Uses of Interface
org.openscience.cdk.interfaces.IAtomContainer
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Uses of IAtomContainer in org.openscience.cdk
Classes in org.openscience.cdk that implement IAtomContainer Modifier and Type Class 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.Fields in org.openscience.cdk declared as IAtomContainer Modifier and Type Field Description protected IAtomContainer[]
AtomContainerSet. atomContainers
Array of AtomContainers.Methods in org.openscience.cdk that return IAtomContainer Modifier and Type Method Description IAtomContainer
AtomContainer. clone()
Clones thisIChemObject
.IAtomContainer
ConformerContainer. get(int i)
Get the conformer at a specified position.IAtomContainer
AtomContainerSet. getAtomContainer(int number)
Returns the AtomContainer at positionnumber
in the container.IAtomContainer
Atom. getContainer()
Access theIAtomContainer
of which this atom is a member of.IAtomContainer
AtomRef. getContainer()
Access theIAtomContainer
of which this atom is a member of.IAtomContainer
Bond. getContainer()
IAtomContainer
BondRef. getContainer()
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)
Methods in org.openscience.cdk that return types with arguments of type IAtomContainer Modifier and Type Method 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)
Methods in org.openscience.cdk with parameters of type IAtomContainer Modifier and Type Method Description void
AtomContainer. add(IAtomContainer that)
Adds all atoms and electronContainers of a given atomcontainer to this container.void
ConformerContainer. add(int i, IAtomContainer atomContainer)
boolean
ConformerContainer. add(IAtomContainer atomContainer)
Add a conformer to the end of the list.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.Method parameters in org.openscience.cdk with type arguments of type IAtomContainer Modifier and Type Method Description boolean
ConformerContainer. addAll(int i, Collection<? extends IAtomContainer> iAtomContainers)
boolean
ConformerContainer. addAll(Collection<? extends IAtomContainer> atomContainers)
void
AtomContainerSet. sortAtomContainers(Comparator<IAtomContainer> comparator)
Sort the AtomContainers and multipliers using a provided Comparator.Constructors in org.openscience.cdk with parameters of type IAtomContainer Constructor 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. -
Uses of IAtomContainer in org.openscience.cdk.aromaticity
Methods in org.openscience.cdk.aromaticity with parameters of type IAtomContainer Modifier and Type Method Description boolean
Aromaticity. apply(IAtomContainer molecule)
Apply this aromaticity model to a molecule.static boolean
CDKHueckelAromaticityDetector. detectAromaticity(IAtomContainer atomContainer)
Deprecated.static boolean
DoubleBondAcceptingAromaticityDetector. detectAromaticity(IAtomContainer atomContainer)
Deprecated.Set<IBond>
Aromaticity. findBonds(IAtomContainer molecule)
Find the bonds of amolecule
which this model determined were aromatic.static boolean
AromaticityCalculator. isAromatic(IRing ring, IAtomContainer atomContainer)
Deprecated.Tests thering
in themolecule
for aromaticity.static void
Kekulization. kekulize(IAtomContainer ac)
Assign a Kekulé representation to the aromatic systems of a compound. -
Uses of IAtomContainer in org.openscience.cdk.atomtype
Methods in org.openscience.cdk.atomtype with parameters of type IAtomContainer Modifier and Type Method Description IAtomType
CDKAtomTypeMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
Method that assigns an atom type to a given atom belonging to an atom container.IAtomType
EStateAtomTypeMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
IAtomType
IAtomTypeMatcher. findMatchingAtomType(IAtomContainer container, IAtom atom)
Method that assigns an atom type to a given atom belonging to an atom container.IAtomType
MM2AtomTypeMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atomInterface)
Deprecated.Assign the mm2 atom type to a given atom.IAtomType
MMFF94AtomTypeMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atomInterface)
Deprecated.Assign the mmff94 atom type to a given atom.IAtomType
StructGenMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state.IAtomType
SybylAtomTypeMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
Sybyl atom type perception for a single atom.IAtomType[]
CDKAtomTypeMatcher. findMatchingAtomTypes(IAtomContainer atomContainer)
Method that assigns atom types to atoms in the given atom container.IAtomType[]
EStateAtomTypeMatcher. findMatchingAtomTypes(IAtomContainer atomContainer)
IAtomType[]
IAtomTypeMatcher. findMatchingAtomTypes(IAtomContainer container)
Method that assigns atom types to atoms in the given atom container.IAtomType[]
MM2AtomTypeMatcher. findMatchingAtomTypes(IAtomContainer atomContainer)
Deprecated.IAtomType[]
MMFF94AtomTypeMatcher. findMatchingAtomTypes(IAtomContainer atomContainer)
Deprecated.IAtomType[]
StructGenMatcher. findMatchingAtomTypes(IAtomContainer atomContainer)
IAtomType[]
SybylAtomTypeMatcher. findMatchingAtomTypes(IAtomContainer atomContainer)
Method that assigns atom types to atoms in the given atom container.static boolean
EStateAtomTypeMatcher. inSameAromaticRing(IAtomContainer m, IAtom atom1, IAtom atom2, IRingSet rs)
List<IAtomType>
IAtomTypeGuesser. possibleAtomTypes(IAtomContainer container, IAtom atom)
Method that returns an iterator with a suitable list of atom types given the provided atom.List<IAtomType>
StructGenAtomTypeGuesser. possibleAtomTypes(IAtomContainer atomContainer, IAtom atom)
Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state. -
Uses of IAtomContainer in org.openscience.cdk.charges
Methods in org.openscience.cdk.charges that return IAtomContainer Modifier and Type Method 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 chargesIAtomContainer
AtomTypeCharges. setCharges(IAtomContainer atomContainer)
Sets initial charges for atom types.Methods in org.openscience.cdk.charges with parameters of type IAtomContainer Modifier and Type Method 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 chargesdouble
Polarizability. calculateBondPolarizability(IAtomContainer atomContainer, IBond bond)
calculate bond polarizability.void
AtomTypeCharges. calculateCharges(IAtomContainer container)
void
GasteigerMarsiliPartialCharges. calculateCharges(IAtomContainer container)
void
GasteigerPEPEPartialCharges. calculateCharges(IAtomContainer container)
void
IElectronicPropertyCalculator. calculateCharges(IAtomContainer container)
void
InductivePartialCharges. calculateCharges(IAtomContainer container)
void
MMFF94PartialCharges. calculateCharges(IAtomContainer container)
double
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. -
Uses of IAtomContainer in org.openscience.cdk.config
Methods in org.openscience.cdk.config with parameters of type IAtomContainer Modifier and Type Method 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. -
Uses of IAtomContainer in org.openscience.cdk.debug
Classes in org.openscience.cdk.debug that implement IAtomContainer Modifier and Type Class 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.Methods in org.openscience.cdk.debug that return IAtomContainer Modifier and Type Method Description IAtomContainer
DebugAtomContainer. clone()
Clones thisIChemObject
.IAtomContainer
DebugAtomContainerSet. getAtomContainer(int number)
Returns the AtomContainer at positionnumber
in the container.IAtomContainer
DebugSubstance. getAtomContainer(int number)
Returns the AtomContainer at positionnumber
in the container.IAtomContainer
DebugAtom. getContainer()
Access theIAtomContainer
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.Methods in org.openscience.cdk.debug that return types with arguments of type IAtomContainer Modifier and Type Method Description Iterable<IAtomContainer>
DebugAtomContainerSet. atomContainers()
Get an iterator for this AtomContainerSet.Iterable<IAtomContainer>
DebugSubstance. atomContainers()
Get an iterator for this AtomContainerSet.Methods in org.openscience.cdk.debug with parameters of type IAtomContainer Modifier and Type Method Description void
DebugAminoAcid. 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
DebugBioPolymer. 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
DebugMonomer. 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
DebugRing. add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this container.void
DebugStrand. 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
DebugAtomContainerSet. addAtomContainer(IAtomContainer atomContainer, double multiplier)
Adds an atomContainer to this container with the given multiplier.void
DebugSubstance. addAtomContainer(IAtomContainer atomContainer)
Adds an atomContainer to this container.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
DebugAminoAcid. 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
DebugBioPolymer. 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
DebugMonomer. 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
DebugRing. remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this container.void
DebugStrand. 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.Constructors in org.openscience.cdk.debug with parameters of type IAtomContainer Constructor Description DebugAtomContainer(IAtomContainer container)
DebugCrystal(IAtomContainer container)
DebugRing(IAtomContainer container)
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Uses of IAtomContainer in org.openscience.cdk.depict
Methods in org.openscience.cdk.depict with parameters of type IAtomContainer Modifier and Type Method 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.int
Abbreviations. apply(IAtomContainer mol, Map<IAtom,Integer> atomSets)
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.List<Sgroup>
Abbreviations. generate(IAtomContainer mol, Map<IAtom,Integer> atomSets)
Find all enabled abbreviations in the provided molecule.Method parameters in org.openscience.cdk.depict with type arguments of type IAtomContainer Modifier and Type Method Description Depiction
DepictionGenerator. depict(Iterable<IAtomContainer> mols)
Depict a set of molecules, they will be depicted in a grid.Depiction
DepictionGenerator. depict(Iterable<IAtomContainer> mols, int nrow, int ncol)
Depict a set of molecules, they will be depicted in a grid with the specified number of rows and columns. -
Uses of IAtomContainer in org.openscience.cdk.fingerprint
Methods in org.openscience.cdk.fingerprint with parameters of type IAtomContainer Modifier and Type Method Description void
CircularFingerprinter. calculate(IAtomContainer mol)
Calculates the fingerprints for the givenIAtomContainer
, 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
AtomPairs2DFingerprinter. getBitFingerprint(IAtomContainer container)
IBitFingerprint
CircularFingerprinter. getBitFingerprint(IAtomContainer mol)
Calculates the circular fingerprint for the givenIAtomContainer
, and folds the result into a single bitset (see getSize()).IBitFingerprint
EStateFingerprinter. getBitFingerprint(IAtomContainer atomContainer)
Returns the bit fingerprint for the givenIAtomContainer
.IBitFingerprint
ExtendedFingerprinter. getBitFingerprint(IAtomContainer container)
Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics.IBitFingerprint
ExtendedFingerprinter. getBitFingerprint(IAtomContainer atomContainer, IRingSet ringSet, List<IRingSet> rslist)
Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics.IBitFingerprint
Fingerprinter. getBitFingerprint(IAtomContainer container)
Generates a fingerprint of the default size for the given AtomContainer.IBitFingerprint
Fingerprinter. getBitFingerprint(IAtomContainer container, AllRingsFinder ringFinder)
Generates a fingerprint of the default size for the given AtomContainer.BitSet
GraphOnlyFingerprinter. getBitFingerprint(IAtomContainer container, int size)
IBitFingerprint
IFingerprinter. getBitFingerprint(IAtomContainer container)
Returns the bit fingerprint for the givenIAtomContainer
.IBitFingerprint
LingoFingerprinter. getBitFingerprint(IAtomContainer iAtomContainer)
IBitFingerprint
MACCSFingerprinter. getBitFingerprint(IAtomContainer container)
Returns the bit fingerprint for the givenIAtomContainer
.IBitFingerprint
PubchemFingerprinter. getBitFingerprint(IAtomContainer atomContainer)
Calculate 881 bit Pubchem fingerprint for a molecule.IBitFingerprint
ShortestPathFingerprinter. getBitFingerprint(IAtomContainer ac)
Generates a shortest path based BitSet fingerprint for the given AtomContainer.IBitFingerprint
SignatureFingerprinter. getBitFingerprint(IAtomContainer atomContainer)
IBitFingerprint
SubstructureFingerprinter. getBitFingerprint(IAtomContainer atomContainer)
Returns the bit fingerprint for the givenIAtomContainer
.ICountFingerprint
AtomPairs2DFingerprinter. getCountFingerprint(IAtomContainer mol)
ICountFingerprint
CircularFingerprinter. getCountFingerprint(IAtomContainer mol)
Calculates the circular fingerprint for the givenIAtomContainer
, and returns a datastructure that enumerates all of the fingerprints, and their counts (i.e.ICountFingerprint
EStateFingerprinter. getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the givenIAtomContainer
.ICountFingerprint
ExtendedFingerprinter. getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the givenIAtomContainer
.ICountFingerprint
Fingerprinter. getCountFingerprint(IAtomContainer container)
ICountFingerprint
IFingerprinter. getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the givenIAtomContainer
.ICountFingerprint
LingoFingerprinter. getCountFingerprint(IAtomContainer container)
ICountFingerprint
MACCSFingerprinter. getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the givenIAtomContainer
.ICountFingerprint
PubchemFingerprinter. getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the givenIAtomContainer
.ICountFingerprint
ShortestPathFingerprinter. getCountFingerprint(IAtomContainer iac)
ICountFingerprint
SignatureFingerprinter. getCountFingerprint(IAtomContainer container)
ICountFingerprint
SubstructureFingerprinter. getCountFingerprint(IAtomContainer atomContainer)
Returns the count fingerprint for the givenIAtomContainer
.BitSet
AbstractFingerprinter. getFingerprint(IAtomContainer mol)
Generate a binary fingerprint as a bit.BitSet
ExtendedFingerprinter. getFingerprint(IAtomContainer mol)
BitSet
IFingerprinter. getFingerprint(IAtomContainer mol)
Generate a binary fingerprint as a bit.Map<String,Integer>
AtomPairs2DFingerprinter. getRawFingerprint(IAtomContainer mol)
Map<String,Integer>
CircularFingerprinter. getRawFingerprint(IAtomContainer mol)
Invalid: it is not appropriate to convert the integer hash codes into strings.Map<String,Integer>
EStateFingerprinter. getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.Map<String,Integer>
ExtendedFingerprinter. getRawFingerprint(IAtomContainer container)
Returns the raw representation of the fingerprint for the given IAtomContainer.Map<String,Integer>
Fingerprinter. getRawFingerprint(IAtomContainer container)
Returns the raw representation of the fingerprint for the given IAtomContainer.Map<String,Integer>
IFingerprinter. getRawFingerprint(IAtomContainer container)
Returns the raw representation of the fingerprint for the given IAtomContainer.Map<String,Integer>
LingoFingerprinter. getRawFingerprint(IAtomContainer atomContainer)
Map<String,Integer>
MACCSFingerprinter. getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.Map<String,Integer>
PubchemFingerprinter. getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.Map<String,Integer>
ShortestPathFingerprinter. getRawFingerprint(IAtomContainer ac)
Returns the raw representation of the fingerprint for the given IAtomContainer.Map<String,Integer>
SignatureFingerprinter. getRawFingerprint(IAtomContainer atomContainer)
Map<String,Integer>
SubstructureFingerprinter. getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.Constructors in org.openscience.cdk.fingerprint with parameters of type IAtomContainer Constructor Description ShortestPathWalker(IAtomContainer container)
Create a new shortest path walker for a given container. -
Uses of IAtomContainer in org.openscience.cdk.fingerprint.model
Methods in org.openscience.cdk.fingerprint.model with parameters of type IAtomContainer Modifier and Type Method Description void
Bayesian. addMolecule(IAtomContainer mol, boolean active)
Appends a new row to the model source data, which consists of a molecule and whether or not it is considered active.double
Bayesian. predict(IAtomContainer mol)
For a given molecule, determines its fingerprints and uses them to calculate a Bayesian prediction. -
Uses of IAtomContainer in org.openscience.cdk.forcefield.mmff
Methods in org.openscience.cdk.forcefield.mmff with parameters of type IAtomContainer Modifier and Type Method 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. -
Uses of IAtomContainer in org.openscience.cdk.fragment
Methods in org.openscience.cdk.fragment that return IAtomContainer Modifier and Type Method Description IAtomContainer[]
