup group)
Speed up the search for the automorphism group using the automorphisms in
the supplied group.
|
Partition |
AtomContainerDiscretePartitionRefiner.getAutomorphismPartition(IAtomContainer atomContainer)
Get the automorphism partition (equivalence classes) of the atoms.
|
boolean |
AtomContainerDiscretePartitionRefiner.isCanonical(IAtomContainer atomContainer)
Checks if the atom container is canonical.
|
void |
AtomContainerDiscretePartitionRefiner.refine(IAtomContainer atomContainer)
Refine an atom container, which has the side effect of calculating
the automorphism group.
|
void |
AtomContainerDiscretePartitionRefiner.refine(IAtomContainer atomContainer,
Partition partition)
Refine an atom partition based on the connectivity in the atom container.
|
| Modifier and Type | Method and Description |
|---|---|
int |
AtomEncoder.encode(IAtom atom,
IAtomContainer container)
Encode an invariant attribute of the given atom.
|
long |
MoleculeHashGenerator.generate(IAtomContainer container)
Generate invariant 64-bit hash code for a molecule.
|
long[] |
AtomHashGenerator.generate(IAtomContainer container)
Generate invariant 64-bit hash codes for the atoms of the molecule.
|
| Modifier and Type | Method and Description |
|---|---|
long |
EnsembleHashGenerator.generate(Set<IAtomContainer> ensemble)
Generate invariant 64-bit hash code for an ensemble of molecules.
|
| Modifier and Type | Method and Description |
|---|---|
StereoEncoder |
DoubleBondElementEncoderFactory.create(IAtomContainer container,
int[][] graph)
Create a stereo-encoder for possible stereo-chemical configurations.
|
StereoEncoder |
GeometricDoubleBondEncoderFactory.create(IAtomContainer container,
int[][] graph)
Create a stereo encoder for all potential 2D and 3D double bond stereo
configurations.
|
StereoEncoder |
TetrahedralElementEncoderFactory.create(IAtomContainer container,
int[][] graph)
Create a stereo-encoder for possible stereo-chemical configurations.
|
StereoEncoder |
StereoEncoderFactory.create(IAtomContainer container,
int[][] graph)
Create a stereo-encoder for possible stereo-chemical configurations.
|
StereoEncoder |
GeometricCumulativeDoubleBondFactory.create(IAtomContainer container,
int[][] graph)
Create a stereo encoder for cumulative double bonds.
|
StereoEncoder |
GeometricTetrahedralEncoderFactory.create(IAtomContainer container,
int[][] graph)
Create a stereo encoder for all potential 2D and 3D tetrahedral
elements.
|
| Modifier and Type | Field and Description |
|---|---|
protected IAtomContainer |
InChIGenerator.atomContainer
AtomContainer instance refers to.
|
protected IAtomContainer |
InChIToStructure.molecule |
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
InChIToStructure.getAtomContainer()
Returns generated molecule.
|
| Modifier and Type | Method and Description |
|---|---|
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.
|
| Constructor and Description |
|---|
InChIGenerator(IAtomContainer atomContainer,
boolean ignoreAromaticBonds)
Constructor.
|
InChIGenerator(IAtomContainer atomContainer,
List<net.sf.jniinchi.INCHI_OPTION> options,
boolean ignoreAromaticBonds)
Constructor.
|
InChIGenerator(IAtomContainer atomContainer,
String options,
boolean ignoreAromaticBonds)
Constructor.
|
| Modifier and Type | Interface and Description |
|---|---|
interface |
IAminoAcid
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
|
interface |
IBioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
|
interface |
ICrystal
Class representing a molecular crystal.
|
interface |
IMonomer
A Monomer is an AtomContainer which stores additional monomer specific
informations for a group of Atoms.
|
interface |
IPDBMonomer
Represents the idea of an protein monomer as found in PDB files.
|
interface |
IPDBPolymer
A PDBPolymer is a subclass of a BioPolymer which is supposed to store
additional informations about the BioPolymer which are connected to BioPolymers.
|
interface |
IPolymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
|
interface |
IRing
Class representing a ring structure in a molecule.
|
interface |
IStrand
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
IAtomContainer.clone()
Returns a deep clone of this IChemObject.
|
IAtomContainer |
IAtomContainerSet.getAtomContainer(int number)
Returns the AtomContainer at position
number in the
container. |
IAtomContainer |
IAtom.getContainer()
Access the
IAtomContainer of which this atom is a member of. |
IAtomContainer |
IBond.getContainer() |
IAtomContainer |
IFragmentAtom.getFragment()
Returns the fully expended form of the IFragmentAtom.
|
IAtomContainer |
IChemObjectBuilder.newAtomContainer()
Create a new atom container using the default constructor.
|
| Modifier and Type | Method and Description |
|---|---|
Iterable<IAtomContainer> |
IAtomContainerSet.atomContainers()
Get an Iterable for this AtomContainerSet.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ICrystal.add(IAtomContainer container)
Adds the atoms in the AtomContainer as cell content.
|
void |
IAtomContainer.add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
void |
IReaction.addAgent(IAtomContainer agent)
Adds an agent to this reaction.
|
void |
IAtomContainerSet.addAtomContainer(IAtomContainer atomContainer)
Adds an atomContainer to this container.
|
void |
IAtomContainerSet.addAtomContainer(IAtomContainer atomContainer,
double multiplier)
Adds an atomContainer to this container with the given
multiplier.
|
void |
IReaction.addProduct(IAtomContainer product)
Adds a product to this reaction.
|
void |
IReaction.addProduct(IAtomContainer product,
Double coefficient)
Adds a product to this reaction.
|
void |
IReaction.addReactant(IAtomContainer reactant)
Adds a reactant to this reaction.
|
void |
IReaction.addReactant(IAtomContainer reactant,
Double coefficient)
Adds a reactant to this reaction with a stoichiometry coefficient.
|
boolean |
IRingSet.contains(IAtomContainer container)
True, if this set contains the IAtomContainer.
|
Double |
IAtomContainerSet.getMultiplier(IAtomContainer container)
Returns the multiplier of the given AtomContainer.
|
Double |
IReaction.getProductCoefficient(IAtomContainer product)
Returns the stoichiometry coefficient of the given product.
|
Double |
IReaction.getReactantCoefficient(IAtomContainer reactant)
Returns the stoichiometry coefficient of the given reactant.
|
void |
IAtomContainer.remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
IAtomContainerSet.removeAtomContainer(IAtomContainer atomContainer)
Removes an AtomContainer from this container.
|
void |
IAtomContainerSet.replaceAtomContainer(int position,
IAtomContainer container)
Replace the AtomContainer at a specific position (array has to be large enough).
|
void |
IFragmentAtom.setFragment(IAtomContainer fragment)
Sets the fully expended form of the IFragmentAtom.
|
boolean |
IAtomContainerSet.setMultiplier(IAtomContainer container,
Double multiplier)
Sets the coefficient of a AtomContainer to a given value.
|
boolean |
IReaction.setProductCoefficient(IAtomContainer product,
Double coefficient)
Sets the coefficient of a a product to a given value.
|
boolean |
IReaction.setReactantCoefficient(IAtomContainer reactant,
Double coefficient)
Sets the coefficient of a a reactant to a given value.
|
| Modifier and Type | Method and Description |
|---|---|
void |
IAtomContainerSet.sortAtomContainers(Comparator<IAtomContainer> comparator)
Sort the AtomContainers using a provided Comparator.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
MDLV3000Reader.readConnectionTable(IChemObjectBuilder builder) |
IAtomContainer |
MDLV3000Reader.readMolecule(IChemObjectBuilder builder) |
| Modifier and Type | Method and Description |
|---|---|
void |
MDLV3000Reader.readAtomBlock(IAtomContainer readData)
Reads the atoms, coordinates and charges.
|
void |
MDLV3000Reader.readBondBlock(IAtomContainer readData)
Reads the bond atoms, order and stereo configuration.
|
String |
MDLV3000Reader.readHeader(IAtomContainer readData) |
void |
MDLV3000Reader.readSGroup(IAtomContainer readData)
Reads labels.
|
void |
SMILESWriter.writeAtomContainer(IAtomContainer molecule)
Writes the content from molecule to output.
|
void |
PDBWriter.writeMolecule(IAtomContainer molecule)
Writes a single frame in PDB format to the Writer.
|
void |
Mol2Writer.writeMolecule(IAtomContainer mol)
Writes a single frame in XYZ format to the Writer.
|
void |
XYZWriter.writeMolecule(IAtomContainer mol)
writes a single frame in XYZ format to the Writer.
|
void |
MDLV2000Writer.writeMolecule(IAtomContainer container)
Writes a Molecule to an OutputStream in MDL sdf format.
|
| Modifier and Type | Field and Description |
|---|---|
protected IAtomContainer |
CMLCoreModule.currentMolecule |
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
INChIContentProcessorTool.processFormula(IAtomContainer parsedContent,
String atomsEncoding)
Deprecated.
Processes the content from the formula field of the INChI.
|
| Modifier and Type | Method and Description |
|---|---|
void |
INChIContentProcessorTool.processConnections(String bondsEncoding,
IAtomContainer container,
int source)
Deprecated.
Processes the content from the connections field of the INChI.
|
IAtomContainer |
INChIContentProcessorTool.processFormula(IAtomContainer parsedContent,
String atomsEncoding)
Deprecated.
Processes the content from the formula field of the INChI.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
IteratingSMILESReader.next()
Get the next molecule from the stream.
|
IAtomContainer |
IteratingPCCompoundASNReader.next() |
IAtomContainer |
IteratingPCCompoundXMLReader.next() |
IAtomContainer |
IteratingSDFReader.next()
Returns the next
IAtomContainer. |
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
EventCMLHandler.getAtomContainer() |
IAtomContainer |
EventCMLReader.getAtomContainer() |
IAtomContainer |
IEventChemObjectReader.getAtomContainer() |
| Modifier and Type | Method and Description |
|---|---|
void |
GaussianInputWriter.writeMolecule(IAtomContainer mol)
Writes a molecule for input for Gaussian.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
PubChemXMLHelper.parseMolecule(XMLStreamReader parser,
IChemObjectBuilder builder) |
| Modifier and Type | Method and Description |
|---|---|
void |
PubChemXMLHelper.parseAtomCharges(XMLStreamReader parser,
IAtomContainer molecule) |
void |
PubChemXMLHelper.parseAtomElements(XMLStreamReader parser,
IAtomContainer molecule) |
void |
PubChemXMLHelper.parserAtomBlock(XMLStreamReader parser,
IAtomContainer molecule) |
void |
PubChemXMLHelper.parserBondBlock(XMLStreamReader parser,
IAtomContainer molecule) |
void |
PubChemXMLHelper.parserCompoundInfoData(XMLStreamReader parser,
IAtomContainer molecule) |
void |
PubChemXMLHelper.parserCoordBlock(XMLStreamReader parser,
IAtomContainer molecule) |
| Modifier and Type | Method and Description |
|---|---|
static IAtomContainer |
UniversalIsomorphismTester.project(List<RMap> rMapList,
IAtomContainer g,
int id)
Projects a list of
RMap on a molecule. |
| Modifier and Type | Method and Description |
|---|---|
List<IAtomContainer> |
UniversalIsomorphismTester.getOverlaps(IAtomContainer g1,
IAtomContainer g2)
Returns all the maximal common substructure between two atom containers.
|
static List<IAtomContainer> |
UniversalIsomorphismTester.projectList(List<List<RMap>> rMapsList,
IAtomContainer g,
int id)
Projects a list of RMapsList on a molecule.
|
Iterable<IAtomContainer> |
Mappings.toSubstructures()
Obtain the mapped substructures (atoms/bonds) of the target compound.
|
| Modifier and Type | Method and Description |
|---|---|
static RGraph |
UniversalIsomorphismTester.buildRGraph(IAtomContainer g1,
IAtomContainer g2)
Builds the
RGraph ( resolution graph ), from two atomContainer
(description of the two molecules to compare)
This is the interface point between the CDK model and
the generic MCSS algorithm based on the RGRaph. |
static List<RMap> |
UniversalIsomorphismTester.checkSingleAtomCases(IAtomContainer g1,
IAtomContainer g2)
Checks for single atom cases before doing subgraph/isomorphism search.
