Uses of Interface
org.openscience.cdk.interfaces.IAtomType
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Uses of IAtomType in org.openscience.cdk
Classes in org.openscience.cdk that implement IAtomType Modifier and Type Class Description class
Atom
Represents the idea of an chemical atom.class
AtomRef
An atom ref, references a CDKIAtom
indirectly.class
AtomType
The base class for atom types.class
EnzymeResidueLocator
Atom that represents part of an residue in an enzyme, like Arg255.class
FragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.class
PseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc. -
Uses of IAtomType in org.openscience.cdk.atomtype
Methods in org.openscience.cdk.atomtype that return IAtomType 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.Methods in org.openscience.cdk.atomtype that return types with arguments of type IAtomType Modifier and Type Method Description 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 IAtomType in org.openscience.cdk.config
Methods in org.openscience.cdk.config that return IAtomType Modifier and Type Method Description IAtomType[]
AtomTypeFactory. getAllAtomTypes()
Gets the allAtomTypes attribute of the AtomTypeFactory object.IAtomType
AtomTypeFactory. getAtomType(String identifier)
Get an AtomType with the given ID.IAtomType[]
AtomTypeFactory. getAtomTypes(String symbol)
Get an array of all atomTypes known to the AtomTypeFactory for the given element symbol and atomtype class.Methods in org.openscience.cdk.config that return types with arguments of type IAtomType Modifier and Type Method Description List<IAtomType>
CDKBasedAtomTypeConfigurator. readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the CDK based atom type list.List<IAtomType>
IAtomTypeConfigurator. readAtomTypes(IChemObjectBuilder builder)
Reads a set of configured AtomType's into a List.List<IAtomType>
OWLBasedAtomTypeConfigurator. readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the OWL based atom type list.List<IAtomType>
TXTBasedAtomTypeConfigurator. readAtomTypes(IChemObjectBuilder builder)
Reads a text based configuration file. -
Uses of IAtomType in org.openscience.cdk.config.atomtypes
Methods in org.openscience.cdk.config.atomtypes that return types with arguments of type IAtomType Modifier and Type Method Description List<IAtomType>
AtomTypeHandler. getAtomTypes()
Returns a List with read IAtomType's.List<IAtomType>
OWLAtomTypeHandler. getAtomTypes()
Returns a List with read IAtomType's.List<IAtomType>
AtomTypeReader. readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the data file.List<IAtomType>
OWLAtomTypeReader. readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the data file. -
Uses of IAtomType in org.openscience.cdk.debug
Classes in org.openscience.cdk.debug that implement IAtomType Modifier and Type Class Description class
DebugAtom
Debugging data class.class
DebugAtomType
Debugging data class.class
DebugFragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.class
DebugPDBAtom
Debugging data class.class
DebugPseudoAtom
Debugging data class. -
Uses of IAtomType in org.openscience.cdk.interfaces
Subinterfaces of IAtomType in org.openscience.cdk.interfaces Modifier and Type Interface Description interface
IAtom
Represents the idea of an chemical atom.interface
IFragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.interface
IPDBAtom
A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.interface
IPseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc. -
Uses of IAtomType in org.openscience.cdk.isomorphism.matchers
Subinterfaces of IAtomType in org.openscience.cdk.isomorphism.matchers Modifier and Type Interface Description interface
IQueryAtom
Defines the ability to be matched againstIAtom
's.Classes in org.openscience.cdk.isomorphism.matchers that implement IAtomType Modifier and Type Class Description class
InverseSymbolSetQueryAtom
Deprecated.class
QueryAtom
class
SymbolAndChargeQueryAtom
Deprecated.class
SymbolChargeIDQueryAtom
class
SymbolQueryAtom
Deprecated.class
SymbolSetQueryAtom
Deprecated.Usenew Expr(Element, 6).and(new Expr(Element, 8))