ExhaustiveFragmenter. getFragmentsAsContainers()
Get the fragments generated asIAtomContainer
objects..IAtomContainer[]
IFragmenter. getFragmentsAsContainers()
Get fragments generated asIAtomContainer
objects.IAtomContainer[]
MurckoFragmenter. getFragmentsAsContainers()
Get all frameworks and ring systems asIAtomContainer
objects.IAtomContainer[]
MurckoFragmenter. getFrameworksAsContainers()
Get frameworks asIAtomContainer
as objects.IAtomContainer[]
MurckoFragmenter. getRingSystemsAsContainers()
Get rings systems asIAtomContainer
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.Methods in org.openscience.cdk.fragment that return types with arguments of type IAtomContainer Modifier and Type Method Description protected static List<IAtomContainer>
FragmentUtils. splitMolecule(IAtomContainer atomContainer, IBond bond)
Non destructively split a molecule into two parts at the specified bond.Methods in org.openscience.cdk.fragment with parameters of type IAtomContainer Modifier and Type Method Description void
ExhaustiveFragmenter. generateFragments(IAtomContainer atomContainer)
Generate fragments for the input molecule.void
IFragmenter. generateFragments(IAtomContainer atomContainer)
Generate fragments for the input molecule.void
MurckoFragmenter. generateFragments(IAtomContainer atomContainer)
Perform the fragmentation procedure.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)
-
Uses of IAtomContainer in org.openscience.cdk.geometry
Methods in org.openscience.cdk.geometry with parameters of type IAtomContainer Modifier and Type Method 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 forAtom
atom in the environment of the atoms in theAtomContainer
.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 theAtom
s in the AtomContainer for the 2D coordinates.static javax.vecmath.Point2d
GeometryUtil. get2DCentreOfMass(IAtomContainer ac)
Calculates the center of mass for theAtom
s in the AtomContainer for the 2D coordinates.static GeometryTools.CoordinateCoverage
GeometryTools. get2DCoordinateCoverage(IAtomContainer container)
Deprecated.Determines the coverage of thisIAtomContainer
's 2D coordinates.static GeometryUtil.CoordinateCoverage
GeometryUtil. get2DCoordinateCoverage(IAtomContainer container)
Determines the coverage of thisIAtomContainer
'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 theAtom
s in the AtomContainer for the 2D coordinates.static javax.vecmath.Point3d
GeometryUtil. get3DCentreOfMass(IAtomContainer ac)
Calculates the center of mass for theAtom
s in the AtomContainer.static GeometryTools.CoordinateCoverage
GeometryTools. get3DCoordinateCoverage(IAtomContainer container)
Deprecated.Determines the coverage of thisIAtomContainer
's 3D coordinates.static GeometryUtil.CoordinateCoverage
GeometryUtil. get3DCoordinateCoverage(IAtomContainer container)
Determines the coverage of thisIAtomContainer
'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
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
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
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(double xPosition, double yPosition, IAtomContainer atomCon)
Returns the atom of the given molecule that is closest to the given coordinates.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
GeometryUtil. getClosestAtom(int xPosition, int yPosition, IAtomContainer atomCon)
Returns the atom of the given molecule that is closest to the given coordinates.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 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
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(double xPosition, double yPosition, IAtomContainer atomCon)
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 thisIAtomContainer
's atoms contain 2D coordinates.static boolean
GeometryUtil. has2DCoordinates(IAtomContainer container)
Determines if all thisIAtomContainer
's atoms contain 2D coordinates.static int
GeometryTools. has2DCoordinatesNew(IAtomContainer container)
Deprecated.useGeometryTools.get2DCoordinateCoverage(org.openscience.cdk.interfaces.IAtomContainer)
for determining partial coordinatesstatic int
GeometryUtil. has2DCoordinatesNew(IAtomContainer container)
Deprecated.useGeometryUtil.get2DCoordinateCoverage(org.openscience.cdk.interfaces.IAtomContainer)
for determining partial coordinatesstatic boolean
GeometryTools. has3DCoordinates(IAtomContainer container)
Deprecated.Determines if all thisIAtomContainer
's atoms contain 3D coordinates.static boolean
GeometryUtil. has3DCoordinates(IAtomContainer container)
Determines if all thisIAtomContainer
'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, double scaleFactor)
Deprecated.Multiplies all the coordinates of the atoms of the given molecule with the scalefactor.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
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 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 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 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
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, double transX, double transY)
Translates the given molecule by the given 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. -
Uses of IAtomContainer in org.openscience.cdk.geometry.alignment
Methods in org.openscience.cdk.geometry.alignment with parameters of type IAtomContainer Modifier and Type Method Description void
KabschAlignment. rotateAtomContainer(IAtomContainer ac)
Rotates theIAtomContainer
coordinates by the rotation matrix.Constructors in org.openscience.cdk.geometry.alignment with parameters of type IAtomContainer Constructor 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. -
Uses of IAtomContainer in org.openscience.cdk.geometry.cip
Methods in org.openscience.cdk.geometry.cip that return IAtomContainer Modifier and Type Method Description IAtomContainer
ILigand. getAtomContainer()
IAtomContainer
of which this ligand is part.IAtomContainer
Ligand. getAtomContainer()
IAtomContainer
of which this ligand is part.Methods in org.openscience.cdk.geometry.cip with parameters of type IAtomContainer Modifier and Type Method 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 theIAtomContainer
.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 theIAtomContainer
.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.Constructors in org.openscience.cdk.geometry.cip with parameters of type IAtomContainer Constructor Description ImplicitHydrogenLigand(IAtomContainer container, VisitedAtoms visitedAtoms, IAtom centralAtom)
Ligand(IAtomContainer container, VisitedAtoms visitedAtoms, IAtom centralAtom, IAtom ligandAtom)
-
Uses of IAtomContainer in org.openscience.cdk.geometry.surface
Constructors in org.openscience.cdk.geometry.surface with parameters of type IAtomContainer Constructor 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. -
Uses of IAtomContainer in org.openscience.cdk.geometry.volume
Methods in org.openscience.cdk.geometry.volume with parameters of type IAtomContainer Modifier and Type Method Description static double
VABCVolume. calculate(IAtomContainer molecule)
Calculates the volume for the givenIAtomContainer
. -
Uses of IAtomContainer in org.openscience.cdk.graph
Fields in org.openscience.cdk.graph declared as IAtomContainer Modifier and Type Field Description protected IAtomContainer
AtomContainerPermutor. atomContainer
The atom container that is permuted at each step.Methods in org.openscience.cdk.graph that return IAtomContainer Modifier and Type Method Description IAtomContainer
AtomContainerAtomPermutor. containerFromPermutation(int[] permutation)
Generate the atom container with this permutation of the atoms.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
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.Methods in org.openscience.cdk.graph with parameters of type IAtomContainer Modifier and Type Method 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.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 anIAtomContainer
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)
Split a molecule based on the provided component array.static Cycles
Cycles. relevant(IAtomContainer container)
Find the relevant cycles of a molecule.protected static void
PathTools. resetFlags(IAtomContainer atomContainer)
static void
Cycles. smallRingSizes(IAtomContainer mol, int[] rsizes)
Convenience method to determine the smallest ring size of every atom in the molecule.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 thecontainer
and fill in thebondMap
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
.Constructors in org.openscience.cdk.graph with parameters of type IAtomContainer Constructor Description AllPairsShortestPaths(IAtomContainer container)
Create a new all shortest paths utility for anIAtomContainer
.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. -
Uses of IAtomContainer in org.openscience.cdk.graph.invariant
Methods in org.openscience.cdk.graph.invariant with parameters of type IAtomContainer Modifier and Type Method 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 thecontainer
.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. getEAIDNumber(IAtomContainer atomContainer)
Calculates the extended adjacency matrix index.static double[][]
HuLuIndexTool. getExtendedAdjacencyMatrix(IAtomContainer mol)
Compute the extended adjacency matrix as described in [Chang-Yu Hu and Lu Xu. J. Chem. Inf. Comput. Sci.. 1996. 36].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 ofatomContainer
.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, 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.static long[]
Canon. label(IAtomContainer container, int[][] g, Comparator<IAtom> cmp)
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.Constructors in org.openscience.cdk.graph.invariant with parameters of type IAtomContainer Constructor Description EquivalentClassPartitioner(IAtomContainer atomContainer)
Constructor for the TopologicalEquivalentClass object. -
Uses of IAtomContainer in org.openscience.cdk.graph.matrix
Methods in org.openscience.cdk.graph.matrix with parameters of type IAtomContainer Modifier and Type Method Description static int[][]
AdjacencyMatrix. getMatrix(IAtomContainer container)
Returns the adjacency matrix for the given AtomContainer.static double[][]
ConnectionMatrix. getMatrix(IAtomContainer container)
Returns the connection matrix representation of this AtomContainer.static int[][]
TopologicalMatrix. getMatrix(IAtomContainer container)
Returns the topological matrix for the given AtomContainer. -
Uses of IAtomContainer in org.openscience.cdk.graph.rebond
Methods in org.openscience.cdk.graph.rebond with parameters of type IAtomContainer Modifier and Type Method Description void
RebondTool. rebond(IAtomContainer container)
Rebonding using a Binary Space Partition Tree. -
Uses of IAtomContainer in org.openscience.cdk.group
Methods in org.openscience.cdk.group with parameters of type IAtomContainer Modifier and Type Method 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. -
Uses of IAtomContainer in org.openscience.cdk.hash
Methods in org.openscience.cdk.hash with parameters of type IAtomContainer Modifier and Type Method Description int
AtomEncoder. encode(IAtom atom, IAtomContainer container)
Encode an invariant attribute of the given atom.long[]
AtomHashGenerator. generate(IAtomContainer container)
Generate invariant 64-bit hash codes for the atoms of the molecule.long
MoleculeHashGenerator. generate(IAtomContainer container)
Generate invariant 64-bit hash code for a molecule.Method parameters in org.openscience.cdk.hash with type arguments of type IAtomContainer Modifier and Type Method Description long
EnsembleHashGenerator. generate(Set<IAtomContainer> ensemble)
Generate invariant 64-bit hash code for an ensemble of molecules. -
Uses of IAtomContainer in org.openscience.cdk.hash.stereo
Methods in org.openscience.cdk.hash.stereo with parameters of type IAtomContainer Modifier and Type Method Description StereoEncoder
DoubleBondElementEncoderFactory. 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
GeometricDoubleBondEncoderFactory. create(IAtomContainer container, int[][] graph)
Create a stereo encoder for all potential 2D and 3D double bond stereo configurations.StereoEncoder
GeometricTetrahedralEncoderFactory. create(IAtomContainer container, int[][] graph)
Create a stereo encoder for all potential 2D and 3D tetrahedral elements.StereoEncoder
StereoEncoderFactory. create(IAtomContainer container, int[][] graph)
Create a stereo-encoder for possible stereo-chemical configurations.StereoEncoder
TetrahedralElementEncoderFactory. create(IAtomContainer container, int[][] graph)
Create a stereo-encoder for possible stereo-chemical configurations. -
Uses of IAtomContainer in org.openscience.cdk.inchi
Fields in org.openscience.cdk.inchi declared as IAtomContainer Modifier and Type Field Description protected IAtomContainer
InChIGenerator. atomContainer
AtomContainer instance refers to.protected IAtomContainer
InChIToStructure. molecule
Methods in org.openscience.cdk.inchi that return IAtomContainer Modifier and Type Method Description IAtomContainer
InChIToStructure. getAtomContainer()
Returns generated molecule.Methods in org.openscience.cdk.inchi with parameters of type IAtomContainer Modifier and Type Method Description InChIGenerator
InChIGeneratorFactory. getInChIGenerator(IAtomContainer container)
Gets an Standard InChI generator for aIAtomContainer
.InChIGenerator
InChIGeneratorFactory. getInChIGenerator(IAtomContainer container, io.github.dan2097.jnainchi.InchiFlag... flags)
Get an InChI generator providing flags to customise the generation.InChIGenerator
InChIGeneratorFactory. getInChIGenerator(IAtomContainer container, io.github.dan2097.jnainchi.InchiOptions options)
Get an InChI generator providing flags to customise the generation.InChIGenerator
InChIGeneratorFactory. getInChIGenerator(IAtomContainer container, String options)
Gets InChI generator for CDK IAtomContainer.InChIGenerator
InChIGeneratorFactory. getInChIGenerator(IAtomContainer container, List<INCHI_OPTION> options)
Constructors in org.openscience.cdk.inchi with parameters of type IAtomContainer Constructor Description InChIGenerator(IAtomContainer atomContainer, boolean ignoreAromaticBonds)
Constructor.InChIGenerator(IAtomContainer atomContainer, io.github.dan2097.jnainchi.InchiOptions options, boolean ignoreAromaticBonds)
InChIGenerator(IAtomContainer atomContainer, String optStr, boolean ignoreAromaticBonds)
Constructor.InChIGenerator(IAtomContainer atomContainer, List<INCHI_OPTION> opts, boolean ignoreAromaticBonds)
Deprecated. -
Uses of IAtomContainer in org.openscience.cdk.interfaces
Subinterfaces of IAtomContainer in org.openscience.cdk.interfaces Modifier and Type Interface 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.Methods in org.openscience.cdk.interfaces that return IAtomContainer Modifier and Type Method Description IAtomContainer
IAtomContainer. clone()
Returns a deep clone of this IChemObject.IAtomContainer
IAtomContainerSet. getAtomContainer(int number)
Returns the AtomContainer at positionnumber
in the container.IAtomContainer
IAtom. getContainer()
Access theIAtomContainer
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.Methods in org.openscience.cdk.interfaces that return types with arguments of type IAtomContainer Modifier and Type Method Description Iterable<IAtomContainer>
IAtomContainerSet. atomContainers()
Get an Iterable for this AtomContainerSet.Methods in org.openscience.cdk.interfaces with parameters of type IAtomContainer Modifier and Type Method Description void
IAtomContainer. add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this container.void
ICrystal. add(IAtomContainer container)
Adds the atoms in the AtomContainer as cell content.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.Method parameters in org.openscience.cdk.interfaces with type arguments of type IAtomContainer Modifier and Type Method Description void
IAtomContainerSet. sortAtomContainers(Comparator<IAtomContainer> comparator)
Sort the AtomContainers using a provided Comparator. -
Uses of IAtomContainer in org.openscience.cdk.io
Methods in org.openscience.cdk.io that return IAtomContainer Modifier and Type Method Description IAtomContainer
MDLV3000Reader. readConnectionTable(IChemObjectBuilder builder)
IAtomContainer
MDLV3000Reader. readMolecule(IChemObjectBuilder builder)
Methods in org.openscience.cdk.io with parameters of type IAtomContainer Modifier and Type Method Description void
SMILESWriter. writeAtomContainer(IAtomContainer molecule)
Writes the content from molecule to output.void
MDLV2000Writer. writeMolecule(IAtomContainer container)
Writes a Molecule to an OutputStream in MDL sdf format.void
Mol2Writer. writeMolecule(IAtomContainer mol)
Writes a single frame in XYZ format to the Writer.void
PDBWriter. writeMolecule(IAtomContainer molecule)
Writes a single frame in PDB format to the Writer.void
XYZWriter. writeMolecule(IAtomContainer mol)