|
static Pattern |
Pattern.findIdentical(IAtomContainer query)
Create a pattern which can be used to find molecules which are the same
as the
query structure. |
static Pattern |
VentoFoggia.findIdentical(IAtomContainer query)
Create a pattern which can be used to find molecules which are the same
as the
query structure. |
static Pattern |
VentoFoggia.findIdentical(IAtomContainer query,
AtomMatcher atomMatcher,
BondMatcher bondMatcher)
Create a pattern which can be used to find molecules which are the same
as the
query structure. |
static Pattern |
Pattern.findSubstructure(IAtomContainer query)
Create a pattern which can be used to find molecules which contain the
query structure. |
static Pattern |
VentoFoggia.findSubstructure(IAtomContainer query)
Create a pattern which can be used to find molecules which contain the
query structure. |
static DfPattern |
DfPattern.findSubstructure(IAtomContainer query)
Create a pattern which can be used to find molecules which contain the
query structure. |
static Pattern |
Ullmann.findSubstructure(IAtomContainer query)
Create a pattern which can be used to find molecules which contain the
query structure. |
static Pattern |
VentoFoggia.findSubstructure(IAtomContainer query,
AtomMatcher atomMatcher,
BondMatcher bondMatcher)
Create a pattern which can be used to find molecules which contain the
query structure. |
static BitSet |
UniversalIsomorphismTester.getBitSet(IAtomContainer ac)
Transforms an AtomContainer into a
BitSet (which's size = number of bond
in the atomContainer, all the bit are set to true). |
List<RMap> |
UniversalIsomorphismTester.getIsomorphAtomsMap(IAtomContainer g1,
IAtomContainer g2)
Returns the first isomorph 'atom mapping' found for g2 in g1.
|
List<RMap> |
UniversalIsomorphismTester.getIsomorphMap(IAtomContainer g1,
IAtomContainer g2)
Returns the first isomorph mapping found or null.
|
List<List<RMap>> |
UniversalIsomorphismTester.getIsomorphMaps(IAtomContainer g1,
IAtomContainer g2)
Returns all the isomorph 'mappings' found between two
atom containers.
|
List<IAtomContainer> |
UniversalIsomorphismTester.getOverlaps(IAtomContainer g1,
IAtomContainer g2)
Returns all the maximal common substructure between two atom containers.
|
List<RMap> |
UniversalIsomorphismTester.getSubgraphAtomsMap(IAtomContainer g1,
IAtomContainer g2)
Returns the first subgraph 'atom mapping' found for g2 in g1, where g2 must be a substructure
of g1.
|
List<List<RMap>> |
UniversalIsomorphismTester.getSubgraphAtomsMaps(IAtomContainer g1,
IAtomContainer g2)
Returns all subgraph 'atom mappings' found for g2 in g1, where g2 must be a substructure
of g1.
|
List<RMap> |
UniversalIsomorphismTester.getSubgraphMap(IAtomContainer g1,
IAtomContainer g2)
Returns the first subgraph 'bond mapping' found for g2 in g1.
|
List<List<RMap>> |
UniversalIsomorphismTester.getSubgraphMaps(IAtomContainer g1,
IAtomContainer g2)
Returns all the subgraph 'bond mappings' found for g2 in g1.
|
boolean |
UniversalIsomorphismTester.isIsomorph(IAtomContainer g1,
IAtomContainer g2)
Tests if g1 and g2 are isomorph.
|
boolean |
IsomorphismTester.isIsomorphic(IAtomContainer mol2)
Checks whether a given molecule is isomorphic with the one
that has been assigned to this IsomorphismTester at construction time.
|
boolean |
IsomorphismTester.isIsomorphic(IAtomContainer mol1,
IAtomContainer mol2)
Checks whether a given molecule is isomorphic with the one
that has been assigned to this IsomorphismTester at construction time.
|
boolean |
UniversalIsomorphismTester.isSubgraph(IAtomContainer g1,
IAtomContainer g2)
Deprecated.
Use the Pattern APIs from the cdk-isomorphism module
|
static List<RMap> |
UniversalIsomorphismTester.makeAtomsMapOfBondsMap(List<RMap> l,
IAtomContainer g1,
IAtomContainer g2)
This makes a map of matching atoms out of a map of matching bonds as produced by the
get(Subgraph|Ismorphism)Map methods.
|
static List<List<RMap>> |
UniversalIsomorphismTester.makeAtomsMapsOfBondsMaps(List<List<RMap>> l,
IAtomContainer g1,
IAtomContainer g2)
This makes maps of matching atoms out of a maps of matching bonds as produced by the
get(Subgraph|Ismorphism)Maps methods.
|
static Map<Integer,Integer> |
AtomMappingTools.mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms)
Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest
AtomContainer) atomContainer.
|
abstract int[] |
Pattern.match(IAtomContainer target)
Find a matching of this pattern in the
target. |
int[] |
VentoFoggia.match(IAtomContainer target)
Find a matching of this pattern in the
target. |
int[] |
DfPattern.match(IAtomContainer target)
Find a matching of this pattern in the
target. |
int[] |
Ullmann.match(IAtomContainer target) |
abstract Mappings |
Pattern.matchAll(IAtomContainer target)
Find all mappings of this pattern in the
target. |
Mappings |
VentoFoggia.matchAll(IAtomContainer target)
Find all mappings of this pattern in the
target. |
Mappings |
DfPattern.matchAll(IAtomContainer mol)
Find all mappings of this pattern in the
target. |
Mappings |
Ullmann.matchAll(IAtomContainer target) |
boolean |
Pattern.matches(IAtomContainer target)
Determine if there is a mapping of this pattern in the
target. |
boolean |
DfPattern.matches(IAtomContainer target)
Determine if there is a mapping of this pattern in the
target. |
static IAtomContainer |
UniversalIsomorphismTester.project(List<RMap> rMapList,
IAtomContainer g,
int id)
Projects a list of
RMap on a molecule. |
static List<IAtomContainer> |
UniversalIsomorphismTester.projectList(List<List<RMap>> rMapsList,
IAtomContainer g,
int id)
Projects a list of RMapsList on a molecule.
|
List<List<RMap>> |
UniversalIsomorphismTester.search(IAtomContainer g1,
IAtomContainer g2,
BitSet c1,
BitSet c2,
boolean findAllStructure,
boolean findAllMap)
General
RGraph parsing method (usually not used directly)
This method is the entry point for the recursive search
adapted to the atom container input. |
| Constructor and Description |
|---|
IsomorphismTester(IAtomContainer mol)
Constructor for the IsomorphismTester object
|
SmartsStereoMatch(IAtomContainer query,
IAtomContainer target)
Deprecated.
Create a predicate for checking mappings between a provided
query and target. |
| Modifier and Type | Interface and Description |
|---|---|
interface |
IQueryAtomContainer
General concept of a IAtomContainer aimed at doing molecular subgraph
queries using the UniversalIsomorphismTester.
|
| Modifier and Type | Class and Description |
|---|---|
class |
QueryAtomContainer |
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
QueryBond.getContainer() |
IAtomContainer |
QueryAtom.getContainer()
Access the
IAtomContainer of which this atom is a member of. |
IAtomContainer |
RGroup.getGroup() |
IAtomContainer |
RGroupQuery.getRootStructure() |
IAtomContainer |
IRGroupQuery.getRootStructure()
Getter for the root structure of this R-Group.
|
IAtomContainer |
Expr.subquery()
Access the sub-query, only applicable to recursive types.
|
static IAtomContainer |
QueryAtomContainerCreator.suppressQueryHydrogens(IAtomContainer mol) |
| Modifier and Type | Method and Description |
|---|---|
List<IAtomContainer> |
RGroupQuery.getAllConfigurations() |
List<IAtomContainer> |
IRGroupQuery.getAllConfigurations()
Produces all combinations of the root structure (scaffold) with the R-groups
substituted in valid ways, using each R-group's definitions and conditions.
|
List<IAtomContainer> |
RGroupQuery.getSubstituents() |
List<IAtomContainer> |
IRGroupQuery.getSubstituents()
Return all the substituent atom containers, in other words the atom containers
defined in this RGroupQuery except for the root structure.
|
| Modifier and Type | Method and Description |
|---|---|
void |
QueryAtomContainer.add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
static QueryAtomContainer |
QueryAtomContainer.create(IAtomContainer src,
Expr.Type... opts)
Create a query from a molecule and a provided set of expressions.
|
static void |
QueryAtomContainer.create(IAtomContainer dst,
IAtomContainer src,
Expr.Type... opts)
Populate a query from a molecule and a provided set of expressions.
|
static QueryAtomContainer |
QueryAtomContainerCreator.createAnyAtomAnyBondContainer(IAtomContainer container,
boolean aromaticity)
Creates a QueryAtomContainer with the following settings:
|
static QueryAtomContainer |
QueryAtomContainerCreator.createAnyAtomContainer(IAtomContainer container,
boolean aromaticity)
Creates a QueryAtomContainer with the following settings:
|
static QueryAtomContainer |
QueryAtomContainerCreator.createAnyAtomForPseudoAtomQueryContainer(IAtomContainer container)
Creates a QueryAtomContainer with the following settings:
|
static QueryAtomContainer |
QueryAtomContainerCreator.createBasicQueryContainer(IAtomContainer container)
Creates a QueryAtomContainer with the following settings:
|
static QueryAtomContainer |
QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(IAtomContainer container)
Creates a QueryAtomContainer with the following settings:
|
static QueryAtomContainer |
QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(IAtomContainer container)
Creates a QueryAtomContainer with the following settings:
|
static QueryAtomContainer |
QueryAtomContainerCreator.createSymbolChargeIDQueryContainer(IAtomContainer container) |
void |
QueryAtomContainer.remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
RGroup.setGroup(IAtomContainer group) |
void |
RGroupQuery.setRootStructure(IAtomContainer rootStructure) |
void |
IRGroupQuery.setRootStructure(IAtomContainer rootStructure)
Setter for the root structure of this R-Group.
|
static IAtomContainer |
QueryAtomContainerCreator.suppressQueryHydrogens(IAtomContainer mol) |
| Constructor and Description |
|---|
Expr(Expr.Type op,
IAtomContainer mol)
Creates a recursive atom expression.
|
QueryAtomContainer(IAtomContainer container,
IChemObjectBuilder builder)
Constructs an AtomContainer with a copy of the atoms and electronContainers
of another AtomContainer (A shallow copy, i.e., with the same objects as in
the original AtomContainer).
|
| Modifier and Type | Method and Description |
|---|---|
static void |
SmartsMatchers.prepare(IAtomContainer container,
boolean ringQuery)
Deprecated.
Do not use - temporary method until the SMARTS packages are cleaned up.
|
| Modifier and Type | Method and Description |
|---|---|
protected IAtomContainer |
MoleculeBuilder.buildMolecule(int mainChain,
List<AttachedGroup> attachedSubstituents,
List<AttachedGroup> attachedGroups,
boolean isMainCyclic,
String name)
Start of the process of building a molecule from the parsed data.
|
static IAtomContainer |
NomParser.generate(String stringToParse)
Deprecated.
Parses the chemical name and returns the built molecule.
|
static IAtomContainer |
NomParser.generate(String stringToParse,
IChemObjectBuilder builder)
Deprecated.