etc -
Uses of IAtomType in org.openscience.cdk.isomorphism.matchers.smarts
Classes in org.openscience.cdk.isomorphism.matchers.smarts that implement IAtomType Modifier and Type Class Description class
AliphaticAtom
Deprecated.class
AliphaticSymbolAtom
Deprecated.class
AnyAtom
Deprecated.class
AromaticAtom
Deprecated.class
AromaticSymbolAtom
Deprecated.class
AtomicNumberAtom
Deprecated.class
ChiralityAtom
Deprecated.class
ExplicitConnectionAtom
Deprecated.class
FormalChargeAtom
Deprecated.class
HybridizationNumberAtom
Deprecated.class
HydrogenAtom
Deprecated.class
ImplicitHCountAtom
Deprecated.class
LogicalOperatorAtom
Deprecated.class
MassAtom
Deprecated.class
NonCHHeavyAtom
Deprecated.class
PeriodicGroupNumberAtom
Deprecated.class
ReactionRoleQueryAtom
Deprecated.class
RecursiveSmartsAtom
Deprecated.class
RingIdentifierAtom
Deprecated.class
RingMembershipAtom
Deprecated.class
SmallestRingAtom
Deprecated.class
SMARTSAtom
Deprecated.class
TotalConnectionAtom
Deprecated.class
TotalHCountAtom
Deprecated.class
TotalRingConnectionAtom
Deprecated.class
TotalValencyAtom
Deprecated. -
Uses of IAtomType in org.openscience.cdk.modeling.builder3d
Methods in org.openscience.cdk.modeling.builder3d that return types with arguments of type IAtomType Modifier and Type Method Description List<IAtomType>
ForceFieldConfigurator. getAtomTypes()
Gets the atomTypes attribute of the ForceFieldConfigurator objectList<IAtomType>
MM2BasedParameterSetReader. getAtomTypes()
List<IAtomType>
MMFF94BasedParameterSetReader. getAtomTypes()
Method parameters in org.openscience.cdk.modeling.builder3d with type arguments of type IAtomType Modifier and Type Method Description void
ForceFieldConfigurator. setAtomTypes(List<IAtomType> atomtypes)
Sets the atomTypes attribute of the ForceFieldConfigurator object -
Uses of IAtomType in org.openscience.cdk.pharmacophore
Classes in org.openscience.cdk.pharmacophore that implement IAtomType Modifier and Type Class Description class
PharmacophoreAtom
A representation of a pharmacophore group.class
PharmacophoreQueryAtom
Represents a query pharmacophore group. -
Uses of IAtomType in org.openscience.cdk.protein.data
Classes in org.openscience.cdk.protein.data that implement IAtomType Modifier and Type Class Description class
PDBAtom
Represents the idea of an atom as used in PDB files. -
Uses of IAtomType in org.openscience.cdk.silent
Classes in org.openscience.cdk.silent that implement IAtomType Modifier and Type Class Description class
Atom
Represents the idea of an chemical atom.class
AtomType
The base class for atom types.class
FragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.class
PDBAtom
Represents the idea of an atom as used in PDB files.class
PseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc. -
Uses of IAtomType in org.openscience.cdk.tools
Methods in org.openscience.cdk.tools with parameters of type IAtomType Modifier and Type Method Description 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.boolean
SmilesValencyChecker. couldMatchAtomType(IAtom atom, double bondOrderSum, IBond.Order maxBondOrder, IAtomType type)
Determines if the atom can be of type AtomType. -
Uses of IAtomType in org.openscience.cdk.tools.manipulator
Methods in org.openscience.cdk.tools.manipulator with parameters of type IAtomType Modifier and Type Method Description static void
AtomTypeManipulator. configure(IAtom atom, IAtomType atomType)
Method that assign properties to an atom given a particular atomType.static void
AtomTypeManipulator. configureUnsetProperties(IAtom atom, IAtomType atomType)
Method that assign properties to an atom given a particular atomType. -
Uses of IAtomType in org.openscience.cdk.validate
Methods in org.openscience.cdk.validate with parameters of type IAtomType Modifier and Type Method Description ValidationReport
AbstractValidator. validateAtomType(IAtomType subject)
ValidationReport
IValidator. validateAtomType(IAtomType subject)
ValidationReport
ValidatorEngine. validateAtomType(IAtomType subject)
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