writes a single frame in XYZ format to the Writer. -
Uses of IAtomContainer in org.openscience.cdk.io.cml
Fields in org.openscience.cdk.io.cml declared as IAtomContainer Modifier and Type Field Description protected IAtomContainer
CMLCoreModule. currentMolecule
-
Uses of IAtomContainer in org.openscience.cdk.io.inchi
Methods in org.openscience.cdk.io.inchi that return IAtomContainer Modifier and Type Method Description IAtomContainer
INChIContentProcessorTool. processFormula(IAtomContainer parsedContent, String atomsEncoding)
Deprecated.Processes the content from the formula field of the INChI.Methods in org.openscience.cdk.io.inchi with parameters of type IAtomContainer Modifier and Type Method 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. -
Uses of IAtomContainer in org.openscience.cdk.io.iterator
Methods in org.openscience.cdk.io.iterator that return IAtomContainer Modifier and Type Method Description IAtomContainer
IteratingPCCompoundASNReader. next()
IAtomContainer
IteratingPCCompoundXMLReader. next()
IAtomContainer
IteratingSDFReader. next()
Returns the nextIAtomContainer
.IAtomContainer
IteratingSMILESReader. next()
Get the next molecule from the stream. -
Uses of IAtomContainer in org.openscience.cdk.io.iterator.event
Methods in org.openscience.cdk.io.iterator.event that return IAtomContainer Modifier and Type Method Description IAtomContainer
EventCMLHandler. getAtomContainer()
IAtomContainer
EventCMLReader. getAtomContainer()
IAtomContainer
IEventChemObjectReader. getAtomContainer()
-
Uses of IAtomContainer in org.openscience.cdk.io.program
Methods in org.openscience.cdk.io.program with parameters of type IAtomContainer Modifier and Type Method Description void
GaussianInputWriter. writeMolecule(IAtomContainer mol)
Writes a molecule for input for Gaussian. -
Uses of IAtomContainer in org.openscience.cdk.io.pubchemxml
Methods in org.openscience.cdk.io.pubchemxml that return IAtomContainer Modifier and Type Method Description IAtomContainer
PubChemXMLHelper. parseMolecule(XMLStreamReader parser, IChemObjectBuilder builder)
Methods in org.openscience.cdk.io.pubchemxml with parameters of type IAtomContainer Modifier and Type Method 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)
-
Uses of IAtomContainer in org.openscience.cdk.isomorphism
Methods in org.openscience.cdk.isomorphism that return IAtomContainer Modifier and Type Method Description static IAtomContainer
UniversalIsomorphismTester. project(List<RMap> rMapList, IAtomContainer g, int id)
Projects a list ofRMap
on a molecule.Methods in org.openscience.cdk.isomorphism that return types with arguments of type IAtomContainer Modifier and Type Method 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.Stream<IAtomContainer>
Mappings. toSubstructuresStream()
Obtain the mapped substructures (atoms/bonds) of the target compound.Methods in org.openscience.cdk.isomorphism with parameters of type IAtomContainer Modifier and Type Method Description static RGraph
UniversalIsomorphismTester. buildRGraph(IAtomContainer g1, IAtomContainer g2)
Builds theRGraph
( resolution graph ), from two atomContainer (description of the two molecules to compare) This is the interface point between the CDK model and the generic MCSS algorithm based on the RGRaph.static List<RMap>
UniversalIsomorphismTester. checkSingleAtomCases(IAtomContainer g1, IAtomContainer g2)
Checks for single atom cases before doing subgraph/isomorphism search.static Pattern
Pattern. findIdentical(IAtomContainer query)
Create a pattern which can be used to find molecules which are the same as thequery
structure.static Pattern
VentoFoggia. findIdentical(IAtomContainer query)
Create a pattern which can be used to find molecules which are the same as thequery
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 thequery
structure.static DfPattern
DfPattern. findSubstructure(IAtomContainer query)
Create a pattern which can be used to find molecules which contain thequery
structure.static Pattern
Pattern. findSubstructure(IAtomContainer query)
Create a pattern which can be used to find molecules which contain thequery
structure.static Pattern
Ullmann. findSubstructure(IAtomContainer query)
Create a pattern which can be used to find molecules which contain thequery
structure.static Pattern
VentoFoggia. findSubstructure(IAtomContainer query)
Create a pattern which can be used to find molecules which contain thequery
structure.static Pattern
VentoFoggia. findSubstructure(IAtomContainer query, AtomMatcher atomMatcher, BondMatcher bondMatcher)
Create a pattern which can be used to find molecules which contain thequery
structure.static BitSet
UniversalIsomorphismTester. getBitSet(IAtomContainer ac)
Transforms an AtomContainer into aBitSet
(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 modulestatic 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.int[]
DfPattern. match(IAtomContainer target)
Find a matching of this pattern in thetarget
.abstract int[]
Pattern. match(IAtomContainer target)
Find a matching of this pattern in thetarget
.int[]
Ullmann. match(IAtomContainer target)
int[]
VentoFoggia. match(IAtomContainer target)
Find a matching of this pattern in thetarget
.Mappings
DfPattern. matchAll(IAtomContainer mol)
Find all mappings of this pattern in thetarget
.abstract Mappings
Pattern. matchAll(IAtomContainer target)
Find all mappings of this pattern in thetarget
.Mappings
Ullmann. matchAll(IAtomContainer target)
Mappings
VentoFoggia. matchAll(IAtomContainer target)
Find all mappings of this pattern in thetarget
.boolean
DfPattern. matches(IAtomContainer target)
Determine if there is a mapping of this pattern in thetarget
.boolean
Pattern. matches(IAtomContainer target)
Determine if there is a mapping of this pattern in thetarget
.static IAtomContainer
UniversalIsomorphismTester. project(List<RMap> rMapList, IAtomContainer g, int id)
Projects a list ofRMap
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)
GeneralRGraph
parsing method (usually not used directly) This method is the entry point for the recursive search adapted to the atom container input.Constructors in org.openscience.cdk.isomorphism with parameters of type IAtomContainer Constructor Description IsomorphismTester(IAtomContainer mol)
Constructor for the IsomorphismTester objectSmartsStereoMatch(IAtomContainer query, IAtomContainer target)
Deprecated.Create a predicate for checking mappings between a providedquery
andtarget
. -
Uses of IAtomContainer in org.openscience.cdk.isomorphism.matchers
Subinterfaces of IAtomContainer in org.openscience.cdk.isomorphism.matchers Modifier and Type Interface Description interface
IQueryAtomContainer
General concept of a IAtomContainer aimed at doing molecular subgraph queries using the UniversalIsomorphismTester.Classes in org.openscience.cdk.isomorphism.matchers that implement IAtomContainer Modifier and Type Class Description class
QueryAtomContainer
Methods in org.openscience.cdk.isomorphism.matchers that return IAtomContainer Modifier and Type Method Description IAtomContainer
QueryAtom. getContainer()
Access theIAtomContainer
of which this atom is a member of.IAtomContainer
QueryBond. getContainer()
IAtomContainer
IRGroup. getGroup()
Get the connection table of atoms/bonds for this Rgroup.IAtomContainer
RGroup. getGroup()
IAtomContainer
IRGroupQuery. getRootStructure()
Getter for the root structure of this R-Group.IAtomContainer
RGroupQuery. getRootStructure()
IAtomContainer
Expr. subquery()
Access the sub-query, only applicable to recursive types.static IAtomContainer
QueryAtomContainerCreator. suppressQueryHydrogens(IAtomContainer mol)
Methods in org.openscience.cdk.isomorphism.matchers that return types with arguments of type IAtomContainer Modifier and Type Method Description 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. getAllConfigurations()
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.List<IAtomContainer>
RGroupQuery. getSubstituents()
Methods in org.openscience.cdk.isomorphism.matchers with parameters of type IAtomContainer Modifier and Type Method Description void
QueryAtomContainer. add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this container.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
QueryAtomContainer. create(IAtomContainer src, Expr.Type... opts)
Create 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
IRGroupQuery. setRootStructure(IAtomContainer rootStructure)
Setter for the root structure of this R-Group.void
RGroupQuery. setRootStructure(IAtomContainer rootStructure)
static IAtomContainer
QueryAtomContainerCreator. suppressQueryHydrogens(IAtomContainer mol)
Constructors in org.openscience.cdk.isomorphism.matchers with parameters of type IAtomContainer Constructor 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). -
Uses of IAtomContainer in org.openscience.cdk.isomorphism.matchers.smarts
Methods in org.openscience.cdk.isomorphism.matchers.smarts with parameters of type IAtomContainer Modifier and Type Method Description static void
SmartsMatchers. prepare(IAtomContainer container, boolean ringQuery)
Deprecated.Do not use - temporary method until the SMARTS packages are cleaned up. -
Uses of IAtomContainer in org.openscience.cdk.iupac.parser
Methods in org.openscience.cdk.iupac.parser that return IAtomContainer Modifier and Type Method Description protected IAtomContainer
MoleculeBuilder. buildMolecule(int mainChain, List<AttachedGroup> attachedSubstituents, List<AttachedGroup> attachedGroups, boolean isMainCyclic, String name)
Start of the process of building a molecule from the parsed data.static IAtomContainer
NomParser. generate(String stringToParse)
Deprecated.Parses the chemical name and returns the built molecule.static IAtomContainer
NomParser. generate(String stringToParse, IChemObjectBuilder builder)
Deprecated.Parses the chemical name and returns the built molecule. -
Uses of IAtomContainer in org.openscience.cdk.layout
Fields in org.openscience.cdk.layout with type parameters of type IAtomContainer Modifier and Type Field Description static Comparator<IAtomContainer>
StructureDiagramGenerator. LARGEST_FIRST_COMPARATOR
Methods in org.openscience.cdk.layout that return IAtomContainer Modifier and Type Method 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
AtomPlacer. getMolecule()
Return the molecule the AtomPlacer currently works withIAtomContainer
RingPlacer. getMolecule()
IAtomContainer
StructureDiagramGenerator. getMolecule()
Returns the molecule, usually used after a call of generateCoordinates()static IAtomContainer
AtomPlacer. getPlacedAtoms(IAtomContainer ac)
Get all the placed atoms in an AtomContainerIAtomContainer
TemplateHandler. getTemplateAt(int position)
Gets the templateAt attribute of the TemplateHandler objectIAtomContainer
RingPlacer. placeRingSubstituents(IRingSet rs, double bondLength)
Positions the aliphatic substituents of a ring systemIAtomContainer
TemplateHandler. removeMolecule(IAtomContainer molecule)
Methods in org.openscience.cdk.layout with parameters of type IAtomContainer Modifier and Type Method 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 placedstatic 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 AtomContainerstatic 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.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.String
AtomPlacer. listPlaced(IAtomContainer ac)
Returns a string with the numbers of all placed atoms in an AtomContainerboolean
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 placedstatic void
AtomPlacer. markPlaced(IAtomContainer ac)
Marks all the atoms in the given AtomContainer as placedvoid
RingPlacer. partitionNonRingPartners(IAtom atom, IRing ring, IAtomContainer ringAtoms, IAtomContainer nonRingAtoms)
Partition the bonding partners of a given atom into ring atoms and non-ring atomsvoid
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
AtomPlacer. setMolecule(IAtomContainer molecule)
Sets the molecule the AtomPlacer currently works withvoid
RingPlacer. setMolecule(IAtomContainer molecule)
void
StructureDiagramGenerator. setMolecule(IAtomContainer molecule)
Assings a molecule to be layed out.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.Method parameters in org.openscience.cdk.layout with type arguments of type IAtomContainer Modifier and Type Method Description static TemplateHandler
TemplateHandler. createFromSubstructure(Pattern ptrn, Iterable<IAtomContainer> mols)
Create a template from a substructure pattern.Constructors in org.openscience.cdk.layout with parameters of type IAtomContainer Constructor Description StructureDiagramGenerator(IAtomContainer molecule)
Creates an instance of this class while assigning a molecule to be layed out. -
Uses of IAtomContainer in org.openscience.cdk.libio.cml
Methods in org.openscience.cdk.libio.cml with parameters of type IAtomContainer Modifier and Type Method Description org.xmlcml.cml.element.CMLMolecule
Convertor. cdkAtomContainerToCMLMolecule(IAtomContainer structure)
org.xmlcml.cml.element.CMLAtom
Convertor. cdkAtomToCMLAtom(IAtomContainer container, IAtom cdkAtom)
void
ICMLCustomizer. customize(IAtomContainer molecule, Object nodeToAdd)
Customized the nodeToAdd for the given Molecule.void
MDMoleculeCustomizer. customize(IAtomContainer molecule, Object nodeToAdd)
Customize Molecule.void
PDBAtomCustomizer. customize(IAtomContainer molecule, Object nodeToAdd)
void
QSARCustomizer. customize(IAtomContainer molecule, Object nodeToAdd)
-
Uses of IAtomContainer in org.openscience.cdk.libio.jena
Methods in org.openscience.cdk.libio.jena that return IAtomContainer Modifier and Type Method Description static IAtomContainer
Convertor. model2Molecule(org.apache.jena.rdf.model.Model model, IChemObjectBuilder builder)
Methods in org.openscience.cdk.libio.jena with parameters of type IAtomContainer Modifier and Type Method Description static org.apache.jena.rdf.model.Model
Convertor. molecule2Model(IAtomContainer molecule)
Converts aIAtomContainer
into aModel
representation using the CDK OWL. -
Uses of IAtomContainer in org.openscience.cdk.libio.md
Classes in org.openscience.cdk.libio.md that implement IAtomContainer Modifier and Type Class 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.Constructors in org.openscience.cdk.libio.md with parameters of type IAtomContainer Constructor 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. -
Uses of IAtomContainer in org.openscience.cdk.modeling.builder3d
Methods in org.openscience.cdk.modeling.builder3d that return IAtomContainer Modifier and Type Method 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)
Methods in org.openscience.cdk.modeling.builder3d with parameters of type IAtomContainer Modifier and Type Method 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. -
Uses of IAtomContainer in org.openscience.cdk.normalize
Methods in org.openscience.cdk.normalize that return IAtomContainer Modifier and Type Method Description static IAtomContainer
SMSDNormalizer. convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
Deprecated.Returns IAtomContainer without Hydrogen.static IAtomContainer
SMSDNormalizer. makeDeepCopy(IAtomContainer container)
Deprecated.Returns deep copy of the moleculestatic IAtomContainer
SMSDNormalizer. removeHydrogensAndPreserveAtomID(IAtomContainer atomContainer)
Deprecated.Returns IAtomContainer without Hydrogen.Methods in org.openscience.cdk.normalize with parameters of type IAtomContainer Modifier and Type Method 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 moleculestatic boolean
Normalizer. normalize(IAtomContainer ac, Document doc)
Deprecated.The method takes an XML files like the following:
<replace-set>
<replace>O=N=O</replace>
<replacement>[O-][N+]=O</replacement>
</replace-set>
All parts in ac which are the same as replace will be changed according to replacement.static void
SMSDNormalizer. percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Deprecated.Convenience method to perceive atom types for allIAtom
s in theIAtomContainer
, using theCDKAtomTypeMatcher
.static IAtomContainer
SMSDNormalizer. removeHydrogensAndPreserveAtomID(IAtomContainer atomContainer)
Deprecated.Returns IAtomContainer without Hydrogen. -
Uses of IAtomContainer in org.openscience.cdk.pharmacophore
Classes in org.openscience.cdk.pharmacophore that implement IAtomContainer Modifier and Type Class Description class
PharmacophoreQuery
Represents a colleciton of pharmacophore groups and constraints.Methods in org.openscience.cdk.pharmacophore with parameters of type IAtomContainer Modifier and Type Method Description boolean
PharmacophoreMatcher. matches(IAtomContainer atomContainer)
Performs the pharmacophore matching.boolean
PharmacophoreMatcher. matches(IAtomContainer atomContainer, boolean initializeTarget)
Performs the pharmacophore matching. -
Uses of IAtomContainer in org.openscience.cdk.protein.data
Classes in org.openscience.cdk.protein.data that implement IAtomContainer Modifier and Type Class 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. -
Uses of IAtomContainer in org.openscience.cdk.qsar