Parses the chemical name and returns the built molecule.
|
| Modifier and Type | Field and Description |
|---|---|
static Comparator<IAtomContainer> |
StructureDiagramGenerator.LARGEST_FIRST_COMPARATOR |
| Modifier and Type | Method and Description |
|---|---|
static IAtomContainer |
AtomPlacer.getInitialLongestChain(IAtomContainer molecule)
Search an aliphatic molecule for the longest chain.
|
static IAtomContainer |
AtomPlacer.getLongestUnplacedChain(IAtomContainer molecule,
IAtom startAtom)
Search a molecule for the longest unplaced, aliphatic chain in it.
|
IAtomContainer |
StructureDiagramGenerator.getMolecule()
Returns the molecule, usually used after a call of generateCoordinates()
|
IAtomContainer |
RingPlacer.getMolecule() |
IAtomContainer |
AtomPlacer.getMolecule()
Return the molecule the AtomPlacer currently works with
|
static IAtomContainer |
AtomPlacer.getPlacedAtoms(IAtomContainer ac)
Get all the placed atoms in an AtomContainer
|
IAtomContainer |
TemplateHandler.getTemplateAt(int position)
Gets the templateAt attribute of the TemplateHandler object
|
IAtomContainer |
RingPlacer.placeRingSubstituents(IRingSet rs,
double bondLength)
Positions the aliphatic substituents of a ring system
|
IAtomContainer |
TemplateHandler.removeMolecule(IAtomContainer molecule) |
| Modifier and Type | Method and Description |
|---|---|
void |
TemplateHandler.addMolecule(IAtomContainer molecule)
Adds a Molecule to the list of templates use by this TemplateHandler.
|
static boolean |
AtomPlacer.allPlaced(IAtomContainer ac)
True is all the atoms in the given AtomContainer have been placed
|
static void |
AtomPlacer.breadthFirstSearch(IAtomContainer ac,
List<IAtom> sphere,
IAtomContainer[] pathes)
Performs a breadthFirstSearch in an AtomContainer starting with a
particular sphere, which usually consists of one start atom, and searches
for the longest aliphatic chain which is yet unplaced.
|
static void |
AtomPlacer.breadthFirstSearch(IAtomContainer ac,
List<IAtom> sphere,
IAtomContainer[] pathes)
Performs a breadthFirstSearch in an AtomContainer starting with a
particular sphere, which usually consists of one start atom, and searches
for the longest aliphatic chain which is yet unplaced.
|
static TemplateHandler |
TemplateHandler.createFromSubstructure(Pattern ptrn,
IAtomContainer mol)
Create a template from a substructure pattern.
|
static TemplateHandler |
TemplateHandler.createSingleton(IAtomContainer template)
Singleton template instance, mainly useful for aligning molecules.
|
double |
OverlapResolver.displace(IAtomContainer ac,
Vector overlappingAtoms,
Vector overlappingBonds)
Deprecated.
Makes a small displacement to some atoms or rings in the given
atomcontainer.
|
void |
AtomPlacer.distributePartners(IAtom atom,
IAtomContainer placedNeighbours,
javax.vecmath.Point2d sharedAtomsCenter,
IAtomContainer unplacedNeighbours,
double bondLength)
Distribute the bonded atoms (neighbours) of an atom such that they fill the
remaining space around an atom in a geometrically nice way.
|
void |
StructureDiagramGenerator.generateCoordinates(IAtomContainer mol)
Convenience method for generating 2D coordinates.
|
double |
OverlapResolver.getAtomOverlapScore(IAtomContainer ac,
Vector overlappingAtoms)
Deprecated.
Calculates a score based on the overlap of atoms.
|
double |
OverlapResolver.getBondOverlapScore(IAtomContainer ac,
Vector overlappingBonds)
Deprecated.
Calculates a score based on the intersection of bonds.
|
static IAtomContainer |
AtomPlacer.getInitialLongestChain(IAtomContainer molecule)
Search an aliphatic molecule for the longest chain.
|
static IAtomContainer |
AtomPlacer.getLongestUnplacedChain(IAtomContainer molecule,
IAtom startAtom)
Search a molecule for the longest unplaced, aliphatic chain in it.
|
IAtomContainerSet |
TemplateHandler.getMappedSubstructures(IAtomContainer molecule)
Checks if one of the loaded templates is a substructure in the given
Molecule and returns all matched substructures in a IAtomContainerSet.
|
double |
OverlapResolver.getOverlapScore(IAtomContainer ac,
Vector overlappingAtoms,
Vector overlappingBonds)
Deprecated.
Calculates a score based on the overlap of atoms and intersection of bonds.
|
static IAtomContainer |
AtomPlacer.getPlacedAtoms(IAtomContainer ac)
Get all the placed atoms in an AtomContainer
|
static String |
AtomPlacer.listNumbers(IAtomContainer mol,
IAtomContainer ac)
Returns a string with the numbers of all atoms in an AtomContainer relative
to a given molecule.
|
static String |
AtomPlacer.listNumbers(IAtomContainer mol,
List<IAtom> ac)
Returns a string with the numbers of all atoms in a Vector relative to a
given molecule.
|
String |
AtomPlacer.listPlaced(IAtomContainer ac)
Returns a string with the numbers of all placed atoms in an AtomContainer
|
boolean |
TemplateHandler.mapTemplateExact(IAtomContainer molecule)
Checks if one of the loaded templates is isomorph to the given
Molecule.
|
boolean |
TemplateHandler.mapTemplates(IAtomContainer molecule)
Checks if one of the loaded templates is a substructure in the given
Molecule.
|
static void |
AtomPlacer.markNotPlaced(IAtomContainer ac)
Marks all the atoms in the given AtomContainer as not placed
|
static void |
AtomPlacer.markPlaced(IAtomContainer ac)
Marks all the atoms in the given AtomContainer as placed
|
void |
RingPlacer.partitionNonRingPartners(IAtom atom,
IRing ring,
IAtomContainer ringAtoms,
IAtomContainer nonRingAtoms)
Partition the bonding partners of a given atom into ring atoms and non-ring atoms
|
void |
AtomPlacer.partitionPartners(IAtom atom,
IAtomContainer unplacedPartners,
IAtomContainer placedPartners)
Partition the bonding partners of a given atom into placed (coordinates
assinged) and not placed.
|
void |
RingPlacer.placeFusedRing(IRing ring,
IAtomContainer sharedAtoms,
javax.vecmath.Vector2d ringCenterVector,
double bondLength)
Generated coordinates for a given ring, which is fused to another ring.
|
void |
HydrogenPlacer.placeHydrogens2D(IAtomContainer container,
double bondLength)
Place all hydrogens connected to atoms which have already been laid out.
|
void |
HydrogenPlacer.placeHydrogens2D(IAtomContainer container,
IAtom atom)
Place hydrogens connected to the given atom using the average bond length
in the container.
|
void |
HydrogenPlacer.placeHydrogens2D(IAtomContainer container,
IAtom atom,
double bondLength)
Place hydrogens connected to the provided atom atom using the
specified bondLength.
|
void |
AtomPlacer.placeLinearChain(IAtomContainer atomContainer,
javax.vecmath.Vector2d initialBondVector,
double bondLength)
Places the atoms in a linear chain.
|
void |
RingPlacer.placeRing(IRing ring,
IAtomContainer sharedAtoms,
javax.vecmath.Point2d sharedAtomsCenter,
javax.vecmath.Vector2d ringCenterVector,
double bondLength)
Generated coordinates for a given ring.
|
void |
RingPlacer.placeSpiroRing(IRing ring,
IAtomContainer sharedAtoms,
javax.vecmath.Point2d sharedAtomsCenter,
javax.vecmath.Vector2d ringCenterVector,
double bondLength)
Generated coordinates for a given ring, which is connected to a spiro ring.
|
IAtomContainer |
TemplateHandler.removeMolecule(IAtomContainer molecule) |
double |
OverlapResolver.resolveOverlap(IAtomContainer ac,
IRingSet sssr)
Deprecated.
Main method to be called to resolve overlap situations.
|
void |
StructureDiagramGenerator.setMolecule(IAtomContainer molecule)
Assings a molecule to be layed out.
|
void |
RingPlacer.setMolecule(IAtomContainer molecule) |
void |
AtomPlacer.setMolecule(IAtomContainer molecule)
Sets the molecule the AtomPlacer currently works with
|
void |
StructureDiagramGenerator.setMolecule(IAtomContainer mol,
boolean clone) |
void |
StructureDiagramGenerator.setMolecule(IAtomContainer mol,
boolean clone,
Set<IAtom> afix,
Set<IBond> bfix)
Assigns a molecule to be laid out.
|
static boolean |
AtomPlacer.shouldBeLinear(IAtom atom,
IAtomContainer molecule)
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
static TemplateHandler |
TemplateHandler.createFromSubstructure(Pattern ptrn,
Iterable<IAtomContainer> mols)
Create a template from a substructure pattern.
|
| Constructor and Description |
|---|
StructureDiagramGenerator(IAtomContainer molecule)
Creates an instance of this class while assigning a molecule to be layed
out.
|
| Modifier and Type | Method and Description |
|---|---|
org.xmlcml.cml.element.CMLMolecule |
Convertor.cdkAtomContainerToCMLMolecule(IAtomContainer structure) |
org.xmlcml.cml.element.CMLAtom |
Convertor.cdkAtomToCMLAtom(IAtomContainer container,
IAtom cdkAtom) |
void |
PDBAtomCustomizer.customize(IAtomContainer molecule,
Object nodeToAdd) |
void |
MDMoleculeCustomizer.customize(IAtomContainer molecule,
Object nodeToAdd)
Customize Molecule.
|
void |
QSARCustomizer.customize(IAtomContainer molecule,
Object nodeToAdd) |
void |
ICMLCustomizer.customize(IAtomContainer molecule,
Object nodeToAdd)
Customized the nodeToAdd for the given Molecule.
|
| Modifier and Type | Method and Description |
|---|---|
static IAtomContainer |
Convertor.model2Molecule(com.hp.hpl.jena.rdf.model.Model model,
IChemObjectBuilder builder)
|
| Modifier and Type | Method and Description |
|---|---|
static com.hp.hpl.jena.rdf.model.Model |
Convertor.molecule2Model(IAtomContainer molecule)
Converts a
IAtomContainer into a Model representation using the CDK OWL. |
| Modifier and Type | Class and Description |
|---|---|
class |
ChargeGroup
A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule.
|
class |
MDMolecule |
class |
Residue
A residue is a named, numbered collection of atoms in an MDMolecule.
|
| Constructor and Description |
|---|
ChargeGroup(IAtomContainer container,
int number,
MDMolecule parentMolecule)
Constructor to create a ChargeGroup based on an AC, a number, and a MDMolecule.
|
MDMolecule(IAtomContainer container) |
Residue(IAtomContainer container,
int number,
MDMolecule parentMolecule)
Constructor to create a Residue based on an AC, a number, and a MDMolecule.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
TemplateExtractor.createAnyAtomAtomContainer(IAtomContainer atomContainer) |
IAtomContainer |
ModelBuilder3D.generate3DCoordinates(IAtomContainer molecule,
boolean clone)
Generate 3D coordinates with force field information.
|
IAtomContainer |
AtomTetrahedralLigandPlacer3D.getPlacedAtomsInAtomContainer(IAtom atom,
IAtomContainer ac)
Gets all placed neighbouring atoms of a atom.
|
IAtomContainer |
AtomPlacer3D.getPlacedHeavyAtoms(IAtomContainer molecule,
IAtom atom)
Gets the placed Heavy Atoms connected to an atom.
|
IAtomContainer |
TemplateHandler3D.getTemplateAt(int position)
Gets the templateAt attribute of the TemplateHandler object.
|
IAtomContainer |
AtomTetrahedralLigandPlacer3D.getUnsetAtomsInAtomContainer(IAtom atom,
IAtomContainer ac)
Gets the unsetAtomsInAtomContainer attribute of the
AtomTetrahedralLigandPlacer3D object.
|
IAtomContainer |
AtomPlacer3D.markPlaced(IAtomContainer ac)
Mark all atoms in chain as placed.
|
IAtomContainer |
TemplateExtractor.removeLoopBonds(IAtomContainer molecule,
int position) |
IAtomContainer |
TemplateExtractor.resetFlags(IAtomContainer ac) |
| Modifier and Type | Method and Description |
|---|---|
void |
AtomTetrahedralLigandPlacer3D.add3DCoordinatesForSinglyBondedLigands(IAtomContainer atomContainer)
Generate coordinates for all atoms which are singly bonded and have no
coordinates.
|
boolean |
AtomPlacer3D.allHeavyAtomsPlaced(IAtomContainer ac)
True is all the atoms in the given AtomContainer have been placed.