Methods in org.openscience.cdk.qsar that return IAtomContainer Modifier and Type Method Description protected static IAtomContainer
AbstractMolecularDescriptor. clone(IAtomContainer mol)
Methods in org.openscience.cdk.qsar with parameters of type IAtomContainer Modifier and Type Method 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
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.DescriptorValue
IMolecularDescriptor. calculate(IAtomContainer container)
Calculates the descriptor value for the given IAtomContainer.protected static IAtomContainer
AbstractMolecularDescriptor. clone(IAtomContainer mol)
boolean
AbstractAtomicDescriptor. isCachedAtomContainer(IAtomContainer container)
Returns true if the cached IDescriptorResult's are for the given IAtomContainer.boolean
AbstractBondDescriptor. 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. -
Uses of IAtomContainer in org.openscience.cdk.qsar.descriptors.atomic
Methods in org.openscience.cdk.qsar.descriptors.atomic with parameters of type IAtomContainer Modifier and Type Method Description DescriptorValue
AtomDegreeDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculates the number of not-H substituents of an atom.DescriptorValue
AtomHybridizationDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculates the hybridization of an atom.DescriptorValue
AtomHybridizationVSEPRDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculates the hybridization of an atom.DescriptorValue
AtomValenceDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculates the valence of an atom.DescriptorValue
BondsToAtomDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculate the number of bonds on the shortest path between two atoms.DescriptorValue
CovalentRadiusDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculates the Covalent radius of an atom.DescriptorValue
DistanceToAtomDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculate the 3D distance between two atoms.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
InductiveAtomicHardnessDescriptor. calculate(IAtom atom, IAtomContainer ac)
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.DescriptorValue
InductiveAtomicSoftnessDescriptor. calculate(IAtom atom, IAtomContainer ac)
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.DescriptorValue
IPAtomicHOSEDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculates the ionization potential of an atom.DescriptorValue
IPAtomicLearningDescriptor. calculate(IAtom atom, IAtomContainer container)
Deprecated.This method calculates the ionization potential of an atom.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
IsProtonInConjugatedPiSystemDescriptor. calculate(IAtom atom, IAtomContainer atomContainer)
The method is a proton descriptor that evaluates if a proton is joined to a conjugated system.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
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
PartialTChargeMMFF94Descriptor. calculate(IAtom atom, IAtomContainer org)
The method returns partial charges assigned to an heavy atom through MMFF94 method.DescriptorValue
PartialTChargePEOEDescriptor. calculate(IAtom atom, IAtomContainer ac)
The method returns partial total charges assigned to an heavy atom through PEOE method.DescriptorValue
PeriodicTablePositionDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculates the period of an atom.DescriptorValue
PiElectronegativityDescriptor. calculate(IAtom atom, IAtomContainer atomContainer)
The method calculates the pi electronegativity of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
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
RDFProtonDescriptor_G3R. calculate(IAtom atom, IAtomContainer varAtomContainerSet)
DescriptorValue
RDFProtonDescriptor_G3R. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
DescriptorValue
RDFProtonDescriptor_GDR. calculate(IAtom atom, IAtomContainer varAtomContainerSet)
DescriptorValue
RDFProtonDescriptor_GDR. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
DescriptorValue
RDFProtonDescriptor_GHR_topol. calculate(IAtom atom, IAtomContainer varAtomContainerSet)
DescriptorValue
RDFProtonDescriptor_GHR_topol. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
DescriptorValue
RDFProtonDescriptor_GHR. calculate(IAtom atom, IAtomContainer varAtomContainerSet)
DescriptorValue
RDFProtonDescriptor_GHR. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
DescriptorValue
RDFProtonDescriptor_GSR. calculate(IAtom atom, IAtomContainer varAtomContainerSet)
DescriptorValue
RDFProtonDescriptor_GSR. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
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
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
VdWRadiusDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculate the Van der Waals radius of an atom. -
Uses of IAtomContainer in org.openscience.cdk.qsar.descriptors.atompair
Methods in org.openscience.cdk.qsar.descriptors.atompair with parameters of type IAtomContainer Modifier and Type Method Description DescriptorValue
PiContactDetectionDescriptor. calculate(IAtom first, IAtom second, IAtomContainer atomContainer)
The method returns if two atoms have pi-contact. -
Uses of IAtomContainer in org.openscience.cdk.qsar.descriptors.bond
Methods in org.openscience.cdk.qsar.descriptors.bond with parameters of type IAtomContainer Modifier and Type Method Description DescriptorValue
AtomicNumberDifferenceDescriptor. calculate(IBond bond, IAtomContainer ac)
DescriptorValue
BondPartialPiChargeDescriptor. calculate(IBond bond, IAtomContainer ac)
The method calculates the bond-pi Partial charge of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
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
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
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
IPBondLearningDescriptor. calculate(IBond bond, IAtomContainer atomContainer)
Deprecated.This method calculates the ionization potential of a bond. -
Uses of IAtomContainer in org.openscience.cdk.qsar.descriptors.molecular
Methods in org.openscience.cdk.qsar.descriptors.molecular with parameters of type IAtomContainer Modifier and Type Method 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.NaNDescriptorValue
AcidicGroupCountDescriptor. calculate(IAtomContainer atomContainer)
Calculates the descriptor value for the given IAtomContainer.DescriptorValue
ALOGPDescriptor. calculate(IAtomContainer container)
The AlogP descriptor.DescriptorValue
AminoAcidCountDescriptor. calculate(IAtomContainer ac)
Determine the number of amino acids groups the suppliedIAtomContainer
.DescriptorValue
APolDescriptor. calculate(IAtomContainer container)
Calculate the sum of atomic polarizabilities in anIAtomContainer
.DescriptorValue
AromaticAtomsCountDescriptor. calculate(IAtomContainer atomContainer)
Calculate the count of aromatic atoms in the suppliedIAtomContainer
.DescriptorValue
AromaticBondsCountDescriptor. calculate(IAtomContainer atomContainer)
Calculate the count of aromatic atoms in the suppliedIAtomContainer
.DescriptorValue
AtomCountDescriptor. calculate(IAtomContainer container)
This method calculate the number of atoms of a given type in anIAtomContainer
.DescriptorValue
AutocorrelationDescriptorCharge. calculate(IAtomContainer atomContainer)
DescriptorValue
AutocorrelationDescriptorMass. calculate(IAtomContainer atomContainer)
This method calculate the ATS Autocorrelation descriptor.DescriptorValue
AutocorrelationDescriptorPolarizability. calculate(IAtomContainer container)
This method calculate the ATS Autocorrelation descriptor.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
BondCountDescriptor. calculate(IAtomContainer container)
This method calculate the number of bonds of a given type in an atomContainerDescriptorValue
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 moleculeDescriptorValue
CarbonTypesDescriptor. calculate(IAtomContainer container)
Calculates the 9 carbon types descriptorsDescriptorValue
ChiChainDescriptor. calculate(IAtomContainer container)
DescriptorValue
ChiClusterDescriptor. calculate(IAtomContainer container)
DescriptorValue
ChiPathClusterDescriptor. calculate(IAtomContainer container)
DescriptorValue
ChiPathDescriptor. calculate(IAtomContainer container)
DescriptorValue
CPSADescriptor. calculate(IAtomContainer atomContainer)
Evaluates the 29 CPSA descriptors using Gasteiger-Marsilli charges.DescriptorValue
EccentricConnectivityIndexDescriptor. calculate(IAtomContainer container)
Calculates the eccentric connectivityDescriptorValue
FMFDescriptor. calculate(IAtomContainer container)
Calculates the FMF descriptor value for the givenIAtomContainer
.DescriptorValue
FractionalCSP3Descriptor. calculate(IAtomContainer mol)
Calculates the Fsp3 descriptor value for the givenIAtomContainer
.DescriptorValue
FractionalPSADescriptor. calculate(IAtomContainer mol)
Calculates the topological polar surface area and expresses it as a ratio to molecule size.DescriptorValue
FragmentComplexityDescriptor. calculate(IAtomContainer container)
Calculate the complexity in the suppliedIAtomContainer
.DescriptorValue
GravitationalIndexDescriptor. calculate(IAtomContainer container)
Calculates the 9 gravitational indices.DescriptorValue
HBondAcceptorCountDescriptor. calculate(IAtomContainer atomContainer)
Calculates the number of H bond acceptors.DescriptorValue
HBondDonorCountDescriptor. calculate(IAtomContainer atomContainer)
Calculates the number of H bond donors.DescriptorValue
HybridizationRatioDescriptor. calculate(IAtomContainer container)
Calculate sp3/sp2 hybridization ratio in the suppliedIAtomContainer
.DescriptorValue
IPMolecularLearningDescriptor. calculate(IAtomContainer atomContainer)
Deprecated.It calculates the first ionization energy of a molecule.DescriptorValue
JPlogPDescriptor. calculate(IAtomContainer container)
DescriptorValue
KappaShapeIndicesDescriptor. calculate(IAtomContainer container)
calculates the kier shape indices for an atom containerDescriptorValue
KierHallSmartsDescriptor. calculate(IAtomContainer container)
This method calculates occurrences of the Kier & Hall E-state fragments.DescriptorValue
LargestChainDescriptor. calculate(IAtomContainer atomContainer)
Calculate the count of atoms of the largest chain in the suppliedIAtomContainer
.DescriptorValue
LargestPiSystemDescriptor. calculate(IAtomContainer container)
Calculate the count of atoms of the largest pi system in the suppliedIAtomContainer
.DescriptorValue
LengthOverBreadthDescriptor. calculate(IAtomContainer atomContainer)
Evaluate the descriptor for the molecule.DescriptorValue
LongestAliphaticChainDescriptor. calculate(IAtomContainer mol)
Calculate the count of atoms of the longest aliphatic chain in the suppliedIAtomContainer
.DescriptorValue
MannholdLogPDescriptor. calculate(IAtomContainer atomContainer)
Calculates the Mannhold LogP for an atom container.DescriptorValue
MDEDescriptor. calculate(IAtomContainer container)
Calculate the weight of specified element type in the suppliedIAtomContainer
.DescriptorValue
MomentOfInertiaDescriptor. calculate(IAtomContainer container)
Calculates the 3 MI's, 3 ration and the R_gyr value.DescriptorValue
PetitjeanNumberDescriptor. calculate(IAtomContainer atomContainer)
Evaluate the descriptor for the molecule.DescriptorValue
PetitjeanShapeIndexDescriptor. calculate(IAtomContainer container)
Calculates the two Petitjean shape indices.DescriptorValue
RotatableBondsCountDescriptor. calculate(IAtomContainer ac)
The method calculates the number of rotatable bonds of an atom container.DescriptorValue
RuleOfFiveDescriptor. calculate(IAtomContainer mol)
the method take a boolean checkAromaticity: if the boolean is true, it means that aromaticity has to be checked.DescriptorValue
SmallRingDescriptor. calculate(IAtomContainer mol)
Performs the calculation: the graph will be analyzed and ring information will be determined and wrapped up into descriptors.DescriptorValue
SpiroAtomCountDescriptor. calculate(IAtomContainer atomContainer)
Calculates the descriptor value for the given IAtomContainer.DescriptorValue
TPSADescriptor. calculate(IAtomContainer atomContainer)
Calculates the TPSA for an atom container.DescriptorValue
VABCDescriptor. calculate(IAtomContainer atomContainer)
Calculates the descriptor value using theVABCVolume
class.DescriptorValue
VAdjMaDescriptor. calculate(IAtomContainer atomContainer)
calculates the VAdjMa descriptor for an atom containerDescriptorValue
WeightDescriptor. calculate(IAtomContainer container)
Calculate the natural weight of specified elements type in the suppliedIAtomContainer
.DescriptorValue
WeightedPathDescriptor. calculate(IAtomContainer container)
Calculates the weighted path descriptors.DescriptorValue
WHIMDescriptor. calculate(IAtomContainer container)
Calculates 11 directional and 6 non-directional WHIM descriptors for.DescriptorValue
WienerNumbersDescriptor. calculate(IAtomContainer atomContainer)
Calculate the Wiener numbers.DescriptorValue
XLogPDescriptor. calculate(IAtomContainer atomContainer)
Calculates the xlogP for an atom container.DescriptorValue
ZagrebIndexDescriptor. calculate(IAtomContainer atomContainer)
Evaluate the Zagreb Index for a molecule.DescriptorValue
IPMolecularLearningDescriptor. calculatePlus(IAtomContainer container)
Deprecated.It calculates the 1,2,..Map<Integer,Integer>
JPlogPDescriptor.JPlogPCalculator. getMappedHologram(IAtomContainer struct)
Used in Training the model -
Uses of IAtomContainer in org.openscience.cdk.qsar.descriptors.protein
Methods in org.openscience.cdk.qsar.descriptors.protein with parameters of type IAtomContainer Modifier and Type Method Description DescriptorValue
TaeAminoAcidDescriptor. calculate(IAtomContainer container)
Calculates the 147 TAE descriptors for amino acids. -
Uses of IAtomContainer in org.openscience.cdk.renderer
Methods in org.openscience.cdk.renderer that return IAtomContainer Modifier and Type Method Description IAtomContainer
RendererModel. getClipboardContent()
Returns the atoms and bonds on the Renderer2D clipboard.IAtomContainer
RendererModel. getExternalSelectedPart()
Get externally selected atoms.Methods in org.openscience.cdk.renderer that return types with arguments of type IAtomContainer Modifier and Type Method Description List<IGenerator<IAtomContainer>>
AtomContainerRenderer. getGenerators()
Returns aList
ofIGenerator
s for this renderer.Methods in org.openscience.cdk.renderer with parameters of type IAtomContainer Modifier and Type Method Description static Rectangle2D
BoundsCalculator. calculateBounds(IAtomContainer atomContainer)
Calculate the bounding rectangle for an atom container.Rectangle
AtomContainerRenderer. calculateDiagramBounds(IAtomContainer atomContainer)
Given aIChemObject
, 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 parameters in org.openscience.cdk.renderer with type arguments of type IAtomContainer Constructor 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, List<IGenerator<IReaction>> reactionGenerators, 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.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, List<IGenerator<IReaction>> reactionGenerators, IFontManager fontManager)
A renderer that drawsIReaction
s with the passedIGenerator
for bothIAtomContainer
andIReaction
content.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(RendererModel rendererModel, List<IGenerator<IAtomContainer>> generators, IFontManager fontManager)
ReactionSetRenderer(List<IGenerator<IAtomContainer>> generators, List<IGenerator<IReaction>> reactionGenerators, IFontManager fontManager)
A renderer that generates diagrams using the specified generators forIAtomContainer
s andIReactionSet
s and manages fonts with the supplied font manager.ReactionSetRenderer(List<IGenerator<IAtomContainer>> generators, IFontManager fontManager)
A renderer that generates diagrams using the specified generators and manages fonts with the supplied font manager.ReactionSetRenderer(RendererModel rendererModel, List<IGenerator<IAtomContainer>> generators, List<IGenerator<IReaction>> reactionGenerators, IFontManager fontManager)
ReactionSetRenderer(RendererModel rendererModel, List<IGenerator<IAtomContainer>> generators, IFontManager fontManager)
-
Uses of IAtomContainer in org.openscience.cdk.renderer.elements
Methods in org.openscience.cdk.renderer.elements with parameters of type IAtomContainer Modifier and Type Method 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. -
Uses of IAtomContainer in org.openscience.cdk.renderer.generators
Methods in org.openscience.cdk.renderer.generators with parameters of type IAtomContainer Modifier and Type Method Description protected boolean
BasicAtomGenerator. canDraw(IAtom atom, IAtomContainer container, RendererModel model)
Checks an atom to see if it should be drawn.IRenderingElement
AtomContainerBoundsGenerator. generate(IAtomContainer container, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing.IRenderingElement
AtomNumberGenerator. generate(IAtomContainer container, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing.IRenderingElement
BasicAtomGenerator. generate(IAtomContainer atomContainer, IAtom atom, RendererModel model)
Generate the rendering element(s) for a particular atom.IRenderingElement
BasicAtomGenerator. generate(IAtomContainer container, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing.IRenderingElement
BasicBondGenerator. generate(IAtomContainer container, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing.IRenderingElement
BasicGenerator. generate(IAtomContainer ac, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing.IRenderingElement
BasicSceneGenerator. generate(IAtomContainer ac, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing.IRenderingElement
ExtendedAtomGenerator. generate(IAtomContainer container, IAtom atom, RendererModel model)
Generate the rendering element(s) for a particular atom.IRenderingElement
HighlightGenerator. generate(IAtomContainer container, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing.IRenderingElement
LonePairGenerator. generate(IAtomContainer container, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing.IRenderingElement
RadicalGenerator. generate(IAtomContainer container, RendererModel model)
Converts aIChemObject
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. -
Uses of IAtomContainer in org.openscience.cdk.renderer.generators.standard
Methods in org.openscience.cdk.renderer.generators.standard with parameters of type IAtomContainer Modifier and Type Method Description IRenderingElement
StandardGenerator. generate(IAtomContainer container, RendererModel parameters)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing. -
Uses of IAtomContainer in org.openscience.cdk.renderer.selection
Methods in org.openscience.cdk.renderer.selection that return IAtomContainer Modifier and Type Method Description IAtomContainer
IChemObjectSelection. getConnectedAtomContainer()
Make an IAtomContainer where all the bonds only have atoms that are in the selection.Methods in org.openscience.cdk.renderer.selection with parameters of type IAtomContainer Modifier and Type Method Description protected void
AbstractSelection. addToAtomContainer(IAtomContainer ac, IChemObject item)
Utility method to add anIChemObject
to anIAtomContainer
. -
Uses of IAtomContainer in org.openscience.cdk.ringsearch
Methods in org.openscience.cdk.ringsearch that return IAtomContainer Modifier and Type Method 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.Methods in org.openscience.cdk.ringsearch that return types with arguments of type IAtomContainer Modifier and Type Method Description List<IAtomContainer>
RingSearch. fusedRingFragments()
Construct a list ofIAtomContainer
s which only contain fused rings.List<IAtomContainer>
RingSearch. isolatedRingFragments()
Construct a list ofIAtomContainer
s each of which only contains a single isolated ring.Methods in org.openscience.cdk.ringsearch with parameters of type IAtomContainer Modifier and Type Method Description IRingSet
AllRingsFinder. findAllRings(IAtomContainer container)
Compute all rings in the givenIAtomContainer
.IRingSet
AllRingsFinder. findAllRings(IAtomContainer container, int maxRingSize)
Compute all rings up to and including the maxRingSize.IRingSet
AllRingsFinder. findAllRingsInIsolatedRingSystem(IAtomContainer container)
Compute all rings in the givenIAtomContainer
.IRingSet
AllRingsFinder. findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer, int maxRingSize)
Compute all rings up to an including the maxRingSize.IRingSet
FiguerasSSSRFinder. findSSSR(IAtomContainer mol)
Deprecated.Finds the Smallest Set of Smallest Rings.Constructors in org.openscience.cdk.ringsearch with parameters of type IAtomContainer Constructor Description RingSearch(IAtomContainer container)
Create a new RingSearch for the specified container.RingSearch(IAtomContainer container, int[][] graph)
Create a new RingSearch for the specified container and graph.RingSearch(IAtomContainer container, CyclicVertexSearch searcher)
Create a new RingSearch for the specified container using the provided search.SSSRFinder(IAtomContainer container)
Deprecated.Constructs a SSSRFinder for a specified molecule. -
Uses of IAtomContainer in org.openscience.cdk.signature
Methods in org.openscience.cdk.signature that return IAtomContainer Modifier and Type Method 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.Constructors in org.openscience.cdk.signature with parameters of type IAtomContainer Constructor Description AtomSignature(int atomIndex, int height, IAtomContainer molecule)
Create an atom signature starting atatomIndex
and with a maximum height ofheight
.AtomSignature(int atomIndex, int height, signature.AbstractVertexSignature.InvariantType invariantType, IAtomContainer molecule)
Create an atom signature starting atatomIndex
, with maximum height ofheight
, and using a particular invariant type.AtomSignature(int atomIndex, IAtomContainer molecule)
Create an atom signature starting atatomIndex
.AtomSignature(IAtom atom, int height, IAtomContainer molecule)
Create an atom signature for the atomatom
and with a maximum height ofheight
.AtomSignature(IAtom atom, int height, signature.AbstractVertexSignature.InvariantType invariantType, IAtomContainer molecule)
Create an atom signature for the atomatom
, with maximum height ofheight
, and using a particular invariant type.AtomSignature(IAtom atom, IAtomContainer molecule)
Create an atom signature for the atomatom
.MoleculeSignature(IAtomContainer molecule)
Creates a signature that represents this molecule.MoleculeSignature(IAtomContainer molecule, int height)
Creates a signature with a maximum height ofheight
for moleculemolecule
.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 heightheight
. -
Uses of IAtomContainer in org.openscience.cdk.silent
Classes in org.openscience.cdk.silent that implement IAtomContainer Modifier and Type Class 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
PDBMonomer
Represents the idea of an monomer as used in PDB files.class
PDBPolymer
An entry in the PDB database.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.Fields in org.openscience.cdk.silent declared as IAtomContainer Modifier and Type Field Description protected IAtomContainer[]
AtomContainerSet. atomContainers
Array of AtomContainers.Methods in org.openscience.cdk.silent that return IAtomContainer Modifier and Type Method Description IAtomContainer
AtomContainer. clone()
Clones thisIChemObject
.IAtomContainer
AtomContainerSet. getAtomContainer(int number)
Returns the AtomContainer at positionnumber
in the container.IAtomContainer
Atom. getContainer()
Access theIAtomContainer
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.Methods in org.openscience.cdk.silent that return types with arguments of type IAtomContainer Modifier and Type Method Description Iterable<IAtomContainer>
AtomContainerSet. atomContainers()
Get an iterator for this AtomContainerSet.Methods in org.openscience.cdk.silent with parameters of type IAtomContainer Modifier and Type Method 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.Method parameters in org.openscience.cdk.silent with type arguments of type IAtomContainer Modifier and Type Method Description void
AtomContainerSet. sortAtomContainers(Comparator<IAtomContainer> comparator)
Sort the AtomContainers and multipliers using a provided ComparatorConstructors in org.openscience.cdk.silent with parameters of type IAtomContainer Constructor 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. -
Uses of IAtomContainer in org.openscience.cdk.similarity
Methods in org.openscience.cdk.similarity with parameters of type IAtomContainer Modifier and Type Method 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. -
Uses of IAtomContainer in org.openscience.cdk.smarts
Methods in org.openscience.cdk.smarts with parameters of type IAtomContainer Modifier and Type Method 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 thetarget
.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 SmartsResult
Smarts. parseToResult(IAtomContainer mol, String smarts)
Parse the provided SMARTS string appending query atom/bonds to the provided molecule.static SmartsResult
Smarts. parseToResult(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)
Constructors in org.openscience.cdk.smarts with parameters of type IAtomContainer Constructor Description SmartsFragmentExtractor(IAtomContainer mol)
Create a new instance over the provided molecule. -
Uses of IAtomContainer in org.openscience.cdk.smiles
Methods in org.openscience.cdk.smiles that return IAtomContainer Modifier and Type Method 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
).Methods in org.openscience.cdk.smiles with parameters of type IAtomContainer Modifier and Type Method Description String
SmilesGenerator. create(IAtomContainer molecule)
Generate SMILES for the providedmolecule
.String
SmilesGenerator. create(IAtomContainer molecule, int[] order)
Creates a SMILES string of the flavour specified in the constructor and write the output order to the provided array.static String
SmilesGenerator. create(IAtomContainer molecule, int flavour, int[] order)
Creates a SMILES string of the flavour specified as a parameter and write the output order to the provided array.static Comparator<IAtom>
SmilesGenerator. createComparator(IAtomContainer mol, int flavor)
String
SmilesGenerator. createSMILES(IAtomContainer molecule)
Deprecated.use #createIAtomContainer
DeduceBondSystemTool. fixAromaticBondOrders(IAtomContainer atomContainer)
Deprecated.Added missing bond orders based on atom type information.boolean
DeduceBondSystemTool. isOK(IAtomContainer m)
Deprecated.Determines if, according to the algorithms implemented in this class, the given AtomContainer has properly distributed double bonds.IAtomContainer
FixBondOrdersTool. kekuliseAromaticRings(IAtomContainer molecule)
Deprecated.kekuliseAromaticRings - function to add double/single bond order information for molecules having rings containing all atoms marked SP2 or Planar3 hybridisation. -
Uses of IAtomContainer in org.openscience.cdk.smiles.smarts
Methods in org.openscience.cdk.smiles.smarts with parameters of type IAtomContainer Modifier and Type Method Description int[]
SmartsPattern. match(IAtomContainer container)
Deprecated.Find a matching of this pattern in thetarget
.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. -
Uses of IAtomContainer in org.openscience.cdk.smsd
Methods in org.openscience.cdk.smsd that return IAtomContainer Modifier and Type Method 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.Methods in org.openscience.cdk.smsd with parameters of type IAtomContainer Modifier and Type Method 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 atomsstatic 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 -
Uses of IAtomContainer in org.openscience.cdk.smsd.algorithm.matchers
Methods in org.openscience.cdk.smsd.algorithm.matchers with parameters of type IAtomContainer Modifier and Type Method 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
AtomMatcher. matches(IAtomContainer container, IAtom atom)
Deprecated.boolean
BondMatcher. matches(IAtomContainer container, IBond atom)
Deprecated.boolean
DefaultBondMatcher. matches(IAtomContainer targetContainer, IBond targetBond)
Deprecated.boolean
DefaultMCSPlusAtomMatcher. matches(IAtomContainer targetContainer, IAtom targetAtom)
Deprecated.boolean
DefaultRGraphAtomMatcher. matches(IAtomContainer targetContainer, IAtom targetAtom)
Deprecated.Constructors in org.openscience.cdk.smsd.algorithm.matchers with parameters of type IAtomContainer Constructor Description DefaultBondMatcher(IAtomContainer queryMol, IBond queryBond, boolean shouldMatchBonds)
Deprecated.ConstructorDefaultMCSPlusAtomMatcher(IAtomContainer queryContainer, IAtom atom, boolean shouldMatchBonds)
Deprecated.ConstructorDefaultMCSPlusAtomMatcher(IAtomContainer queryContainer, IAtom template, int blockedPositions, boolean shouldMatchBonds)
Deprecated.ConstructorDefaultRGraphAtomMatcher(IAtomContainer queryContainer, IAtom atom, boolean shouldMatchBonds)
Deprecated.ConstructorDefaultRGraphAtomMatcher(IAtomContainer queryContainer, IAtom template, int blockedPositions, boolean shouldMatchBonds)
Deprecated.ConstructorDefaultVFAtomMatcher(IAtomContainer queryContainer, IAtom atom, boolean shouldMatchBonds)
Deprecated.ConstructorDefaultVFAtomMatcher(IAtomContainer queryContainer, IAtom template, int blockedPositions, boolean shouldMatchBonds)
Deprecated.ConstructorDefaultVFBondMatcher(IAtomContainer queryMol, IBond queryBond, boolean shouldMatchBonds)
Deprecated.Constructor -
Uses of IAtomContainer in org.openscience.cdk.smsd.algorithm.mcgregor
Methods in org.openscience.cdk.smsd.algorithm.mcgregor with parameters of type IAtomContainer Modifier and Type Method 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
QueryProcessor. process(IQueryAtomContainer 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 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.Constructors in org.openscience.cdk.smsd.algorithm.mcgregor with parameters of type IAtomContainer Constructor 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. -
Uses of IAtomContainer in org.openscience.cdk.smsd.algorithm.mcsplus
Methods in org.openscience.cdk.smsd.algorithm.mcsplus with parameters of type IAtomContainer Modifier and Type Method 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.Constructors in org.openscience.cdk.smsd.algorithm.mcsplus with parameters of type IAtomContainer Constructor Description GenerateCompatibilityGraph(IAtomContainer source, IAtomContainer target, boolean shouldMatchBonds)
Deprecated.Generates a compatibility graph between two molecules -
Uses of IAtomContainer in org.openscience.cdk.smsd.algorithm.rgraph
Methods in org.openscience.cdk.smsd.algorithm.rgraph that return IAtomContainer Modifier and Type Method Description IAtomContainer
CDKRMapHandler. getSource()
Deprecated.Returns source moleculeIAtomContainer
CDKRMapHandler. getTarget()
Deprecated.Returns target moleculestatic IAtomContainer
CDKMCS. project(List<CDKRMap> rMapList, IAtomContainer graph, int key)
Deprecated.Projects atom list of CDKRMap on atom molecule.Methods in org.openscience.cdk.smsd.algorithm.rgraph that return types with arguments of type IAtomContainer Modifier and Type Method 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.Methods in org.openscience.cdk.smsd.algorithm.rgraph with parameters of type IAtomContainer Modifier and Type Method Description static CDKRGraph
CDKMCS. buildRGraph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
Deprecated.Builds the CDKRGraph ( resolution graph ), from two atomContainer (description of the two molecules to compare) This is the interface point between the CDK model and the generic MCSS algorithm based on the RGRaph.void
CDKRMapHandler. calculateIsomorphs(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
Deprecated.This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprintvoid
CDKRMapHandler. calculateOverlapsAndReduce(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
Deprecated.This function calculates all the possible combinations of MCSvoid
CDKRMapHandler. calculateOverlapsAndReduceExactMatch(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
Deprecated.This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprintvoid
CDKRMapHandler. calculateSubGraphs(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds)
Deprecated.This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprintstatic List<CDKRMap>
CDKMCS. checkSingleAtomCases(IAtomContainer sourceGraph, IAtomContainer targetGraph)
Deprecated.Checks for single atom cases before doing subgraph/isomorphism searchstatic 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
CDKMCSHandler. getUncommon(IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds)
Deprecated.protected IAtomContainerSet
CDKSubGraphHandler. 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
CDKMCSHandler. set(IQueryAtomContainer source, IAtomContainer target)
Deprecated.Initialise the query and target molecule.void
CDKSubGraphHandler. set(IQueryAtomContainer source, IAtomContainer target)
Deprecated.Initialise the query and target molecule.void
CDKRMapHandler. setSource(IAtomContainer aSource)
Deprecated.Set source moleculevoid
CDKRMapHandler. setTarget(IAtomContainer aTarget)
Deprecated.Set target molecule -
Uses of IAtomContainer in org.openscience.cdk.smsd.algorithm.single
Methods in org.openscience.cdk.smsd.algorithm.single with parameters of type IAtomContainer Modifier and Type Method Description protected List<Map<IAtom,IAtom>>
SingleMapping. getOverLaps(IAtomContainer source, IAtomContainer target, boolean removeHydrogen)
Deprecated.Returns single mapping solutions.protected List<Map<IAtom,IAtom>>
SingleMapping. getOverLaps(IQueryAtomContainer source, IAtomContainer target, boolean removeHydrogen)
Deprecated.Returns single mapping solutions.void
SingleMappingHandler. set(IQueryAtomContainer source, IAtomContainer target)