|
IRingSet |
ForceFieldConfigurator.assignAtomTyps(IAtomContainer molecule)
Method assigns atom types to atoms (calculates sssr and aromaticity)
|
IAtomContainer |
TemplateExtractor.createAnyAtomAtomContainer(IAtomContainer atomContainer) |
int[] |
AtomPlacer3D.findHeavyAtomsInChain(IAtomContainer molecule,
IAtomContainer chain)
Count and find first heavy atom(s) (non Hydrogens) in a chain.
|
IAtomContainer |
ModelBuilder3D.generate3DCoordinates(IAtomContainer molecule,
boolean clone)
Generate 3D coordinates with force field information.
|
javax.vecmath.Point3d |
AtomPlacer3D.geometricCenterAllPlacedAtoms(IAtomContainer molecule)
Calculates the geometric center of all placed atoms in the atomcontainer.
|
javax.vecmath.Point3d[] |
AtomTetrahedralLigandPlacer3D.get3DCoordinatesForLigands(IAtom refAtom,
IAtomContainer noCoords,
IAtomContainer withCoords,
IAtom atomC,
int nwanted,
double length,
double angle)
Adds 3D coordinates for singly-bonded ligands of a reference atom (A).
|
javax.vecmath.Point3d[] |
AtomTetrahedralLigandPlacer3D.get3DCoordinatesForSP2Ligands(IAtom refAtom,
IAtomContainer noCoords,
IAtomContainer withCoords,
IAtom atomC,
double length,
double angle)
Main method for the calculation of the ligand coordinates for sp2 atoms.
|
javax.vecmath.Point3d[] |
AtomTetrahedralLigandPlacer3D.get3DCoordinatesForSP3Ligands(IAtom refAtom,
IAtomContainer noCoords,
IAtomContainer withCoords,
IAtom atomC,
int nwanted,
double length,
double angle)
Main method for the calculation of the ligand coordinates for sp3 atoms.
|
javax.vecmath.Point3d |
AtomTetrahedralLigandPlacer3D.get3DCoordinatesForSPLigands(IAtom refAtom,
IAtomContainer withCoords,
double length,
double angle) |
IAtom |
AtomPlacer3D.getFarthestAtom(javax.vecmath.Point3d refAtomPoint,
IAtomContainer ac)
Gets the farthestAtom attribute of the AtomPlacer3D object.
|
IAtom |
AtomPlacer3D.getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer molecule)
Gets the nextPlacedHeavyAtomWithAliphaticPlacedNeigbor from an atom container or molecule.
|
IAtom |
AtomPlacer3D.getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer molecule)
Gets the nextPlacedHeavyAtomWithUnplacedRingNeighbour attribute of the AtomPlacer3D object.
|
IAtom |
AtomPlacer3D.getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer molecule)
Gets the nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour from an atom container or molecule.
|
IAtomContainer |
AtomTetrahedralLigandPlacer3D.getPlacedAtomsInAtomContainer(IAtom atom,
IAtomContainer ac)
Gets all placed neighbouring atoms of a atom.
|
IAtom |
AtomPlacer3D.getPlacedHeavyAtom(IAtomContainer molecule,
IAtom atom)
Returns a placed atom connected to a given atom.
|
IAtom |
AtomPlacer3D.getPlacedHeavyAtom(IAtomContainer molecule,
IAtom atomA,
IAtom atomB)
Gets the first placed Heavy Atom around atomA which is not atomB.
|
IAtom |
AtomTetrahedralLigandPlacer3D.getPlacedHeavyAtomInAtomContainer(IAtom atomA,
IAtom atomB,
IAtomContainer ac)
Returns a placed neighbouring atom of a central atom atomA, which is not
atomB.
|
IAtomContainer |
AtomPlacer3D.getPlacedHeavyAtoms(IAtomContainer molecule,
IAtom atom)
Gets the placed Heavy Atoms connected to an atom.
|
IAtom |
AtomPlacer3D.getUnplacedRingHeavyAtom(IAtomContainer molecule,
IAtom atom)
Gets the unplacedRingHeavyAtom attribute of the AtomPlacer3D object.
|
IAtomContainer |
AtomTetrahedralLigandPlacer3D.getUnsetAtomsInAtomContainer(IAtom atom,
IAtomContainer ac)
Gets the unsetAtomsInAtomContainer attribute of the
AtomTetrahedralLigandPlacer3D object.
|
boolean |
AtomTetrahedralLigandPlacer3D.hasUnsetNeighbour(IAtom atom,
IAtomContainer ac) |
void |
TemplateHandler3D.mapTemplates(IAtomContainer ringSystems,
double numberOfRingAtoms)
|
void |
TemplateHandler3D.mapTemplates(IAtomContainer mol,
int numberOfRingAtoms)
Checks if one of the loaded templates is a substructure in the given
Molecule.
|
IAtomContainer |
AtomPlacer3D.markPlaced(IAtomContainer ac)
Mark all atoms in chain as placed.
|
int |
AtomPlacer3D.numberOfUnplacedHeavyAtoms(IAtomContainer ac)
Gets numberOfUnplacedHeavyAtoms (no Flag ISPLACED, no Hydrogens)
|
void |
AtomPlacer3D.placeAliphaticHeavyChain(IAtomContainer molecule,
IAtomContainer chain)
Method assigns 3D coordinates to the heavy atoms in an aliphatic chain.
|
IAtomContainer |
TemplateExtractor.removeLoopBonds(IAtomContainer molecule,
int position) |
IAtomContainer |
TemplateExtractor.resetFlags(IAtomContainer ac) |
void |
AtomPlacer3D.zmatrixChainToCartesian(IAtomContainer molecule,
boolean flagBranched)
Takes the given Z Matrix coordinates and converts them to cartesian coordinates.
|
| Modifier and Type | Method and Description |
|---|---|
static IAtomContainer |
SMSDNormalizer.convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
Deprecated.
Returns IAtomContainer without Hydrogen.
|
static IAtomContainer |
SMSDNormalizer.makeDeepCopy(IAtomContainer container)
Deprecated.
Returns deep copy of the molecule
|
static IAtomContainer |
SMSDNormalizer.removeHydrogensAndPreserveAtomID(IAtomContainer atomContainer)
Deprecated.
Returns IAtomContainer without Hydrogen.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
SMSDNormalizer.aromatizeMolecule(IAtomContainer mol)
Deprecated.
This function finds rings and uses aromaticity detection code to
aromatize the molecule.
|
static IAtomContainer |
SMSDNormalizer.convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
Deprecated.
Returns IAtomContainer without Hydrogen.
|
static int |
SMSDNormalizer.getExplicitHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
Deprecated.
Returns The number of explicit hydrogens for a given IAtom.
|
static int |
SMSDNormalizer.getHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
Deprecated.
The summed implicit + explicit hydrogens of the given IAtom.
|
static int |
SMSDNormalizer.getImplicitHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
Deprecated.
Returns The number of Implicit Hydrogen Count for a given IAtom.
|
static IAtomContainer |
SMSDNormalizer.makeDeepCopy(IAtomContainer container)
Deprecated.
Returns deep copy of the molecule
|
static boolean |
Normalizer.normalize(IAtomContainer ac,
Document doc)
Deprecated.
The method takes an XML files like the following:
<replace-set> <replace>O=N=O</replace> <replacement>[O-][N+]=O</replacement> </replace-set> All parts in ac which are the same as replace will be changed according to replacement. |
static void |
SMSDNormalizer.percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Deprecated.
Convenience method to perceive atom types for all
IAtoms in the
IAtomContainer, using the CDKAtomTypeMatcher. |
static IAtomContainer |
SMSDNormalizer.removeHydrogensAndPreserveAtomID(IAtomContainer atomContainer)
Deprecated.
Returns IAtomContainer without Hydrogen.
|
| Modifier and Type | Class and Description |
|---|---|
class |
PharmacophoreQuery
Represents a colleciton of pharmacophore groups and constraints.
|
| Modifier and Type | Method and Description |
|---|---|
boolean |
PharmacophoreMatcher.matches(IAtomContainer atomContainer)
Performs the pharmacophore matching.
|
boolean |
PharmacophoreMatcher.matches(IAtomContainer atomContainer,
boolean initializeTarget)
Performs the pharmacophore matching.
|
| Modifier and Type | Class and Description |
|---|---|
class |
PDBMonomer
Represents the idea of an monomer as used in PDB files.
|
class |
PDBPolymer
An entry in the PDB database.
|
class |
PDBStrand
An entry in the PDB database.
|
| Modifier and Type | Method and Description |
|---|---|
protected static IAtomContainer |
AbstractMolecularDescriptor.clone(IAtomContainer mol) |
| Modifier and Type | Method and Description |
|---|---|
void |
AbstractAtomicDescriptor.cacheDescriptorValue(IAtom atom,
IAtomContainer container,
IDescriptorResult value)
Caches a DescriptorValue for a given IAtom.
|
void |
AbstractBondDescriptor.cacheDescriptorValue(IBond bond,
IAtomContainer container,
IDescriptorResult doubleResult)
Caches a DescriptorValue for a given IBond.
|
DescriptorValue |
IMolecularDescriptor.calculate(IAtomContainer container)
Calculates the descriptor value for the given IAtomContainer.
|
DescriptorValue |
IAtomicDescriptor.calculate(IAtom atom,
IAtomContainer container)
Calculates the descriptor value for the given IAtom.
|
DescriptorValue |
IAtomPairDescriptor.calculate(IAtom atom,
IAtom atom2,
IAtomContainer container)
Calculates the descriptor value for the given IAtom.
|
DescriptorValue |
IBondDescriptor.calculate(IBond bond,
IAtomContainer atomContainer)
Calculates the descriptor value for the given IBond.
|
protected static IAtomContainer |
AbstractMolecularDescriptor.clone(IAtomContainer mol) |
boolean |
AbstractBondDescriptor.isCachedAtomContainer(IAtomContainer container)
Returns true if the cached IDescriptorResult's are for the given IAtomContainer.
|
boolean |
AbstractAtomicDescriptor.isCachedAtomContainer(IAtomContainer container)
Returns true if the cached IDescriptorResult's are for the given IAtomContainer.
|
void |
DescriptorEngine.process(IAtomContainer molecule)
Calculates all available (or only those specified) descriptors for a molecule.
|
| Modifier and Type | Method and Description |
|---|---|
DescriptorValue |
IPAtomicLearningDescriptor.calculate(IAtom atom,
IAtomContainer container)
Deprecated.
This method calculates the ionization potential of an atom.
|
DescriptorValue |
PartialTChargeMMFF94Descriptor.calculate(IAtom atom,
IAtomContainer org)
The method returns partial charges assigned to an heavy atom through
MMFF94 method.
|
DescriptorValue |
IPAtomicHOSEDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the ionization potential of an atom.
|
DescriptorValue |
CovalentRadiusDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the Covalent radius of an atom.
|
DescriptorValue |
RDFProtonDescriptor_GDR.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
DescriptorValue |
RDFProtonDescriptor_GHR.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
DescriptorValue |
AtomValenceDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the valence of an atom.
|
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 |
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 |
AtomHybridizationDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the hybridization of an atom.
|
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 |
DistanceToAtomDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculate the 3D distance between two atoms.
|
DescriptorValue |
VdWRadiusDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculate the Van der Waals radius of an atom.
|
DescriptorValue |
InductiveAtomicHardnessDescriptor.calculate(IAtom atom,
IAtomContainer ac)
It is needed to call the addExplicitHydrogensToSatisfyValency method from
the class tools.HydrogenAdder, and 3D coordinates.
|
DescriptorValue |
BondsToAtomDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculate the number of bonds on the shortest path between two atoms.
|
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 |
RDFProtonDescriptor_GSR.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
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 |
ProtonAffinityHOSEDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the protonation affinity of an atom.
|
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 |
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_GHR_topol.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
DescriptorValue |
PeriodicTablePositionDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the period of an atom.
|
DescriptorValue |
AtomHybridizationVSEPRDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the hybridization 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 |
AtomDegreeDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the number of not-H substituents of an atom.
|
DescriptorValue |
RDFProtonDescriptor_G3R.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
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 |
PartialTChargePEOEDescriptor.calculate(IAtom atom,
IAtomContainer ac)
The method returns partial total charges assigned to an heavy atom through PEOE method.
|
DescriptorValue |
RDFProtonDescriptor_GDR.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_GHR.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_GSR.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_GHR_topol.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_G3R.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
| Modifier and Type | Method and Description |
|---|---|
DescriptorValue |
PiContactDetectionDescriptor.calculate(IAtom first,
IAtom second,
IAtomContainer atomContainer)
The method returns if two atoms have pi-contact.
|
| Modifier and Type | Method and Description |
|---|---|
DescriptorValue |
IPBondLearningDescriptor.calculate(IBond bond,
IAtomContainer atomContainer)
Deprecated.