Deprecated.Initialise the query and target molecule. -
Uses of IAtomContainer in org.openscience.cdk.smsd.algorithm.vflib
Methods in org.openscience.cdk.smsd.algorithm.vflib with parameters of type IAtomContainer Modifier and Type Method Description void
VFlibMCSHandler. set(IQueryAtomContainer source, IAtomContainer target)
Deprecated.Initialise the query and target molecule.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. -
Uses of IAtomContainer in org.openscience.cdk.smsd.algorithm.vflib.builder
Constructors in org.openscience.cdk.smsd.algorithm.vflib.builder with parameters of type IAtomContainer Constructor Description TargetProperties(IAtomContainer container)
Deprecated. -
Uses of IAtomContainer in org.openscience.cdk.smsd.algorithm.vflib.interfaces
Methods in org.openscience.cdk.smsd.algorithm.vflib.interfaces with parameters of type IAtomContainer Modifier and Type Method 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. -
Uses of IAtomContainer in org.openscience.cdk.smsd.algorithm.vflib.map
Methods in org.openscience.cdk.smsd.algorithm.vflib.map with parameters of type IAtomContainer Modifier and Type Method Description int
VFMapper. countMaps(IAtomContainer target)
Deprecated.Returns solution map count.int
VFMCSMapper. countMaps(IAtomContainer target)
Deprecated.Returns solution map count.Map<INode,IAtom>
VFMapper. getFirstMap(IAtomContainer target)
Deprecated.Returns first solution map.Map<INode,IAtom>
VFMCSMapper. getFirstMap(IAtomContainer target)
Deprecated.Returns first solution map.List<Map<INode,IAtom>>
VFMapper. getMaps(IAtomContainer target)
Deprecated.Returns all solution map.List<Map<INode,IAtom>>
VFMCSMapper. getMaps(IAtomContainer target)
Deprecated.Returns all solution map.boolean
VFMapper. hasMap(IAtomContainer targetMolecule)
Deprecated.checks if a map exits for a molecule.boolean
VFMCSMapper. hasMap(IAtomContainer targetMolecule)
Deprecated.checks if a map exits for a molecule.Constructors in org.openscience.cdk.smsd.algorithm.vflib.map with parameters of type IAtomContainer Constructor Description VFMapper(IAtomContainer queryMolecule, boolean bondMatcher)
Deprecated.VFMCSMapper(IAtomContainer queryMolecule, boolean bondMatcher)
Deprecated. -
Uses of IAtomContainer in org.openscience.cdk.smsd.algorithm.vflib.query
Constructors in org.openscience.cdk.smsd.algorithm.vflib.query with parameters of type IAtomContainer Constructor Description QueryCompiler(IAtomContainer molecule, boolean shouldMatchBonds)
Deprecated.Construct query object from the molecule -
Uses of IAtomContainer in org.openscience.cdk.smsd.filters
Constructors in org.openscience.cdk.smsd.filters with parameters of type IAtomContainer Constructor 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. -
Uses of IAtomContainer in org.openscience.cdk.smsd.interfaces
Methods in org.openscience.cdk.smsd.interfaces that return IAtomContainer Modifier and Type Method 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.Methods in org.openscience.cdk.smsd.interfaces with parameters of type IAtomContainer Modifier and Type Method Description abstract void
AbstractMCS. init(IAtomContainer source, IAtomContainer target, boolean removeHydrogen, boolean cleanAndConfigureMolecule)
Deprecated.initialize query and target molecules.abstract void
AbstractMCS. init(IQueryAtomContainer source, IAtomContainer target)
Deprecated.initialize query and target molecules.void
IMCSBase. set(IQueryAtomContainer source, IAtomContainer target)
Deprecated.Initialise the query and target molecule. -
Uses of IAtomContainer in org.openscience.cdk.smsd.labelling
Methods in org.openscience.cdk.smsd.labelling that return IAtomContainer Modifier and Type Method Description IAtomContainer
CanonicalLabellingAdaptor. getCanonicalMolecule(IAtomContainer container)
Deprecated.IAtomContainer
ICanonicalMoleculeLabeller. getCanonicalMolecule(IAtomContainer container)
Deprecated.IAtomContainer
MoleculeSignatureLabellingAdaptor. getCanonicalMolecule(IAtomContainer container)
Deprecated.IAtomContainer
AtomContainerAtomPermutor. next()
Deprecated.static IAtomContainer
AtomContainerAtomPermutor. permute(int[] p, IAtomContainer atomContainer)
Deprecated.Methods in org.openscience.cdk.smsd.labelling with parameters of type IAtomContainer Modifier and Type Method Description IAtomContainer
CanonicalLabellingAdaptor. getCanonicalMolecule(IAtomContainer container)
Deprecated.IAtomContainer
ICanonicalMoleculeLabeller. getCanonicalMolecule(IAtomContainer container)
Deprecated.IAtomContainer
MoleculeSignatureLabellingAdaptor. getCanonicalMolecule(IAtomContainer container)
Deprecated.int[]
CanonicalLabellingAdaptor. getCanonicalPermutation(IAtomContainer container)
Deprecated.int[]
ICanonicalMoleculeLabeller. getCanonicalPermutation(IAtomContainer container)
Deprecated.int[]
MoleculeSignatureLabellingAdaptor. getCanonicalPermutation(IAtomContainer container)
Deprecated.static IAtomContainer
AtomContainerAtomPermutor. permute(int[] p, IAtomContainer atomContainer)
Deprecated.String
AtomContainerPrinter. toString(IAtomContainer atomContainer)
Deprecated.Constructors in org.openscience.cdk.smsd.labelling with parameters of type IAtomContainer Constructor Description AtomContainerAtomPermutor(IAtomContainer atomContainer)
Deprecated. -
Uses of IAtomContainer in org.openscience.cdk.smsd.ring
Methods in org.openscience.cdk.smsd.ring with parameters of type IAtomContainer Modifier and Type Method Description void
RingFilter. filterAtoms(IAtomContainer molecule, Collection<IAtom> atoms)
Deprecated.Collection<List<IAtom>>
HanserRingFinder. findRings(IAtomContainer molecule)
Deprecated.Returns a collection of rings.Collection<List<IAtom>>
RingFinder. findRings(IAtomContainer molecule)
Deprecated.Returns Collection of atoms in Rings based on Hanser Ring Finding methodIRingSet
HanserRingFinder. getRingSet(IAtomContainer molecule)
Deprecated.Returns Ring set based on Hanser Ring Finding methodIRingSet
RingFinder. getRingSet(IAtomContainer molecule)
Deprecated.Returns CDK object Ring set based on Hanser Ring Finding methodConstructors in org.openscience.cdk.smsd.ring with parameters of type IAtomContainer Constructor Description PathGraph(IAtomContainer molecule)
Deprecated. -
Uses of IAtomContainer in org.openscience.cdk.smsd.tools
Methods in org.openscience.cdk.smsd.tools that return IAtomContainer Modifier and Type Method Description static IAtomContainer
MoleculeSanityCheck. checkAndCleanMolecule(IAtomContainer molecule)
Deprecated.Modules for cleaning a moleculestatic IAtomContainer
ExtAtomContainerManipulator. convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
Deprecated.Returns IAtomContainer without Hydrogen.IAtomContainer
MolHandler. getMolecule()
Deprecated.Returns the modified containerstatic IAtomContainer
ExtAtomContainerManipulator. makeDeepCopy(IAtomContainer container)
Deprecated.Retrurns deep copy of the moleculestatic IAtomContainer
ExtAtomContainerManipulator. removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer atomContainer)
Deprecated.Returns IAtomContainer without Hydrogen.Methods in org.openscience.cdk.smsd.tools with parameters of type IAtomContainer Modifier and Type Method 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 moleculestatic 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 moleculestatic void
ExtAtomContainerManipulator. percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Deprecated.Convenience method to perceive atom types for allIAtom
s in theIAtomContainer
, using theCDKAtomTypeMatcher
.static IAtomContainer
ExtAtomContainerManipulator. removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer atomContainer)
Deprecated.Returns IAtomContainer without Hydrogen.Constructors in org.openscience.cdk.smsd.tools with parameters of type IAtomContainer Constructor Description MolHandler(IAtomContainer container, boolean removeHydrogen, boolean cleanMolecule)
Deprecated.Creates a new instance of MolHandler -
Uses of IAtomContainer in org.openscience.cdk.stereo
Fields in org.openscience.cdk.stereo declared as IAtomContainer Modifier and Type Field Description protected IAtomContainer
StereoElementFactory. container
Native CDK structure representation.Methods in org.openscience.cdk.stereo with parameters of type IAtomContainer Modifier and Type Method Description static IBond
ExtendedCisTrans. findCentralBond(IAtomContainer mol, IAtom atom)
Locate the central double-bond in a chain of cumulated double bonds.static IAtom[]
ExtendedCisTrans. findTerminalAtoms(IAtomContainer container, IBond focus)
Helper method to locate two terminal atoms in a container for this extended Cis/Trans element.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 int
ExtendedTetrahedral. getLength(IAtomContainer container, IAtom focus)
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).Constructors in org.openscience.cdk.stereo with parameters of type IAtomContainer Constructor Description StereoElementFactory(IAtomContainer container, int[][] graph, GraphUtil.EdgeToBondMap bondMap)
Internal constructor. -
Uses of IAtomContainer in org.openscience.cdk.structgen
Methods in org.openscience.cdk.structgen that return IAtomContainer Modifier and Type Method 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.Methods in org.openscience.cdk.structgen that return types with arguments of type IAtomContainer Modifier and Type Method 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.Methods in org.openscience.cdk.structgen with parameters of type IAtomContainer Modifier and Type Method Description void
RandomGenerator. mutate(IAtomContainer ac)
Randomly chooses four atoms and alters the bonding pattern between them according to rules described in "Faulon, JCICS 1996, 36, 731".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.void
SingleStructureRandomGenerator. setAtomContainer(IAtomContainer ac)
Sets the AtomContainer attribute of the SingleStructureRandomGenerator object.void
RandomGenerator. setMolecule(IAtomContainer molecule)
Assigns a starting structure to this generator.Constructors in org.openscience.cdk.structgen with parameters of type IAtomContainer Constructor Description RandomGenerator(IAtomContainer molecule)
Constructs a RandomGenerator with a given starting structure. -
Uses of IAtomContainer in org.openscience.cdk.structgen.maygen
Methods in org.openscience.cdk.structgen.maygen that return IAtomContainer Modifier and Type Method Description IAtomContainer
Maygen. buildAtomContainerFromMatrix(int[][] mat, IAtomContainer atomContainer)
Building an atom container for an adjacency matrix.IAtomContainer
Maygen. buildContainer4SDF(int[][] mat)
Building an atom container for an adjacency matrix.IAtomContainer
Maygen. buildContainer4SDF(String[] symbols)
Building an atom container for SDF output from its symbolsIAtomContainer
Maygen. buildContainer4SDF(IAtomContainer ac, int[][] mat)
Building an atom container for an adjacency matrix.IAtomContainer
Maygen. initAC(IAtomContainer ac, String[] symbolArrayCopy)
Building an atom container from a string of atom-implicit hydrogen information.Methods in org.openscience.cdk.structgen.maygen with parameters of type IAtomContainer Modifier and Type Method Description IAtomContainer
Maygen. buildAtomContainerFromMatrix(int[][] mat, IAtomContainer atomContainer)
Building an atom container for an adjacency matrix.IAtomContainer
Maygen. buildContainer4SDF(IAtomContainer ac, int[][] mat)
Building an atom container for an adjacency matrix.void
Maygen.Consumer. consume(IAtomContainer mol)
void
Maygen. emit(IAtomContainer mol)
Emits a molecule to whomever is listening.int[][]
Maygen. forward(IAtomContainer ac, String[] symbolArrayCopy, int[][] a, int[] indices, int[] degrees, int[] initialPartition, int[][] partitionList, boolean[] callForward, int[] connectivityIndices, boolean[] learningFromConnectivity, int[] nonCanonicalIndices, List<ArrayList<Permutation>> formerPermutations, int[] hydrogens, int[] partSize, int[] r, int[] y, int[] z, int[][][] max, int[][][] l, int[][][] c, int[][] ys, int[][] zs, boolean[] learningFromCanonicalTest)
Setting successor indices entry if there is a possible filling.int[][]
Maygen. forward(IAtomContainer ac, String[] symbolArrayCopy, int lInverse, int cInverse, int maximalX, int i, int j, int[][] a, int[] indices, int[] initialPartition, int[][] partitionList, boolean[] callForward, int[] connectivityIndices, boolean[] learningFromConnectivity, int[] nonCanonicalIndices, List<ArrayList<Permutation>> formerPermutations, int[] hydrogens, int[] partSize, int[] r, int[] y, int[] z, int[][][] max, int[][][] l, int[][][] c, int[][] ys, int[][] zs, boolean[] learningFromCanonicalTest)
void
Maygen. generate(IAtomContainer ac, String[] symbolArrayCopy, int[] degreeList, int[] initialPartition, int[][] partitionList, int[] connectivityIndices, boolean[] learningFromConnectivity, int[] nonCanonicalIndices, List<ArrayList<Permutation>> formerPermutations, int[] hydrogens, int[] partSize, int[] r, int[] y, int[] z, int[][] ys, int[][] zs, boolean[] learningFromCanonicalTest)
Initialization of global variables for the generate of structures for given degree list.IAtomContainer
Maygen. initAC(IAtomContainer ac, String[] symbolArrayCopy)
Building an atom container from a string of atom-implicit hydrogen information.void
Maygen. nextStep(IAtomContainer ac, String[] symbolArrayCopy, int[][] a, int[] indices, int[] degrees, int[] initialPartition, int[][] partitionList, boolean[] callForward, int[] connectivityIndices, boolean[] learningFromConnectivity, int[] nonCanonicalIndices, List<ArrayList<Permutation>> formerPermutations, int[] hydrogens, int[] partSize, int[] r, int[] y, int[] z, int[][][] max, int[][][] l, int[][][] c, int[][] ys, int[][] zs, boolean[] learningFromCanonicalTest, boolean[] flag)
Calling foward or backward function in a nextstep function. -
Uses of IAtomContainer in org.openscience.cdk.structgen.stochastic
Methods in org.openscience.cdk.structgen.stochastic that return IAtomContainer Modifier and Type Method Description IAtomContainer
PartialFilledStructureMerger. generate(IAtomContainerSet atomContainers)
Randomly generates a single, connected, correctly bonded structure from a number of fragments. -
Uses of IAtomContainer in org.openscience.cdk.structgen.stochastic.operator
Methods in org.openscience.cdk.structgen.stochastic.operator that return types with arguments of type IAtomContainer Modifier and Type Method Description List<IAtomContainer>
CrossoverMachine. doCrossover(IAtomContainer dad, IAtomContainer mom)
Performs the n point crossover of twoIAtomContainer
.Methods in org.openscience.cdk.structgen.stochastic.operator with parameters of type IAtomContainer Modifier and Type Method Description List<IAtomContainer>
CrossoverMachine. doCrossover(IAtomContainer dad, IAtomContainer mom)
Performs the n point crossover of twoIAtomContainer
.Constructors in org.openscience.cdk.structgen.stochastic.operator with parameters of type IAtomContainer Constructor Description ChemGraph(IAtomContainer chrom)
-
Uses of IAtomContainer in org.openscience.cdk.tautomers
Methods in org.openscience.cdk.tautomers that return types with arguments of type IAtomContainer Modifier and Type Method Description List<IAtomContainer>
InChITautomerGenerator. getTautomers(IAtomContainer mol)
Public method to get tautomers for an input molecule, based on the InChI which will be calculated by JNI-InChI.List<IAtomContainer>
InChITautomerGenerator. getTautomers(IAtomContainer mol, String inchi)
Deprecated.useInChITautomerGenerator.getTautomers(IAtomContainer)
directlyMethods in org.openscience.cdk.tautomers with parameters of type IAtomContainer Modifier and Type Method Description List<IAtomContainer>
InChITautomerGenerator. getTautomers(IAtomContainer mol)
Public method to get tautomers for an input molecule, based on the InChI which will be calculated by JNI-InChI.List<IAtomContainer>
InChITautomerGenerator. getTautomers(IAtomContainer mol, String inchi)
Deprecated.useInChITautomerGenerator.getTautomers(IAtomContainer)
directly -
Uses of IAtomContainer in org.openscience.cdk.templates
Methods in org.openscience.cdk.templates that return IAtomContainer Modifier and Type Method Description static IAtomContainer
MoleculeFactory. loadMolecule(String inFile)
Deprecated.static IAtomContainer
MoleculeFactory. make123Triazole()
Deprecated.Returns 1,2,3-triazole without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. make123Triazole()
Returns 1,2,3-triazole without explicit hydrogens.static IAtomContainer
MoleculeFactory. make124Triazole()
Deprecated.Returns 1,2,4-triazole without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. make124Triazole()
Returns 1,2,4-triazole without explicit hydrogens.static IAtomContainer
MoleculeFactory. make4x3CondensedRings()
Deprecated.static IAtomContainer
TestMoleculeFactory. make4x3CondensedRings()
static IAtomContainer
MoleculeFactory. makeAdenine()
Deprecated.static IAtomContainer
TestMoleculeFactory. makeAdenine()
static IAtomContainer
MoleculeFactory. makeAlkane(int chainLength)
Deprecated.Generate an Alkane (chain of carbons with no hydrogens) of a given length.static IAtomContainer
TestMoleculeFactory. makeAlkane(int chainLength)
Generate an Alkane (chain of carbons with no hydrogens) of a given length.static IAtomContainer
MoleculeFactory. makeAlphaPinene()
Deprecated.static IAtomContainer
TestMoleculeFactory. makeAlphaPinene()
static IAtomContainer
TestMoleculeFactory. makeAnthracene()
static IAtomContainer
MoleculeFactory. makeAzulene()
Deprecated.Returns azulene without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeAzulene()
Returns azulene without explicit hydrogens.static IAtomContainer
MoleculeFactory. makeBenzene()
Deprecated.static IAtomContainer
TestMoleculeFactory. makeBenzene()
static IAtomContainer
MoleculeFactory. makeBicycloRings()
Deprecated.static IAtomContainer
TestMoleculeFactory. makeBicycloRings()
static IAtomContainer
MoleculeFactory. makeBiphenyl()
Deprecated.Returns biphenyl without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeBiphenyl()
Returns biphenyl without explicit hydrogens.static IAtomContainer
MoleculeFactory. makeBranchedAliphatic()
Deprecated.static IAtomContainer
TestMoleculeFactory. makeBranchedAliphatic()
static IAtomContainer
MoleculeFactory. makeCyclobutadiene()
Deprecated.Returns cyclobutadiene without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeCyclobutadiene()
Returns cyclobutadiene without explicit hydrogens.static IAtomContainer
MoleculeFactory. makeCyclobutane()
Deprecated.Returns cyclobutane without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeCyclobutane()
Returns cyclobutane without explicit hydrogens.static IAtomContainer
MoleculeFactory. makeCyclohexane()
Deprecated.Returns cyclohexane without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeCyclohexane()
Returns cyclohexane without explicit hydrogens.static IAtomContainer
MoleculeFactory. makeCyclohexene()
Deprecated.Returns cyclohexene without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeCyclohexene()
Returns cyclohexene without explicit hydrogens.static IAtomContainer
MoleculeFactory. makeCyclopentane()
Deprecated.Returns cyclopentane without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeCyclopentane()
Returns cyclopentane without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeCyclophaneLike()
octacyclo[17.2.2.2¹,⁴.2⁴,⁷.2⁷,¹⁰.2¹⁰,¹³.2¹³,¹⁶.2¹⁶,¹⁹]pentatriacontanestatic IAtomContainer
MoleculeFactory. makeDiamantane()
Deprecated.static IAtomContainer
TestMoleculeFactory. makeDiamantane()
static IAtomContainer
MoleculeFactory. makeEthylCyclohexane()
Deprecated.static IAtomContainer
TestMoleculeFactory. makeEthylCyclohexane()
static IAtomContainer
MoleculeFactory. makeEthylPropylPhenantren()
Deprecated.static IAtomContainer
TestMoleculeFactory. makeEthylPropylPhenantren()
static IAtomContainer
MoleculeFactory. makeFusedRings()
Deprecated.static IAtomContainer
TestMoleculeFactory. makeFusedRings()
static IAtomContainer
TestMoleculeFactory. makeGappedCyclophaneLike()
octacyclo[24.2.2.2²,⁵.2⁶,⁹.2¹⁰,¹³.2¹⁴,¹⁷.2¹⁸,²¹.2²²,²⁵]dotetracontanestatic IAtomContainer
MoleculeFactory. makeImidazole()
Deprecated.Returns imidazole without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeImidazole()
Returns imidazole without explicit hydrogens.static IAtomContainer
MoleculeFactory. makeIndole()
Deprecated.Returns indole without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeIndole()
Returns indole without explicit hydrogens.static IAtomContainer
MoleculeFactory. makeIsothiazole()
Deprecated.Returns isothiazole without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeIsothiazole()
Returns isothiazole without explicit hydrogens.static IAtomContainer
MoleculeFactory. makeIsoxazole()
Deprecated.Returns Isoxazole without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeIsoxazole()
Returns Isoxazole without explicit hydrogens.static IAtomContainer
MoleculeFactory. makeMethylDecaline()
Deprecated.static IAtomContainer
TestMoleculeFactory. makeMethylDecaline()
static IAtomContainer
TestMoleculeFactory. makeNaphthalene()
InChI=1/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8Hstatic IAtomContainer
MoleculeFactory. makeOxadiazole()
Deprecated.Returns oxadiazole without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeOxadiazole()
Returns oxadiazole without explicit hydrogens.static IAtomContainer
MoleculeFactory. makeOxazole()
Deprecated.Returns Oxazole without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeOxazole()
Returns Oxazole without explicit hydrogens.static IAtomContainer
MoleculeFactory. makePhenylAmine()
Deprecated.static IAtomContainer
TestMoleculeFactory. makePhenylAmine()
static IAtomContainer
MoleculeFactory. makePhenylEthylBenzene()
Deprecated.static IAtomContainer
TestMoleculeFactory. makePhenylEthylBenzene()
static IAtomContainer
MoleculeFactory. makePiperidine()
Deprecated.static IAtomContainer
TestMoleculeFactory. makePiperidine()
static IAtomContainer
MoleculeFactory. makePropylCycloPropane()
Deprecated.static IAtomContainer
TestMoleculeFactory. makePropylCycloPropane()
static IAtomContainer
MoleculeFactory. makePyrazole()
Deprecated.Returns pyrazole without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makePyrazole()
Returns pyrazole without explicit hydrogens.static IAtomContainer
MoleculeFactory. makePyridazine()
Deprecated.Returns pyridazine without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makePyridazine()
Returns pyridazine without explicit hydrogens.static IAtomContainer
MoleculeFactory. makePyridine()
Deprecated.Returns pyridine without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makePyridine()
Returns pyridine without explicit hydrogens.static IAtomContainer
MoleculeFactory. makePyridineOxide()
Deprecated.Returns pyridine oxide without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makePyridineOxide()
Returns pyridine oxide without explicit hydrogens.static IAtomContainer
MoleculeFactory. makePyrimidine()
Deprecated.Returns pyrimidine without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makePyrimidine()
Returns pyrimidine without explicit hydrogens.static IAtomContainer
MoleculeFactory. makePyrrole()
Deprecated.Returns pyrrole without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makePyrrole()
Returns pyrrole without explicit hydrogens.static IAtomContainer
MoleculeFactory. makePyrroleAnion()
Deprecated.Returns pyrrole anion without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makePyrroleAnion()
Returns pyrrole anion without explicit hydrogens.static IAtomContainer
MoleculeFactory. makeQuinone()
Deprecated.static IAtomContainer
TestMoleculeFactory. makeQuinone()
static IAtomContainer
MoleculeFactory. makeSingleRing()
Deprecated.static IAtomContainer
TestMoleculeFactory. makeSingleRing()
static IAtomContainer
MoleculeFactory. makeSpiroRings()
Deprecated.static IAtomContainer
TestMoleculeFactory. makeSpiroRings()
static IAtomContainer
MoleculeFactory. makeSteran()
Deprecated.static IAtomContainer
TestMoleculeFactory. makeSteran()
static IAtomContainer
MoleculeFactory. makeTetrahydropyran()
Deprecated.static IAtomContainer
TestMoleculeFactory. makeTetrahydropyran()
static IAtomContainer
MoleculeFactory. makeTetrazole()
Deprecated.Returns tetrazole without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeTetrazole()
Returns tetrazole without explicit hydrogens.static IAtomContainer
MoleculeFactory. makeThiadiazole()
Deprecated.Returns thiadiazole without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeThiadiazole()
Returns thiadiazole without explicit hydrogens.static IAtomContainer
MoleculeFactory. makeThiazole()
Deprecated.Returns thiazole without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeThiazole()
Returns thiazole without explicit hydrogens.static IAtomContainer
MoleculeFactory. makeTriazine()
Deprecated.Returns triazine without explicit hydrogens.static IAtomContainer
TestMoleculeFactory. makeTriazine()
Returns triazine without explicit hydrogens. -
Uses of IAtomContainer in org.openscience.cdk.templates.saturatedhydrocarbons
Methods in org.openscience.cdk.templates.saturatedhydrocarbons that return IAtomContainer Modifier and Type Method Description static IAtomContainer
IsoAlkanes. getIsobutane(IChemObjectBuilder builder)
static IAtomContainer
IsoAlkanes. getIsohexane(IChemObjectBuilder builder)
static IAtomContainer
IsoAlkanes. getIsopentane(IChemObjectBuilder builder)
-
Uses of IAtomContainer in org.openscience.cdk.tools
Fields in org.openscience.cdk.tools declared as IAtomContainer Modifier and Type Field Description protected IAtomContainer
HOSECodeGenerator. atomContainer
The molecular structure on which we workMethods in org.openscience.cdk.tools that return IAtomContainer Modifier and Type Method Description IAtomContainer
StructureResonanceGenerator. getContainer(IAtomContainer molecule, IAtom atom)
Get the container which the atom is found on resonance from aIAtomContainer
.IAtomContainer
StructureResonanceGenerator. getContainer(IAtomContainer molecule, IBond bond)
Get the container which the bond is found on resonance from aIAtomContainer
.Methods in org.openscience.cdk.tools with parameters of type IAtomContainer Modifier and Type Method Description void
CDKHydrogenAdder. addImplicitHydrogens(IAtomContainer container)
Sets implicit hydrogen counts for all atoms in the given IAtomContainer.void
CDKHydrogenAdder. addImplicitHydrogens(IAtomContainer container, IAtom atom)
Sets the implicit hydrogen count for the indicated IAtom in the given IAtomContainer.boolean
LonePairElectronChecker. allSaturated(IAtomContainer ac)
Determines of all atoms on the AtomContainer have the right number the lone pair electrons.boolean
SaturationChecker. allSaturated(IAtomContainer ac)
boolean
SmilesValencyChecker. allSaturated(IAtomContainer ac)
IRingSet
AtomTypeTools. assignAtomTypePropertiesToAtom(IAtomContainer molecule)
IRingSet
AtomTypeTools. assignAtomTypePropertiesToAtom(IAtomContainer molecule, boolean aromaticity)
Method assigns certain properties to an atom.boolean
AtomTypeAwareSaturationChecker. bondOrderCanBeIncreased(IBond bond, IAtomContainer atomContainer)
Check if the bond order can be increased.int
SaturationChecker. calculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container)
Calculate the number of missing hydrogens by subtracting the number of bonds for the atom from the expected number of bonds.int
SaturationChecker. calculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container, boolean throwExceptionForUnknowAtom)
int
SmilesValencyChecker. calculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container)
boolean
SaturationChecker. couldMatchAtomType(IAtomContainer atomContainer, IAtom atom, IAtomType atomType)
Determines if the atom can be of type AtomType.boolean
SmilesValencyChecker. couldMatchAtomType(IAtomContainer container, IAtom atom, IAtomType type)
Determines if the atom can be of type AtomType.static void
DeAromatizationTool. Dearomatize(IAtomContainer molecule)
Deprecated.void
AtomTypeAwareSaturationChecker. decideBondOrder(IAtomContainer atomContainer)
This method decides the bond order on bonds that has theSINGLE_OR_DOUBLE
-flag raised.void
AtomTypeAwareSaturationChecker. decideBondOrder(IAtomContainer atomContainer, boolean atomsSaturated)
This method decides the bond order on bonds that has theSINGLE_OR_DOUBLE
-flag raised.static void
CDKUtilities. fixAromaticityForXLogP(IAtomContainer m)
Deprecated.static boolean
CDKUtilities. fixNitroGroups2(IAtomContainer m)
Deprecated.static void
CDKUtilities. fixSulphurH(IAtomContainer m)
Deprecated.IAtomContainer
StructureResonanceGenerator. getContainer(IAtomContainer molecule, IAtom atom)
Get the container which the atom is found on resonance from aIAtomContainer
.IAtomContainer
StructureResonanceGenerator. getContainer(IAtomContainer molecule, IBond bond)
Get the container which the bond is found on resonance from aIAtomContainer
.IAtomContainerSet
StructureResonanceGenerator. getContainers(IAtomContainer molecule)
Get the container which is found resonance from aIAtomContainer
.double
SaturationChecker. getCurrentMaxBondOrder(IAtom atom, IAtomContainer ac)
Returns the currently maximum formable bond order for this atom.String
HOSECodeGenerator. getHOSECode(IAtomContainer ac, IAtom root, int noOfSpheres)
String
HOSECodeGenerator. getHOSECode(IAtomContainer ac, IAtom root, int noOfSpheres, boolean ringsize)
static double[]
IonizationPotentialTool. getQSARs(IAtomContainer container, IAtom atom)
Deprecated.Get the results of 7 qsar descriptors been applied.static double[]
IonizationPotentialTool. getQSARs(IAtomContainer container, IBond bond)
Deprecated.Get the results of 7 qsar descriptors been applied.List<IAtom>[]
HOSECodeGenerator. getSpheres(IAtomContainer ac, IAtom root, int noOfSpheres, boolean ringsize)
This method is intended to be used to get the atoms around an atom in spheres.IAtomContainerSet
StructureResonanceGenerator. getStructures(IAtomContainer molecule)
Get the resonance structures from anIAtomContainer
.static int
DataFeaturesTool. getSupportedDataFeatures(IAtomContainer molecule)
Determines the features present in the givenIAtomContainer
.boolean
SaturationChecker. hasPerfectConfiguration(IAtom atom, IAtomContainer ac)
boolean
SaturationChecker. isOverSaturated(IAtom atom, IAtomContainer ac)
Checks if the current atom has exceeded its bond order sum value.boolean
AtomTypeAwareSaturationChecker. isSaturated(IAtomContainer container)
boolean
AtomTypeAwareSaturationChecker. isSaturated(IAtom atom, IAtomContainer container)
boolean
CDKValencyChecker. isSaturated(IAtomContainer atomContainer)
boolean
CDKValencyChecker. isSaturated(IAtom atom, IAtomContainer container)
boolean
IValencyChecker. isSaturated(IAtomContainer ac)
boolean
IValencyChecker. isSaturated(IAtom atom, IAtomContainer container)
boolean
LonePairElectronChecker. isSaturated(IAtomContainer container)
Determines of all atoms on the AtomContainer have the right number the lone pair electrons.boolean
LonePairElectronChecker. isSaturated(IAtom atom, IAtomContainer ac)
Checks if an Atom is saturated their lone pair electrons by comparing it with known AtomTypes.boolean
SaturationChecker. isSaturated(IAtomContainer container)
Determines of all atoms on the AtomContainer are saturated.boolean
SaturationChecker. isSaturated(IAtom atom, IAtomContainer ac)
Checks whether an Atom is saturated by comparing it with known AtomTypes.boolean
SaturationChecker. isSaturated(IBond bond, IAtomContainer atomContainer)
Returns whether a bond is saturated.boolean
SmilesValencyChecker. isSaturated(IAtomContainer container)
Determines of all atoms on the AtomContainer are saturated.boolean
SmilesValencyChecker. isSaturated(IAtom atom, IAtomContainer container)
Checks whether an Atom is saturated by comparing it with known AtomTypes.boolean
SmilesValencyChecker. isSaturated(IBond bond, IAtomContainer atomContainer)
Returns whether a bond is saturated.boolean
SaturationChecker. isUnsaturated(IBond bond, IAtomContainer atomContainer)
Returns whether a bond is unsaturated.boolean
SmilesValencyChecker. isUnsaturated(IBond bond, IAtomContainer atomContainer)
Returns whether a bond is unsaturated.void
SaturationChecker. newSaturate(IAtomContainer atomContainer)
Saturates a molecule by setting appropriate bond orders.boolean
SaturationChecker. newSaturate(IBond[] bonds, IAtomContainer atomContainer)
Saturates a set of Bonds in an AtomContainer.boolean
SaturationChecker. newSaturate(IBond bond, IAtomContainer atomContainer)
Saturate atom by adjusting its bond orders.static double
IonizationPotentialTool. predictIP(IAtomContainer container, IAtom atom)
Deprecated.Method which is predict the Ionization Potential from given atom.static double
IonizationPotentialTool. predictIP(IAtomContainer container, IBond bond)
Deprecated.Method which is predict the Ionization Potential from given atom.void
AtomTypeAwareSaturationChecker. saturate(IAtomContainer container)
void
IDeduceBondOrderTool. saturate(IAtomContainer ac)
void
LonePairElectronChecker. saturate(IAtomContainer atomContainer)
Saturates a molecule by setting appropriate number lone pair electrons.void
LonePairElectronChecker. saturate(IAtom atom, IAtomContainer ac)
Saturates an IAtom by adding the appropriate number lone pairs.void
SaturationChecker. saturate(IAtomContainer atomContainer)
The method is known to fail for certain compounds.void
SmilesValencyChecker. saturate(IAtomContainer atomContainer)
Saturates a molecule by setting appropriate bond orders.boolean
SmilesValencyChecker. saturate(IBond[] bonds, IAtomContainer atomContainer)
Saturates a set of Bonds in an AtomContainer.boolean
SmilesValencyChecker. saturateByIncreasingBondOrder(IBond bond, IAtomContainer atomContainer)
Tries to saturate a bond by increasing its bond orders by 1.0.void
SaturationChecker. saturateRingSystems(IAtomContainer atomContainer)
void
SaturationChecker. unsaturate(IAtomContainer atomContainer)
Resets the bond orders of all atoms to 1.0.void