This method calculates the ionization potential of a bond.
|
DescriptorValue |
AtomicNumberDifferenceDescriptor.calculate(IBond bond,
IAtomContainer ac) |
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 |
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 |
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.
|
| Modifier and Type | Method and Description |
|---|---|
protected Double |
JPlogPDescriptor.JPlogPCalculator.calcLogP(IAtomContainer struct)
Given a structure in the correct configuration (explicit H and aromatised) it will return the logP as a Double
or if it is out of domain (encounters an unknown atomtype) it will return Double.NaN
|
DescriptorValue |
IPMolecularLearningDescriptor.calculate(IAtomContainer atomContainer)
Deprecated.
It calculates the first ionization energy of a molecule.
|
DescriptorValue |
AminoAcidCountDescriptor.calculate(IAtomContainer ac)
Determine the number of amino acids groups the supplied
IAtomContainer. |
DescriptorValue |
BondCountDescriptor.calculate(IAtomContainer container)
This method calculate the number of bonds of a given type in an atomContainer
|
DescriptorValue |
HBondAcceptorCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the number of H bond acceptors.
|
DescriptorValue |
AutocorrelationDescriptorPolarizability.calculate(IAtomContainer container)
This method calculate the ATS Autocorrelation descriptor.
|
DescriptorValue |
AromaticAtomsCountDescriptor.calculate(IAtomContainer atomContainer)
Calculate the count of aromatic atoms in the supplied
IAtomContainer. |
DescriptorValue |
KappaShapeIndicesDescriptor.calculate(IAtomContainer container)
calculates the kier shape indices for an atom container
|
DescriptorValue |
FragmentComplexityDescriptor.calculate(IAtomContainer container)
Calculate the complexity in the supplied
IAtomContainer. |
DescriptorValue |
AutocorrelationDescriptorMass.calculate(IAtomContainer atomContainer)
This method calculate the ATS Autocorrelation descriptor.
|
DescriptorValue |
LargestPiSystemDescriptor.calculate(IAtomContainer container)
Calculate the count of atoms of the largest pi system in the supplied
IAtomContainer. |
DescriptorValue |
FractionalPSADescriptor.calculate(IAtomContainer mol)
Calculates the topological polar surface area and expresses it as a ratio to molecule size.
|
DescriptorValue |
ChiPathClusterDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
CarbonTypesDescriptor.calculate(IAtomContainer container)
Calculates the 9 carbon types descriptors
|
DescriptorValue |
ChiChainDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
LengthOverBreadthDescriptor.calculate(IAtomContainer atomContainer)
Evaluate the descriptor for the molecule.
|
DescriptorValue |
GravitationalIndexDescriptor.calculate(IAtomContainer container)
Calculates the 9 gravitational indices.
|
DescriptorValue |
CPSADescriptor.calculate(IAtomContainer atomContainer)
Evaluates the 29 CPSA descriptors using Gasteiger-Marsilli charges.
|
DescriptorValue |
AutocorrelationDescriptorCharge.calculate(IAtomContainer atomContainer) |
DescriptorValue |
TPSADescriptor.calculate(IAtomContainer atomContainer)
Calculates the TPSA for an atom container.
|
DescriptorValue |
FMFDescriptor.calculate(IAtomContainer container)
Calculates the FMF descriptor value for the given
IAtomContainer. |
DescriptorValue |
MomentOfInertiaDescriptor.calculate(IAtomContainer container)
Calculates the 3 MI's, 3 ration and the R_gyr value.
|
DescriptorValue |
RotatableBondsCountDescriptor.calculate(IAtomContainer ac)
The method calculates the number of rotatable bonds of an atom container.
|
DescriptorValue |
ChiPathDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
WeightDescriptor.calculate(IAtomContainer container)
Calculate the natural weight of specified elements type in the supplied
IAtomContainer. |
DescriptorValue |
WeightedPathDescriptor.calculate(IAtomContainer container)
Calculates the weighted path descriptors.
|
DescriptorValue |
ZagrebIndexDescriptor.calculate(IAtomContainer atomContainer)
Evaluate the Zagreb Index for a molecule.
|
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 |
APolDescriptor.calculate(IAtomContainer container)
Calculate the sum of atomic polarizabilities in an
IAtomContainer. |
DescriptorValue |
XLogPDescriptor.calculate(IAtomContainer atomContainer)
Calculates the xlogP for an atom container.
|
DescriptorValue |
AcidicGroupCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the descriptor value for the given IAtomContainer.
|
DescriptorValue |
LargestChainDescriptor.calculate(IAtomContainer atomContainer)
Calculate the count of atoms of the largest chain in the supplied
IAtomContainer. |
DescriptorValue |
JPlogPDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
VAdjMaDescriptor.calculate(IAtomContainer atomContainer)
calculates the VAdjMa descriptor for an atom container
|
DescriptorValue |
EccentricConnectivityIndexDescriptor.calculate(IAtomContainer container)
Calculates the eccentric connectivity
|
DescriptorValue |
VABCDescriptor.calculate(IAtomContainer atomContainer)
Calculates the descriptor value using the
VABCVolume class. |
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 |
SpiroAtomCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the descriptor value for the given IAtomContainer.
|
DescriptorValue |
PetitjeanShapeIndexDescriptor.calculate(IAtomContainer container)
Calculates the two Petitjean shape indices.
|
DescriptorValue |
PetitjeanNumberDescriptor.calculate(IAtomContainer atomContainer)
Evaluate the descriptor for the molecule.
|
DescriptorValue |
FractionalCSP3Descriptor.calculate(IAtomContainer mol)
Calculates the Fsp3 descriptor value for the given
IAtomContainer. |
DescriptorValue |
BasicGroupCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the descriptor value for the given IAtomContainer.
|
DescriptorValue |
BCUTDescriptor.calculate(IAtomContainer container)
Calculates the three classes of BCUT descriptors.
|
DescriptorValue |
HBondDonorCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the number of H bond donors.
|
DescriptorValue |
KierHallSmartsDescriptor.calculate(IAtomContainer container)
This method calculates occurrences of the Kier & Hall E-state fragments.
|
DescriptorValue |
WHIMDescriptor.calculate(IAtomContainer container)
Calculates 11 directional and 6 non-directional WHIM descriptors for.
|
DescriptorValue |
ALOGPDescriptor.calculate(IAtomContainer container)
The AlogP descriptor.
|
DescriptorValue |
MDEDescriptor.calculate(IAtomContainer container)
Calculate the weight of specified element type in the supplied
IAtomContainer. |
DescriptorValue |
LongestAliphaticChainDescriptor.calculate(IAtomContainer mol)
Calculate the count of atoms of the longest aliphatic chain in the supplied
IAtomContainer. |
DescriptorValue |
AromaticBondsCountDescriptor.calculate(IAtomContainer atomContainer)
Calculate the count of aromatic atoms in the supplied
IAtomContainer. |
DescriptorValue |
AtomCountDescriptor.calculate(IAtomContainer container)
This method calculate the number of atoms of a given type in an
IAtomContainer. |
DescriptorValue |
HybridizationRatioDescriptor.calculate(IAtomContainer container)
Calculate sp3/sp2 hybridization ratio in the supplied
IAtomContainer. |
DescriptorValue |
ChiClusterDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
SmallRingDescriptor.calculate(IAtomContainer mol)
Performs the calculation: the graph will be analyzed and ring information will be determined and wrapped
up into descriptors.
|
DescriptorValue |
MannholdLogPDescriptor.calculate(IAtomContainer atomContainer)
Calculates the Mannhold LogP for an atom container.
|
DescriptorValue |
WienerNumbersDescriptor.calculate(IAtomContainer atomContainer)
Calculate the Wiener numbers.
|
DescriptorValue |
IPMolecularLearningDescriptor.calculatePlus(IAtomContainer container)
Deprecated.
It calculates the 1,2,..
|
Map<Integer,Integer> |
JPlogPDescriptor.JPlogPCalculator.getMappedHologram(IAtomContainer struct)
Used in Training the model
|
| Modifier and Type | Method and Description |
|---|---|
DescriptorValue |
TaeAminoAcidDescriptor.calculate(IAtomContainer container)
Calculates the 147 TAE descriptors for amino acids.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
RendererModel.getClipboardContent()
Returns the atoms and bonds on the Renderer2D clipboard.
|
IAtomContainer |
RendererModel.getExternalSelectedPart()
Get externally selected atoms.
|
| Modifier and Type | Method and Description |
|---|---|
List<IGenerator<IAtomContainer>> |
AtomContainerRenderer.getGenerators()
Returns a
List of IGenerators for this renderer. |
| Modifier and Type | Method and Description |
|---|---|
static Rectangle2D |
BoundsCalculator.calculateBounds(IAtomContainer atomContainer)
Calculate the bounding rectangle for an atom container.
|
Rectangle |
AtomContainerRenderer.calculateDiagramBounds(IAtomContainer atomContainer)
Given a
IChemObject, calculates the bounding rectangle in screen
space. |
Rectangle |
AtomContainerRenderer.paint(IAtomContainer atomContainer,
IDrawVisitor drawVisitor)
Paint an IChemObject.
|
void |
AtomContainerRenderer.paint(IAtomContainer atomContainer,
IDrawVisitor drawVisitor,
Rectangle2D bounds,
boolean resetCenter)
Paint a molecule (an IAtomContainer).
|
void |
RendererModel.setClipboardContent(IAtomContainer content)
Sets the atoms and bonds on the Renderer2D clipboard.
|
void |
RendererModel.setExternalSelectedPart(IAtomContainer externalSelectedPart)
Set externally selected atoms.
|
void |
AtomContainerRenderer.setScale(IAtomContainer atomContainer)
Set the scale for an IAtomContainer.
|
void |
AtomContainerRenderer.setup(IAtomContainer atomContainer,
Rectangle screen)
Setup the transformations necessary to draw this Atom Container.
|
| Constructor and Description |
|---|
AtomContainerRenderer(List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager)
A renderer that generates diagrams using the specified
generators and manages fonts with the supplied font manager.
|
AtomContainerRenderer(RendererModel rendererModel,
List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager) |
ChemModelRenderer(List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager)
A renderer that generates diagrams using the specified
generators and manages fonts with the supplied font manager.
|
ChemModelRenderer(List<IGenerator<IAtomContainer>> generators,
List<IGenerator<IReaction>> reactionGenerators,
IFontManager fontManager) |
MoleculeSetRenderer(List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager)
A renderer that generates diagrams using the specified
generators and manages fonts with the supplied font manager.
|
MoleculeSetRenderer(RendererModel rendererModel,
List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager) |
ReactionRenderer(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,
List<IGenerator<IReaction>> reactionGenerators,
IFontManager fontManager)
A renderer that draws
IReactions with the passed IGenerator
for both IAtomContainer and IReaction content. |
ReactionRenderer(RendererModel rendererModel,
List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager) |
ReactionSetRenderer(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,
List<IGenerator<IReaction>> reactionGenerators,
IFontManager fontManager)
A renderer that generates diagrams using the specified
generators for
IAtomContainers and IReactionSets
and manages fonts with the supplied font manager. |
ReactionSetRenderer(RendererModel rendererModel,
List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager) |
ReactionSetRenderer(RendererModel rendererModel,
List<IGenerator<IAtomContainer>> generators,
List<IGenerator<IReaction>> reactionGenerators,
IFontManager fontManager) |
| Modifier and Type | Method and Description |
|---|---|
static MarkedElement |
MarkedElement.markupMol(IRenderingElement elem,
IAtomContainer mol)
Markup a molecule with the class 'mol' and optionally the ids/classes
from it's properties.