SaturationChecker. unsaturateBonds(IAtomContainer container)
Resets the bond order of the Bond to 1.0. -
Uses of IAtomContainer in org.openscience.cdk.tools.features
Methods in org.openscience.cdk.tools.features with parameters of type IAtomContainer Modifier and Type Method Description static boolean
MoleculeFeaturesTool. hasElementSymbols(IAtomContainer molecule)
static boolean
MoleculeFeaturesTool. hasFormalCharges(IAtomContainer molecule)
static boolean
MoleculeFeaturesTool. hasGraphRepresentation(IAtomContainer molecule)
Checks whether all bonds have exactly two atoms.static boolean
MoleculeFeaturesTool. hasPartialCharges(IAtomContainer molecule)
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Uses of IAtomContainer in org.openscience.cdk.tools.manipulator
Methods in org.openscience.cdk.tools.manipulator that return IAtomContainer Modifier and Type Method Description static IAtomContainer
AtomContainerManipulator. anonymise(IAtomContainer src)
Anonymise the provided container to single-bonded carbon atoms.static IAtomContainer
AtomContainerManipulator. copyAndSuppressedHydrogens(IAtomContainer org)
Copy the input container and suppress any explicit hydrogens.static IAtomContainer
AtomContainerManipulator. createAllCarbonAllSingleNonAromaticBondAtomContainer(IAtomContainer atomContainer)
Deprecated.not all attributes are removed producing unexpected results, useAtomContainerManipulator.anonymise(org.openscience.cdk.interfaces.IAtomContainer)
static IAtomContainer
ChemModelManipulator. createNewMolecule(IChemModel chemModel)
Adds a new Molecule to the MoleculeSet inside a given ChemModel.static IAtomContainer
AtomContainerManipulator. extractSubstructure(IAtomContainer atomContainer, int... atomIndices)
Deprecated.static IAtomContainer
AtomContainerManipulator. extractSubstructure(IAtomContainer source, Collection<IAtom> atoms)
Extract a substructure from a 'source' molecule to the provideddest
ination based on the collection of atoms.static IAtomContainer
RingSetManipulator. getAllInOneContainer(IRingSet ringSet)
Puts all rings of a ringSet in a single atomContainerstatic IAtomContainer
MolecularFormulaManipulator. getAtomContainer(String formulaString, IChemObjectBuilder builder)
Converts a formula string (like "C2H4") into an atom container with atoms but no bonds.static IAtomContainer
MolecularFormulaManipulator. getAtomContainer(IMolecularFormula formula)
Method that actually does the work of convert the IMolecularFormula to IAtomContainer.static IAtomContainer
MolecularFormulaManipulator. getAtomContainer(IMolecularFormula formula, IAtomContainer atomContainer)
Method that actually does the work of convert the IMolecularFormula to IAtomContainer given a IAtomContainer.static IAtomContainer
AtomContainerManipulator. getIntersection(IAtomContainer container1, IAtomContainer container2)
Compares this AtomContainer with another given AtomContainer and returns the Intersection between them.static IAtomContainer
AtomContainerSetManipulator. getRelevantAtomContainer(IAtomContainerSet containerSet, IAtom atom)
static IAtomContainer
AtomContainerSetManipulator. getRelevantAtomContainer(IAtomContainerSet containerSet, IBond bond)
static IAtomContainer
ChemModelManipulator. getRelevantAtomContainer(IChemModel chemModel, IAtom atom)
This badly named methods tries to determine which AtomContainer in the ChemModel is best suited to contain added Atom's and Bond's.static IAtomContainer
ChemModelManipulator. getRelevantAtomContainer(IChemModel chemModel, IBond bond)
Retrieves the first IAtomContainer containing a given IBond from an IChemModel.static IAtomContainer
MoleculeSetManipulator. getRelevantAtomContainer(IAtomContainerSet moleculeSet, IAtom atom)
static IAtomContainer
MoleculeSetManipulator. getRelevantAtomContainer(IAtomContainerSet moleculeSet, IBond bond)
static IAtomContainer
ReactionManipulator. getRelevantAtomContainer(IReaction reaction, IAtom atom)
static IAtomContainer
ReactionManipulator. getRelevantAtomContainer(IReaction reaction, IBond bond)
static IAtomContainer
ReactionSetManipulator. getRelevantAtomContainer(IReactionSet set, IAtom atom)
static IAtomContainer
ReactionSetManipulator. getRelevantAtomContainer(IReactionSet set, IBond bond)
static IAtomContainer
AtomContainerManipulator. removeHydrogens(IAtomContainer org)
Create an copy of theorg
structure with explicit hydrogens removed.static IAtomContainer
AtomContainerManipulator. removeHydrogensPreserveMultiplyBonded(IAtomContainer ac)
Deprecated.AtomContainerManipulator.suppressHydrogens(org.openscience.cdk.interfaces.IAtomContainer)
will now not removed bridging hydrogens by defaultstatic IAtomContainer
AtomContainerManipulator. removeNonChiralHydrogens(IAtomContainer org)
Produces an AtomContainer without explicit non stereo-relevant Hs but with H count from one with Hs.static IAtomContainer
AtomContainerManipulator. setSingleOrDoubleFlags(IAtomContainer ac)
AssignsCDKConstants.SINGLE_OR_DOUBLE
flags to the bonds of a container.static IAtomContainer
AtomContainerManipulator. skeleton(IAtomContainer src)
Create a skeleton copy of the provided structure.static IAtomContainer
AtomContainerManipulator. suppressHydrogens(IAtomContainer org)
Suppress any explicit hydrogens in the provided container.static IAtomContainer
ReactionManipulator. toMolecule(IReaction rxn)
Converts a reaction to an 'inlined' reaction stored as a molecule.Methods in org.openscience.cdk.tools.manipulator that return types with arguments of type IAtomContainer Modifier and Type Method Description static List<IAtomContainer>
AtomContainerSetManipulator. getAllAtomContainers(IAtomContainerSet set)
Returns all the AtomContainer's of a MoleculeSet.static List<IAtomContainer>
ChemFileManipulator. getAllAtomContainers(IChemFile file)
Returns all the AtomContainer's of a ChemFile.static List<IAtomContainer>
ChemModelManipulator. getAllAtomContainers(IChemModel chemModel)
Returns all the AtomContainer's of a ChemModel.static List<IAtomContainer>
ChemSequenceManipulator. getAllAtomContainers(IChemSequence sequence)
Returns all the AtomContainer's of a ChemSequence.static List<IAtomContainer>
MoleculeSetManipulator. getAllAtomContainers(IAtomContainerSet set)
Returns all the AtomContainer's of a MoleculeSet.static List<IAtomContainer>
ReactionManipulator. getAllAtomContainers(IReaction reaction)
Returns allIAtomContainers
of the given reaction.static List<IAtomContainer>
ReactionSetManipulator. getAllAtomContainers(IReactionSet set)
Returns all the AtomContainer's of a Reaction.static List<IAtomContainer>
RingSetManipulator. getAllAtomContainers(IRingSet set)
Returns all the AtomContainer's in a RingSet.Methods in org.openscience.cdk.tools.manipulator with parameters of type IAtomContainer Modifier and Type Method Description static IAtomContainer
AtomContainerManipulator. anonymise(IAtomContainer src)
Anonymise the provided container to single-bonded carbon atoms.static void
AtomContainerManipulator. clearAtomConfigurations(IAtomContainer container)
This method will reset all atom configuration to UNSET.int
AtomContainerComparator. compare(IAtomContainer o1, IAtomContainer o2)
int
AtomContainerComparatorBy2DCenter. compare(IAtomContainer a, IAtomContainer b)
Compare two AtomContainers based on their 2D position.static void
AtomContainerManipulator. convertImplicitToExplicitHydrogens(IAtomContainer atomContainer)
Adds explicit hydrogens (without coordinates) to the IAtomContainer, equaling the number of set implicit hydrogens.static void
AtomContainerManipulator. copy(IAtomContainer dest, IAtomContainer source, Collection<IAtom> atoms)
Copy atoms in the collection from a 'source' molecule to the provideddest
ination.static void
AtomContainerManipulator. copy(IAtomContainer dest, IAtomContainer source, Predicate<IAtom> atomFilter)
Copy selected atoms from a 'source' molecule to the provideddest
ination.static void
AtomContainerManipulator. copy(IAtomContainer dest, IAtomContainer source, Predicate<IAtom> atomFilter, Predicate<IBond> bondFilter)
Copy selected atoms/bonds from a 'source' molecule to the provideddest
ination.static IAtomContainer
AtomContainerManipulator. copyAndSuppressedHydrogens(IAtomContainer org)
Copy the input container and suppress any explicit hydrogens.static int
AtomContainerManipulator. countExplicitHydrogens(IAtomContainer atomContainer, IAtom atom)
Count explicit hydrogens.static int
AtomContainerManipulator. countHydrogens(IAtomContainer atomContainer, IAtom atom)
static IAtomContainer
AtomContainerManipulator. createAllCarbonAllSingleNonAromaticBondAtomContainer(IAtomContainer atomContainer)
Deprecated.not all attributes are removed producing unexpected results, useAtomContainerManipulator.anonymise(org.openscience.cdk.interfaces.IAtomContainer)
static IAtomContainer
AtomContainerManipulator. extractSubstructure(IAtomContainer atomContainer, int... atomIndices)
Deprecated.static IAtomContainer
AtomContainerManipulator. extractSubstructure(IAtomContainer source, Collection<IAtom> atoms)
Extract a substructure from a 'source' molecule to the provideddest
ination based on the collection of atoms.static List<String>
AtomContainerManipulator. getAllIDs(IAtomContainer mol)
static IAtom[]
AtomContainerManipulator. getAtomArray(IAtomContainer container)
Constructs an array of Atom objects from an AtomContainer.static IAtom
AtomContainerManipulator. getAtomById(IAtomContainer ac, String id)
Returns an atom in an atomcontainer identified by idstatic IAtomContainer
MolecularFormulaManipulator. getAtomContainer(IMolecularFormula formula, IAtomContainer atomContainer)
Method that actually does the work of convert the IMolecularFormula to IAtomContainer given a IAtomContainer.static ArrayList<IAtomContainerSet>
ReactionSchemeManipulator. getAtomContainerSet(IAtomContainer origenMol, IAtomContainer finalMol, IReactionScheme reactionScheme)
Extract the list of AtomContainers taking part in the IReactionScheme to originate a product given a reactant.static IBond[]
AtomContainerManipulator. getBondArray(IAtomContainer container)
Constructs an array of Bond objects from an AtomContainer.static double
AtomContainerManipulator. getBondOrderSum(IAtomContainer container, IAtom atom)
Returns the sum of the bond order equivalents for a given IAtom.static IElectronContainer[]
AtomContainerManipulator. getElectronContainerArray(IAtomContainer container)
Constructs an array of Bond objects from an AtomContainer.static List<IAtom>
AtomContainerManipulator. getHeavyAtoms(IAtomContainer container)
Returns a set of nodes excluding all the hydrogens.static int
AtomContainerManipulator. getImplicitHydrogenCount(IAtomContainer container)
Counts the number of implicit hydrogens on the provided IAtomContainer.static IAtomContainer
AtomContainerManipulator. getIntersection(IAtomContainer container1, IAtomContainer container2)
Compares this AtomContainer with another given AtomContainer and returns the Intersection between them.static double
AtomContainerManipulator. getMass(IAtomContainer mol)
Calculate the mass of a molecule, this function takes an optional 'mass flavour' that switches the computation type.static double
AtomContainerManipulator. getMass(IAtomContainer mol, int flav)
Calculate the mass of a molecule, this function takes an optional 'mass flavour' that switches the computation type.static IBond.Order
AtomContainerManipulator. getMaximumBondOrder(IAtomContainer container)
static IMolecularFormula
MolecularFormulaManipulator. getMolecularFormula(IAtomContainer atomContainer)
Method that actually does the work of convert the atomContainer to IMolecularFormula.static IMolecularFormula
MolecularFormulaManipulator. getMolecularFormula(IAtomContainer atomContainer, IMolecularFormula formula)
Method that actually does the work of convert the atomContainer to IMolecularFormula given a IMolecularFormula.static double
AtomContainerManipulator. getMolecularWeight(IAtomContainer mol)
static IMolecularFormula
MolecularFormulaManipulator. getMostAbundant(IAtomContainer mol)
Compute the most abundant MF.static double
AtomContainerManipulator. getNaturalExactMass(IAtomContainer mol)
static IReactionSet
ReactionSetManipulator. getRelevantReactions(IReactionSet reactSet, IAtomContainer molecule)
Get all Reactions object containing a Molecule from a set of Reactions.static IReactionSet
ReactionSetManipulator. getRelevantReactionsAsProduct(IReactionSet reactSet, IAtomContainer molecule)
Get all Reactions object containing a Molecule as a Product from a set of Reactions.static IReactionSet
ReactionSetManipulator. getRelevantReactionsAsReactant(IReactionSet reactSet, IAtomContainer molecule)
Get all Reactions object containing a Molecule as a Reactant from a set of Reactions.static int
AtomContainerManipulator. getSingleBondEquivalentSum(IAtomContainer container)
Returns the sum of bond orders, where a single bond counts as one single bond equivalent, a double as two, etc.static double
AtomContainerManipulator. getTotalCharge(IAtomContainer atomContainer)
Get the summed charge of all atoms in an AtomContainerstatic double
AtomContainerManipulator. getTotalExactMass(IAtomContainer mol)
static int
AtomContainerManipulator. getTotalFormalCharge(IAtomContainer atomContainer)
Get the total formal charge on a molecule.static int
AtomContainerManipulator. getTotalHydrogenCount(IAtomContainer container)
Counts the number of hydrogens on the provided IAtomContainer.static double
AtomContainerManipulator. getTotalNaturalAbundance(IAtomContainer atomContainer)
Get the summed natural abundance of all atoms in an AtomContainerstatic int
AtomContainerManipulator. getTotalNegativeFormalCharge(IAtomContainer atomContainer)
Get the total formal negative charge on a molecule.static int
AtomContainerManipulator. getTotalPositiveFormalCharge(IAtomContainer atomContainer)
Get the total positive formal charge on a molecule.static IChemModel
ChemModelManipulator. newChemModel(IAtomContainer atomContainer)
Create a new ChemModel containing an IAtomContainer.static void
AtomContainerManipulator. percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Convenience method to perceive atom types for allIAtom
s in theIAtomContainer
, using theCDKAtomTypeMatcher
.static void
AtomContainerManipulator. percieveAtomTypesAndConfigureUnsetProperties(IAtomContainer container)
Convenience method to perceive atom types for allIAtom
s in theIAtomContainer
, using theCDKAtomTypeMatcher
.static IAtomContainer
AtomContainerManipulator. removeHydrogens(IAtomContainer org)
Create an copy of theorg
structure with explicit hydrogens removed.static IAtomContainer
AtomContainerManipulator. removeHydrogensPreserveMultiplyBonded(IAtomContainer ac)
Deprecated.AtomContainerManipulator.suppressHydrogens(org.openscience.cdk.interfaces.IAtomContainer)
will now not removed bridging hydrogens by defaultstatic IAtomContainer
AtomContainerManipulator. removeNonChiralHydrogens(IAtomContainer org)
Produces an AtomContainer without explicit non stereo-relevant Hs but with H count from one with Hs.static boolean
AtomContainerManipulator. replaceAtomByAtom(IAtomContainer container, IAtom oldAtom, IAtom newAtom)
Substitute one atom in a container for another adjusting bonds, single electrons, lone pairs, and stereochemistry as required.static void
AtomContainerManipulator. setAtomProperties(IAtomContainer container, Object propKey, Object propVal)
Sets a property on allAtom
s in the given container.static IAtomContainer
AtomContainerManipulator. setSingleOrDoubleFlags(IAtomContainer ac)
AssignsCDKConstants.SINGLE_OR_DOUBLE
flags to the bonds of a container.static IAtomContainer
AtomContainerManipulator. skeleton(IAtomContainer src)
Create a skeleton copy of the provided structure.static IAtomContainer
AtomContainerManipulator. suppressHydrogens(IAtomContainer org)
Suppress any explicit hydrogens in the provided container.static IReaction
ReactionManipulator. toReaction(IAtomContainer mol)
Converts an 'inlined' reaction stored in a molecule back to a reaction.static void
AtomContainerManipulator. unregisterAtomListeners(IAtomContainer container)
A method to remove AtomListeners.static void
AtomContainerManipulator. unregisterElectronContainerListeners(IAtomContainer container)
A method to remove ElectronContainerListeners. -
Uses of IAtomContainer in org.openscience.cdk.validate
Methods in org.openscience.cdk.validate with parameters of type IAtomContainer Modifier and Type Method Description ValidationReport
AbstractValidator. validateAtomContainer(IAtomContainer subject)
ValidationReport
IValidator. validateAtomContainer(IAtomContainer subject)
ValidationReport
ValidatorEngine. validateAtomContainer(IAtomContainer subject)
ValidationReport
AbstractValidator. validateMolecule(IAtomContainer subject)
ValidationReport
BasicValidator. validateMolecule(IAtomContainer subject)
ValidationReport
IValidator. validateMolecule(IAtomContainer subject)
ValidationReport
ValidatorEngine. validateMolecule(IAtomContainer subject)
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