|
| Modifier and Type | Method and Description |
|---|---|
protected boolean |
BasicAtomGenerator.canDraw(IAtom atom,
IAtomContainer container,
RendererModel model)
Checks an atom to see if it should be drawn.
|
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 |
HighlightGenerator.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 |
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 |
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 |
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 |
BasicSceneGenerator.generate(IAtomContainer ac,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
BasicGenerator.generate(IAtomContainer ac,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
BasicBondGenerator.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. |
protected IRingSet |
BasicBondGenerator.getRingSet(IAtomContainer atomContainer)
Determine the ring set for this atom container.
|
protected boolean |
BasicAtomGenerator.invisibleCarbon(IAtom atom,
IAtomContainer atomContainer,
RendererModel model)
Checks an atom to see if it is an 'invisible carbon' - that is, it is:
a) a carbon atom and b) this carbon should not be shown.
|
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.
|
protected boolean |
BasicAtomGenerator.showCarbon(IAtom carbonAtom,
IAtomContainer container,
RendererModel model)
Checks a carbon atom to see if it should be shown.
|
| Modifier and Type | Method and Description |
|---|---|
IRenderingElement |
StandardGenerator.generate(IAtomContainer container,
RendererModel parameters)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
IChemObjectSelection.getConnectedAtomContainer()
Make an IAtomContainer where all the bonds
only have atoms that are in the selection.
|
| Modifier and Type | Method and Description |
|---|---|
protected void |
AbstractSelection.addToAtomContainer(IAtomContainer ac,
IChemObject item)
Utility method to add an
IChemObject to an IAtomContainer. |
| Modifier and Type | Method and Description |
|---|---|
static IAtomContainer |
RingPartitioner.convertToAtomContainer(IRingSet ringSet)
Converts a RingSet to an AtomContainer.
|
IAtomContainer |
RingSearch.ringFragments()
Extract the cyclic atom and bond fragments of the container.
|
| Modifier and Type | Method and Description |
|---|---|
List<IAtomContainer> |
RingSearch.fusedRingFragments()
Construct a list of
IAtomContainers which only contain fused
rings. |
List<IAtomContainer> |
RingSearch.isolatedRingFragments()
Construct a list of
IAtomContainers each of which only contains a
single isolated ring. |
| Modifier and Type | Method and Description |
|---|---|
IRingSet |
AllRingsFinder.findAllRings(IAtomContainer container)
Compute all rings in the given
IAtomContainer. |
IRingSet |
AllRingsFinder.findAllRings(IAtomContainer container,
int maxRingSize)
Compute all rings up to and including the maxRingSize.
|
IRingSet |
AllRingsFinder.findAllRingsInIsolatedRingSystem(IAtomContainer container)
Compute all rings in the given
IAtomContainer. |
IRingSet |
AllRingsFinder.findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer,
int maxRingSize)
Compute all rings up to an including the maxRingSize.
|
IRingSet |
FiguerasSSSRFinder.findSSSR(IAtomContainer mol)
Deprecated.
Finds the Smallest Set of Smallest Rings.
|
| Constructor and Description |
|---|
RingSearch(IAtomContainer container)
Create a new RingSearch for the specified container.
|
RingSearch(IAtomContainer container,
CyclicVertexSearch searcher)
Create a new RingSearch for the specified container using the provided
search.
|
RingSearch(IAtomContainer container,
int[][] graph)
Create a new RingSearch for the specified container and graph.
|
SSSRFinder(IAtomContainer container)
Deprecated.
Constructs a SSSRFinder for a specified molecule.
|
| Modifier and Type | Method and Description |
|---|---|
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.
|
| Constructor and Description |
|---|
AtomSignature(IAtom atom,
IAtomContainer molecule)
Create an atom signature for the atom
atom. |
AtomSignature(IAtom atom,
int height,
signature.AbstractVertexSignature.InvariantType invariantType,
IAtomContainer molecule)
Create an atom signature for the atom
atom, with maximum
height of height, and using a particular invariant type. |
AtomSignature(IAtom atom,
int height,
IAtomContainer molecule)
Create an atom signature for the atom
atom and with a
maximum height of height. |
AtomSignature(int atomIndex,
IAtomContainer molecule)
Create an atom signature starting at
atomIndex. |
AtomSignature(int atomIndex,
int height,
signature.AbstractVertexSignature.InvariantType invariantType,
IAtomContainer molecule)
Create an atom signature starting at
atomIndex, with maximum
height of height, and using a particular invariant type. |
AtomSignature(int atomIndex,
int height,
IAtomContainer molecule)
Create an atom signature starting at
atomIndex and with a
maximum height of height. |
MoleculeSignature(IAtomContainer molecule)
Creates a signature that represents this molecule.
|
MoleculeSignature(IAtomContainer molecule,
int height)
Creates a signature with a maximum height of
height
for molecule molecule. |
SignatureQuotientGraph(IAtomContainer atomContainer)
Construct a quotient graph from the symmetry classes generated from the
atom container.
|
SignatureQuotientGraph(IAtomContainer atomContainer,
int height)
Construct a quotient graph using symmetry classes defined by signatures
of height
height. |
| Modifier and Type | Field and Description |
|---|---|
protected IAtomContainer[] |
AtomContainerSet.atomContainers
Array of AtomContainers.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
AtomContainer.clone()
Clones this
IChemObject. |
IAtomContainer |
AtomContainerSet.getAtomContainer(int number)
Returns the AtomContainer at position
number in the
container. |
IAtomContainer |
Atom.getContainer()
Access the
IAtomContainer of which this atom is a member of. |
IAtomContainer |
Bond.getContainer() |
IAtomContainer |
FragmentAtom.getFragment() |
IAtomContainer |
SilentChemObjectBuilder.newAtomContainer()
Create a new atom container using the default constructor.
|
| Modifier and Type | Method and Description |
|---|---|
Iterable<IAtomContainer> |
AtomContainerSet.atomContainers()
Get an iterator for this AtomContainerSet.
|
| Modifier and Type | Method and Description |
|---|---|
void |
AtomContainer.add(IAtomContainer that)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
void |
Reaction.addAgent(IAtomContainer agent)
Adds an agent to this reaction.
|
void |
AtomContainerSet.addAtomContainer(IAtomContainer atomContainer)
Adds an atomContainer to this container.
|
void |
AtomContainerSet.addAtomContainer(IAtomContainer atomContainer,
double multiplier)
Adds an atomContainer to this container with the given
multiplier.
|
void |
Reaction.addProduct(IAtomContainer product)
Adds a product to this reaction.
|
void |
Reaction.addProduct(IAtomContainer product,
Double coefficient)
Adds a product to this reaction.
|
void |
Reaction.addReactant(IAtomContainer reactant)
Adds a reactant to this reaction.
|
void |
Reaction.addReactant(IAtomContainer reactant,
Double coefficient)
Adds a reactant to this reaction with a stoichiometry coefficient.
|
boolean |
RingSet.contains(IAtomContainer ring)
Checks for presence of a ring in this RingSet.
|
Double |
AtomContainerSet.getMultiplier(IAtomContainer container)
Returns the multiplier of the given AtomContainer.
|
Double |
Reaction.getProductCoefficient(IAtomContainer product)
Returns the stoichiometry coefficient of the given product.
|
Double |
Reaction.getReactantCoefficient(IAtomContainer reactant)
Returns the stoichiometry coefficient of the given reactant.
|
void |
AtomContainer.remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
AtomContainerSet.removeAtomContainer(IAtomContainer atomContainer)
Removes an AtomContainer from this container.
|
void |
AtomContainerSet.replaceAtomContainer(int position,
IAtomContainer container)
Replace the AtomContainer at a specific position (array has to be large enough).
|
void |
FragmentAtom.setFragment(IAtomContainer fragment) |
boolean |
AtomContainerSet.setMultiplier(IAtomContainer container,
Double multiplier)
Sets the coefficient of a AtomContainer to a given value.
|
boolean |
Reaction.setProductCoefficient(IAtomContainer product,
Double coefficient)
Sets the coefficient of a a product to a given value.
|
boolean |
Reaction.setReactantCoefficient(IAtomContainer reactant,
Double coefficient)
Sets the coefficient of a a reactant to a given value.
|
| Modifier and Type | Method and Description |
|---|---|
void |
AtomContainerSet.sortAtomContainers(Comparator<IAtomContainer> comparator)
Sort the AtomContainers and multipliers using a provided Comparator
|
| Constructor and Description |
|---|
AtomContainer(IAtomContainer container)
Constructs an AtomContainer with a copy of the atoms and electronContainers
of another AtomContainer (A shallow copy, i.e., with the same objects as in
the original AtomContainer).
|
Crystal(IAtomContainer container)
Constructs a new crystal with zero length cell axis
and adds the atoms in the AtomContainer as cell content.
|
Ring(IAtomContainer atomContainer)
Constructs a ring from the atoms in an IAtomContainer object.
|
| Modifier and Type | Method and Description |
|---|---|
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 |
|---|---|
static String |
Smarts.generate(IAtomContainer mol)
Generate a SMARTS string from the provided molecule.
|
int[] |
SmartsPattern.match(IAtomContainer container)
Find a matching of this pattern in the
target. |
Mappings |
SmartsPattern.matchAll(IAtomContainer target)
Obtain the mappings of the query pattern against the target compound.
|
static boolean |
Smarts.parse(IAtomContainer mol,
String smarts)
Parse the provided SMARTS string appending query atom/bonds to the
provided molecule.
|
static boolean |
Smarts.parse(IAtomContainer mol,
String smarts,
int flavor)
Parse the provided SMARTS string appending query atom/bonds to the
provided molecule.
|
static void |
SmartsPattern.prepare(IAtomContainer target) |
| Constructor and Description |
|---|
SmartsFragmentExtractor(IAtomContainer mol)
Create a new instance over the provided molecule.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
DeduceBondSystemTool.fixAromaticBondOrders(IAtomContainer atomContainer)
Deprecated.
Added missing bond orders based on atom type information.
|
IAtomContainer |
FixBondOrdersTool.kekuliseAromaticRings(IAtomContainer molecule)
Deprecated.
kekuliseAromaticRings - function to add double/single bond order information for molecules having rings containing all atoms marked SP2 or Planar3 hybridisation.
|
IAtomContainer |
SmilesParser.parseSmiles(String smiles)
Parses a SMILES string and returns a structure (
IAtomContainer). |
| Modifier and Type | Method and Description |
|---|---|
String |
SmilesGenerator.create(IAtomContainer molecule)
Generate SMILES for the provided
molecule. |
String |
SmilesGenerator.create(IAtomContainer molecule,
int[] order)
Creates a SMILES string of the flavour specified in the constructor
and write the output order to the provided array.
|
static String |
SmilesGenerator.create(IAtomContainer molecule,
int flavour,
int[] order)
Creates a SMILES string of the flavour specified as a parameter
and write the output order to the provided array.
|
static Comparator<IAtom> |
SmilesGenerator.createComparator(IAtomContainer mol,
int flavor) |
String |
SmilesGenerator.createSMILES(IAtomContainer molecule)
Deprecated.
use #create
|
IAtomContainer |
DeduceBondSystemTool.fixAromaticBondOrders(IAtomContainer atomContainer)
Deprecated.
Added missing bond orders based on atom type information.
|
boolean |
DeduceBondSystemTool.isOK(IAtomContainer m)
Deprecated.
Determines if, according to the algorithms implemented in this class, the given
AtomContainer has properly distributed double bonds.
|
IAtomContainer |
FixBondOrdersTool.kekuliseAromaticRings(IAtomContainer molecule)
Deprecated.
kekuliseAromaticRings - function to add double/single bond order information for molecules having rings containing all atoms marked SP2 or Planar3 hybridisation.
|
| Modifier and Type | Method and Description |
|---|---|
int[] |
SmartsPattern.match(IAtomContainer container)
Deprecated.
Find a matching of this pattern in the
target. |
Mappings |
SmartsPattern.matchAll(IAtomContainer target)
Deprecated.
Obtain the mappings of the query pattern against the target compound.
|
boolean |
SMARTSQueryTool.matches(IAtomContainer atomContainer)
Deprecated.
Perform a SMARTS match and check whether the query is present in the target molecule.
|
boolean |
SMARTSQueryTool.matches(IAtomContainer atomContainer,
boolean forceInitialization)
Deprecated.
Perform a SMARTS match and check whether the query is present in the target molecule.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
Isomorphism.getProductMolecule()
Deprecated.
Returns modified target molecule on which mapping was
performed.
|
IAtomContainer |
Isomorphism.getReactantMolecule()
Deprecated.
Returns modified query molecule on which mapping was
performed.
|
| Modifier and Type | Method and Description |
|---|---|
void |
Isomorphism.init(IAtomContainer reactant,
IAtomContainer product,
boolean removeHydrogen,
boolean cleanAndConfigureMolecule)
Deprecated.
initialize query and target molecules.
|
void |
Isomorphism.init(IQueryAtomContainer reactant,
IAtomContainer product)
Deprecated.
|
static Map<IBond,IBond> |
Isomorphism.makeBondMapOfAtomMap(IAtomContainer ac1,
IAtomContainer ac2,
Map<IAtom,IAtom> mapping)
Deprecated.
Returns bond map between source and target molecules based on the atoms
|
static List<Map<IBond,IBond>> |
Isomorphism.makeBondMapsOfAtomMaps(IAtomContainer ac1,
IAtomContainer ac2,
List<Map<IAtom,IAtom>> mappings)
Deprecated.
Returns bond maps between source and target molecules based on the atoms
|
| Modifier and Type | Method and Description |
|---|---|
static boolean |
DefaultMatcher.isAtomMatch(AtomMatcher atomMatcher1,
AtomMatcher atomMatcher2,
IAtomContainer ac2,
IBond bondA2,
boolean shouldMatchBonds)
Deprecated.
|
static boolean |
DefaultMatcher.isBondMatch(BondMatcher bondMatcher,
IAtomContainer ac2,
IBond bondA2,
boolean shouldMatchBonds)
Deprecated.
|
boolean |
DefaultMCSPlusAtomMatcher.matches(IAtomContainer targetContainer,
IAtom targetAtom)
Deprecated.
|
boolean |
AtomMatcher.matches(IAtomContainer container,
IAtom atom)
Deprecated.
|
boolean |
DefaultRGraphAtomMatcher.matches(IAtomContainer targetContainer,
IAtom targetAtom)
Deprecated.
|
boolean |
BondMatcher.matches(IAtomContainer container,
IBond atom)
Deprecated.
|
boolean |
DefaultBondMatcher.matches(IAtomContainer targetContainer,
IBond targetBond)
Deprecated.
|
| Constructor and Description |
|---|
DefaultBondMatcher(IAtomContainer queryMol,
IBond queryBond,
boolean shouldMatchBonds)
Deprecated.
Constructor
|
DefaultMCSPlusAtomMatcher(IAtomContainer queryContainer,
IAtom atom,
boolean shouldMatchBonds)
Deprecated.
Constructor
|
DefaultMCSPlusAtomMatcher(IAtomContainer queryContainer,
IAtom template,
int blockedPositions,
boolean shouldMatchBonds)
Deprecated.
Constructor
|
DefaultRGraphAtomMatcher(IAtomContainer queryContainer,
IAtom atom,
boolean shouldMatchBonds)
Deprecated.
Constructor
|
DefaultRGraphAtomMatcher(IAtomContainer queryContainer,
IAtom template,
int blockedPositions,
boolean shouldMatchBonds)
Deprecated.
Constructor
|
DefaultVFAtomMatcher(IAtomContainer queryContainer,
IAtom atom,
boolean shouldMatchBonds)
Deprecated.
Constructor
|
DefaultVFAtomMatcher(IAtomContainer queryContainer,
IAtom template,
int blockedPositions,
boolean shouldMatchBonds)
Deprecated.
Constructor
|
DefaultVFBondMatcher(IAtomContainer queryMol,
IBond queryBond,
boolean shouldMatchBonds)
Deprecated.
Constructor
|
| Modifier and Type | Method and Description |
|---|---|
protected static int |
McGregorChecks.changeCharBonds(int correspondingAtom,
String newSymbol,
int neighborBondNum,
IAtomContainer atomContainer,
List<String> cBondNeighbors)
Deprecated.
|
protected static List<String> |
McGregorChecks.generateCTabCopy(IAtomContainer atomContainer)
Deprecated.
|
protected static boolean |
McGregorChecks.isFurtherMappingPossible(IAtomContainer source,
IAtomContainer target,
int neighborBondNumA,
int neighborBondNumB,
List<Integer> iBondNeighborAtomsA,
List<Integer> iBondNeighborAtomsB,
List<String> cBondNeighborsA,
List<String> cBondNeighborsB,
boolean shouldMatchBonds)
Deprecated.
|
protected static boolean |
McGregorChecks.isMatchFeasible(IAtomContainer ac1,
IBond bondA1,
IAtomContainer ac2,
IBond bondA2,
boolean shouldMatchBonds)
Deprecated.
|
protected void |
QueryProcessor.process(IAtomContainer query,
IAtomContainer target,
List<Integer> unmappedAtomsMolA,
List<Integer> mappedAtoms,
int counter)
Deprecated.
|
protected void |
TargetProcessor.process(IAtomContainer target,
List<Integer> unmappedAtomsMolB,
int mappingSize,
List<Integer> iBondSetB,
List<String> cBondSetB,
List<Integer> mappedAtoms,
int counter)
Deprecated.
|
protected void |
QueryProcessor.process(IQueryAtomContainer query,
IAtomContainer target,
List<Integer> unmappedAtomsMolA,
List<Integer> mappedAtoms,
int counter)
Deprecated.
|
protected static List<Integer> |
McGregorChecks.setArcs(IAtomContainer source,
IAtomContainer target,
int neighborBondNumA,
int neighborBondNumB,
List<Integer> iBondNeighborAtomsA,
List<Integer> iBondNeighborAtomsB,
List<String> cBondNeighborsA,
List<String> cBondNeighborsB,
List<Integer> modifiedARCS,
boolean shouldMatchBonds)
Deprecated.
|
| Constructor and Description |
|---|
McGregor(IAtomContainer source,
IAtomContainer target,
List<List<Integer>> mappings,
boolean shouldMatchBonds)
Deprecated.
Constructor for the McGregor algorithm.
|
McGregor(IQueryAtomContainer source,
IAtomContainer target,
List<List<Integer>> mappings)
Deprecated.
Constructor for the McGregor algorithm.
|
| Modifier and Type | Method and Description |
|---|---|
protected List<List<Integer>> |
MCSPlus.getOverlaps(IAtomContainer ac1,
IAtomContainer ac2,
boolean shouldMatchBonds)
Deprecated.
|
void |
MCSPlusHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
Initialise the query and target molecule.
|
| Constructor and Description |
|---|
GenerateCompatibilityGraph(IAtomContainer source,
IAtomContainer target,
boolean shouldMatchBonds)
Deprecated.
Generates a compatibility graph between two molecules
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
CDKRMapHandler.getSource()
Deprecated.
Returns source molecule
|
IAtomContainer |
CDKRMapHandler.getTarget()
Deprecated.
Returns target molecule
|
static IAtomContainer |
CDKMCS.project(List<CDKRMap> rMapList,
IAtomContainer graph,
int key)
Deprecated.
Projects atom list of CDKRMap on atom molecule.
|
| Modifier and Type | Method and Description |
|---|---|
static List<IAtomContainer> |
CDKMCS.getOverlaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns all the maximal common substructure between 2 atom containers.
|
static ArrayList<IAtomContainer> |
CDKMCS.projectList(List<List<CDKRMap>> rMapsList,
IAtomContainer graph,
int key)
Deprecated.
Projects atom list of RMapsList on atom molecule.
|
| Modifier and Type | Method and Description |
|---|---|
static CDKRGraph |
CDKMCS.buildRGraph(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Builds the CDKRGraph ( resolution graph ), from two atomContainer
(description of the two molecules to compare)
This is the interface point between the CDK model and
the generic MCSS algorithm based on the RGRaph.
|
void |
CDKRMapHandler.calculateIsomorphs(IAtomContainer molecule1,
IAtomContainer molecule2,
boolean shouldMatchBonds)
Deprecated.
This function calculates only one solution (exact) because we are looking at the
molecules which are exactly same in terms of the bonds and atoms determined by the
Fingerprint
|
void |
CDKRMapHandler.calculateOverlapsAndReduce(IAtomContainer molecule1,
IAtomContainer molecule2,
boolean shouldMatchBonds)
Deprecated.
This function calculates all the possible combinations of MCS
|
void |
CDKRMapHandler.calculateOverlapsAndReduceExactMatch(IAtomContainer molecule1,
IAtomContainer molecule2,
boolean shouldMatchBonds)
Deprecated.
This function calculates only one solution (exact) because we are looking at the
molecules which are exactly same in terms of the bonds and atoms determined by the
Fingerprint
|
void |
CDKRMapHandler.calculateSubGraphs(IAtomContainer molecule1,
IAtomContainer molecule2,
boolean shouldMatchBonds)
Deprecated.
This function calculates only one solution (exact) because we are looking at the
molecules which are exactly same in terms of the bonds and atoms determined by the
Fingerprint
|
static List<CDKRMap> |
CDKMCS.checkSingleAtomCases(IAtomContainer sourceGraph,
IAtomContainer targetGraph)
Deprecated.
Checks for single atom cases before doing subgraph/isomorphism search
|
static BitSet |
CDKMCS.getBitSet(IAtomContainer atomContainer)
Deprecated.
Transforms an AtomContainer into atom BitSet (which's size = number of bondA1
in the atomContainer, all the bit are set to true).
|
static List<CDKRMap> |
CDKMCS.getIsomorphAtomsMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns the first isomorph 'atom mapping' found for targetGraph in sourceGraph.
|
static List<CDKRMap> |
CDKMCS.getIsomorphMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns the first isomorph mapping found or null.
|
static List<List<CDKRMap>> |
CDKMCS.getIsomorphMaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns all the isomorph 'mappings' found between two
atom containers.
|
static List<IAtomContainer> |
CDKMCS.getOverlaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns all the maximal common substructure between 2 atom containers.
|
static List<CDKRMap> |
CDKMCS.getSubgraphAtomsMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns the first subgraph 'atom mapping' found for targetGraph in sourceGraph.
|
static List<List<CDKRMap>> |
CDKMCS.getSubgraphAtomsMaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns all subgraph 'atom mappings' found for targetGraph in sourceGraph.
|
static List<CDKRMap> |
CDKMCS.getSubgraphMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns the first subgraph 'bondA1 mapping' found for targetGraph in sourceGraph.
|
static List<List<CDKRMap>> |
CDKMCS.getSubgraphMaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Returns all the subgraph 'bondA1 mappings' found for targetGraph in sourceGraph.
|
protected IAtomContainerSet |
CDKSubGraphHandler.getUncommon(IAtomContainer mol,
IAtomContainer mcss,
boolean shouldMatchBonds)
Deprecated.
|
protected IAtomContainerSet |
CDKMCSHandler.getUncommon(IAtomContainer mol,
IAtomContainer mcss,
boolean shouldMatchBonds)
Deprecated.
|
protected void |
CDKRMapHandler.identifyMatchedParts(List<List<CDKRMap>> list,
IAtomContainer source,
IAtomContainer target)
Deprecated.
|
protected void |
CDKRMapHandler.identifySingleAtomsMatchedParts(List<CDKRMap> list,
IAtomContainer source,
IAtomContainer target)
Deprecated.
|
static boolean |
CDKMCS.isIsomorph(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Tests if sourceGraph and targetGraph are isomorph.
|
static boolean |
CDKMCS.isSubgraph(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Deprecated.
Tests if targetGraph atom subgraph of sourceGraph.
|
static List<CDKRMap> |
CDKMCS.makeAtomsMapOfBondsMap(List<CDKRMap> list,
IAtomContainer sourceGraph,
IAtomContainer targetGraph)
Deprecated.
This makes atom map of matching atoms out of atom map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
|
static List<List<CDKRMap>> |
CDKMCS.makeAtomsMapsOfBondsMaps(List<List<CDKRMap>> list,
IAtomContainer sourceGraph,
IAtomContainer targetGraph)
Deprecated.
This makes maps of matching atoms out of atom maps of matching bonds as produced by the get(Subgraph|Ismorphism)Maps methods.
|
static IAtomContainer |
CDKMCS.project(List<CDKRMap> rMapList,
IAtomContainer graph,
int key)
Deprecated.
Projects atom list of CDKRMap on atom molecule.
|
static ArrayList<IAtomContainer> |
CDKMCS.projectList(List<List<CDKRMap>> rMapsList,
IAtomContainer graph,
int key)
Deprecated.
Projects atom list of RMapsList on atom molecule.
|
static List<List<CDKRMap>> |
CDKMCS.search(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
BitSet sourceBitSet,
BitSet targetBitSet,
boolean findAllStructure,
boolean findAllMap,
boolean shouldMatchBonds)
Deprecated.
General Rgraph parsing method (usually not used directly)
This method is the entry point for the recursive search
adapted to the atom container input.
|
void |
CDKSubGraphHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
Initialise the query and target molecule.
|
void |
CDKMCSHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
Initialise the query and target molecule.
|
void |
CDKRMapHandler.setSource(IAtomContainer aSource)
Deprecated.
Set source molecule
|
void |
CDKRMapHandler.setTarget(IAtomContainer aTarget)
Deprecated.
Set target molecule
|
| Modifier and Type | Method and Description |
|---|---|
protected List<Map<IAtom,IAtom>> |
SingleMapping.getOverLaps(IAtomContainer source,
IAtomContainer target,
boolean removeHydrogen)
Deprecated.
Returns single mapping solutions.
|
protected List<Map<IAtom,IAtom>> |
SingleMapping.getOverLaps(IQueryAtomContainer source,
IAtomContainer target,
boolean removeHydrogen)
Deprecated.
Returns single mapping solutions.
|
void |
SingleMappingHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
Initialise the query and target molecule.
|
| Modifier and Type | Method and Description |
|---|---|
void |
VFlibSubStructureHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
Initialise the query and target molecule.
|
void |
VFlibTurboHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
Initialise the query and target molecule.
|
void |
VFlibMCSHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
Initialise the query and target molecule.
|
| Constructor and Description |
|---|
TargetProperties(IAtomContainer container)
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
int |
IMapper.countMaps(IAtomContainer target)
Deprecated.
Returns solution map count.
|
Map<INode,IAtom> |
IMapper.getFirstMap(IAtomContainer target)
Deprecated.
Returns first solution map.
|
List<Map<INode,IAtom>> |
IMapper.getMaps(IAtomContainer target)
Deprecated.
Returns all solution map.
|
boolean |
IMapper.hasMap(IAtomContainer molecule)
Deprecated.
checks if a map exits for a molecule.
|
| Modifier and Type | Method and Description |
|---|---|
int |
VFMCSMapper.countMaps(IAtomContainer target)
Deprecated.
Returns solution map count.
|
int |
VFMapper.countMaps(IAtomContainer target)
Deprecated.
Returns solution map count.
|
Map<INode,IAtom> |
VFMCSMapper.getFirstMap(IAtomContainer target)
Deprecated.
Returns first solution map.
|
Map<INode,IAtom> |
VFMapper.getFirstMap(IAtomContainer target)
Deprecated.
Returns first solution map.
|
List<Map<INode,IAtom>> |
VFMCSMapper.getMaps(IAtomContainer target)
Deprecated.
Returns all solution map.
|
List<Map<INode,IAtom>> |
VFMapper.getMaps(IAtomContainer target)
Deprecated.
Returns all solution map.
|
boolean |
VFMCSMapper.hasMap(IAtomContainer targetMolecule)
Deprecated.
checks if a map exits for a molecule.
|
boolean |
VFMapper.hasMap(IAtomContainer targetMolecule)
Deprecated.
checks if a map exits for a molecule.
|
| Constructor and Description |
|---|
VFMapper(IAtomContainer queryMolecule,
boolean bondMatcher)
Deprecated.
|
VFMCSMapper(IAtomContainer queryMolecule,
boolean bondMatcher)
Deprecated.
|
| Constructor and Description |
|---|
QueryCompiler(IAtomContainer molecule,
boolean shouldMatchBonds)
Deprecated.
Construct query object from the molecule
|
| 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)
Deprecated.
This class has all the three chemical filters supported by the SMSD.
|
| Modifier and Type | Method and Description |
|---|---|
abstract IAtomContainer |
AbstractMCS.getProductMolecule()
Deprecated.
Returns modified target molecule on which mapping was
performed.
|
abstract IAtomContainer |
AbstractMCS.getReactantMolecule()
Deprecated.
Returns modified query molecule on which mapping was
performed.
|
| Modifier and Type | Method and Description |
|---|---|
abstract void |
AbstractMCS.init(IAtomContainer source,
IAtomContainer target,
boolean removeHydrogen,
boolean cleanAndConfigureMolecule)
Deprecated.
initialize query and target molecules.
|
abstract void |
AbstractMCS.init(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
initialize query and target molecules.
|
void |
IMCSBase.set(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
Initialise the query and target molecule.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
ICanonicalMoleculeLabeller.getCanonicalMolecule(IAtomContainer container)
Deprecated.
|
IAtomContainer |
MoleculeSignatureLabellingAdaptor.getCanonicalMolecule(IAtomContainer container)
Deprecated.
|
IAtomContainer |
CanonicalLabellingAdaptor.getCanonicalMolecule(IAtomContainer container)
Deprecated.
|
IAtomContainer |
AtomContainerAtomPermutor.next()
Deprecated.
|
static IAtomContainer |
AtomContainerAtomPermutor.permute(int[] p,
IAtomContainer atomContainer)
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
ICanonicalMoleculeLabeller.getCanonicalMolecule(IAtomContainer container)
Deprecated.
|
IAtomContainer |
MoleculeSignatureLabellingAdaptor.getCanonicalMolecule(IAtomContainer container)
Deprecated.
|
IAtomContainer |
CanonicalLabellingAdaptor.getCanonicalMolecule(IAtomContainer container)
Deprecated.
|
int[] |
ICanonicalMoleculeLabeller.getCanonicalPermutation(IAtomContainer container)
Deprecated.
|
int[] |
MoleculeSignatureLabellingAdaptor.getCanonicalPermutation(IAtomContainer container)
Deprecated.
|
int[] |
CanonicalLabellingAdaptor.getCanonicalPermutation(IAtomContainer container)
Deprecated.
|
static IAtomContainer |
AtomContainerAtomPermutor.permute(int[] p,
IAtomContainer atomContainer)
Deprecated.
|
String |
AtomContainerPrinter.toString(IAtomContainer atomContainer)
Deprecated.
|
| Constructor and Description |
|---|
AtomContainerAtomPermutor(IAtomContainer atomContainer)
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
void |
RingFilter.filterAtoms(IAtomContainer molecule,
Collection<IAtom> atoms)
Deprecated.
|
Collection<List<IAtom>> |
RingFinder.findRings(IAtomContainer molecule)
Deprecated.
Returns Collection of atoms in Rings based on Hanser Ring Finding method
|
Collection<List<IAtom>> |
HanserRingFinder.findRings(IAtomContainer molecule)
Deprecated.
Returns a collection of rings.
|
IRingSet |
RingFinder.getRingSet(IAtomContainer molecule)
Deprecated.
Returns CDK object Ring set based on Hanser Ring Finding method
|
IRingSet |
HanserRingFinder.getRingSet(IAtomContainer molecule)
Deprecated.
Returns Ring set based on Hanser Ring Finding method
|
| Constructor and Description |
|---|
PathGraph(IAtomContainer molecule)
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
static IAtomContainer |
MoleculeSanityCheck.checkAndCleanMolecule(IAtomContainer molecule)
Deprecated.
Modules for cleaning a molecule
|
static IAtomContainer |
ExtAtomContainerManipulator.convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
Deprecated.
Returns IAtomContainer without Hydrogen.
|
IAtomContainer |
MolHandler.getMolecule()
Deprecated.
Returns the modified container
|
static IAtomContainer |
ExtAtomContainerManipulator.makeDeepCopy(IAtomContainer container)
Deprecated.
Retrurns deep copy of the molecule
|
static IAtomContainer |
ExtAtomContainerManipulator.removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer atomContainer)
Deprecated.
Returns IAtomContainer without Hydrogen.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
ExtAtomContainerManipulator.aromatizeMolecule(IAtomContainer mol)
Deprecated.
This function finds rings and uses aromaticity detection code to
aromatize the molecule.
|
static IAtomContainer |
MoleculeSanityCheck.checkAndCleanMolecule(IAtomContainer molecule)
Deprecated.
Modules for cleaning a molecule
|
static void |
MoleculeSanityCheck.configure(IAtomContainer mol)
Deprecated.
Fixes Aromaticity of the molecule
i.e.
|
static IAtomContainer |
ExtAtomContainerManipulator.convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
Deprecated.
Returns IAtomContainer without Hydrogen.
|
static int |
ExtAtomContainerManipulator.getExplicitHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
Deprecated.
Returns The number of explicit hydrogens for a given IAtom.
|
static int |
ExtAtomContainerManipulator.getHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
Deprecated.
The summed implicit + explicit hydrogens of the given IAtom.
|
static IAtomContainer |
ExtAtomContainerManipulator.makeDeepCopy(IAtomContainer container)
Deprecated.
Retrurns deep copy of the molecule
|
static void |
ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Deprecated.
Convenience method to perceive atom types for all
IAtoms in the
IAtomContainer, using the CDKAtomTypeMatcher. |
static IAtomContainer |
ExtAtomContainerManipulator.removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer atomContainer)
Deprecated.
Returns IAtomContainer without Hydrogen.
|
| Constructor and Description |
|---|
MolHandler(IAtomContainer container,
boolean removeHydrogen,
boolean cleanMolecule)
Deprecated.
Creates a new instance of MolHandler
|
| Modifier and Type | Field and Description |
|---|---|
protected IAtomContainer |
StereoElementFactory.container
Native CDK structure representation.
|
| Modifier and Type | Method and Description |
|---|---|
IAtom[] |
ExtendedTetrahedral.findTerminalAtoms(IAtomContainer container)
Helper method to locate two terminal atoms in a container for this
extended tetrahedral element.
|
static IAtom[] |
ExtendedTetrahedral.findTerminalAtoms(IAtomContainer container,
IAtom focus)
Helper method to locate two terminal atoms in a container for a given
focus.
|
static IAtom[] |
ExtendedCisTrans.findTerminalAtoms(IAtomContainer container,
IBond focus)
Helper method to locate two terminal atoms in a container for this
extended Cis/Trans element.
|
static Stereocenters |
Stereocenters.of(IAtomContainer container)
Determine the stereocenter atoms in the provided container based on
connectivity.
|
static StereoElementFactory |
StereoElementFactory.using2DCoordinates(IAtomContainer container)
Create a stereo element factory for creating stereo elements using 2D
coordinates and depiction labels (up/down, wedge/hatch).
|
static StereoElementFactory |
StereoElementFactory.using3DCoordinates(IAtomContainer container)
Create a stereo element factory for creating stereo elements using 3D
coordinates and depiction labels (up/down, wedge/hatch).
|
| Constructor and Description |
|---|
StereoElementFactory(IAtomContainer container,
int[][] graph,
GraphUtil.EdgeToBondMap bondMap)
Internal constructor.
|
| Modifier and Type | Method and Description |
|---|---|
IAtomContainer |
SingleStructureRandomGenerator.generate()
Generates a random structure based on the atoms in the given IAtomContainer.
|
IAtomContainer |
RandomGenerator.getMolecule()
Returns the molecule which reflects the current state of this
stochastic structure generator.
|
IAtomContainer |
RandomGenerator.proposeStructure()
Proposes a structure which can be accepted or rejected by an external
entity.
|
| Modifier and Type | Method and Description |
|---|---|
static List<IAtomContainer> |
VicinitySampler.sample(IAtomContainer ac)
Choose any possible quadruple of the set of atoms
in ac and establish all of the possible bonding schemes according to
Faulon's equations.
|