Modifier and Type | Class and Description |
---|---|
class |
Atom
Represents the idea of an chemical atom.
|
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.
|
Modifier and Type | Method and Description |
---|---|
IAtomType |
SybylAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atom)
Sybyl atom type perception for a single atom.
|
IAtomType |
EStateAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atom) |
IAtomType |
MMFF94AtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atomInterface)
Deprecated.
Assign the mmff94 atom type to a given atom.
|
IAtomType |
MM2AtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atomInterface)
Deprecated.
Assign the mm2 atom type to a given atom.
|
IAtomType |
StructGenMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atom)
Finds the AtomType matching the Atom's element symbol, formal charge and
hybridization state.
|
IAtomType |
IAtomTypeMatcher.findMatchingAtomType(IAtomContainer container,
IAtom atom)
Method that assigns an atom type to a given atom belonging to an atom
container.
|
IAtomType |
CDKAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atom)
Method that assigns an atom type to a given atom belonging to an atom
container.
|
IAtomType[] |
SybylAtomTypeMatcher.findMatchingAtomTypes(IAtomContainer atomContainer)
Method that assigns atom types to atoms in the given atom container.
|
IAtomType[] |
EStateAtomTypeMatcher.findMatchingAtomTypes(IAtomContainer atomContainer) |
IAtomType[] |
MMFF94AtomTypeMatcher.findMatchingAtomTypes(IAtomContainer atomContainer)
Deprecated.
|
IAtomType[] |
MM2AtomTypeMatcher.findMatchingAtomTypes(IAtomContainer atomContainer)
Deprecated.
|
IAtomType[] |
StructGenMatcher.findMatchingAtomTypes(IAtomContainer atomContainer) |
IAtomType[] |
IAtomTypeMatcher.findMatchingAtomTypes(IAtomContainer container)
Method that assigns atom types to atoms in the given atom container.
|
IAtomType[] |
CDKAtomTypeMatcher.findMatchingAtomTypes(IAtomContainer atomContainer)
Method that assigns atom types to atoms in the given atom container.
|
Modifier and Type | Method and Description |
---|---|
List<IAtomType> |
StructGenAtomTypeGuesser.possibleAtomTypes(IAtomContainer atomContainer,
IAtom atom)
Finds the AtomType matching the Atom's element symbol, formal charge and
hybridization state.
|
List<IAtomType> |
IAtomTypeGuesser.possibleAtomTypes(IAtomContainer container,
IAtom atom)
Method that returns an iterator with a suitable list of atom types
given the provided atom.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
List<IAtomType> |
TXTBasedAtomTypeConfigurator.readAtomTypes(IChemObjectBuilder builder)
Reads a text based configuration file.
|
List<IAtomType> |
OWLBasedAtomTypeConfigurator.readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the OWL based atom type list.
|
List<IAtomType> |
IAtomTypeConfigurator.readAtomTypes(IChemObjectBuilder builder)
Reads a set of configured AtomType's into a List.
|
List<IAtomType> |
CDKBasedAtomTypeConfigurator.readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the CDK based atom type list.
|
Modifier and Type | Method and Description |
---|---|
List<IAtomType> |
OWLAtomTypeHandler.getAtomTypes()
Returns a List with read IAtomType's.
|
List<IAtomType> |
AtomTypeHandler.getAtomTypes()
Returns a List with read IAtomType's.
|
List<IAtomType> |
OWLAtomTypeReader.readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the data file.
|
List<IAtomType> |
AtomTypeReader.readAtomTypes(IChemObjectBuilder builder)
Reads the atom types from the data file.
|
Modifier and Type | Class and 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.
|
Modifier and Type | Interface and 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.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IQueryAtom
Defines the ability to be matched against
IAtom 's. |
Modifier and Type | Class and Description |
---|---|
class |
InverseSymbolSetQueryAtom
A QueryAtom that matches all symbols but those in this container.
|
class |
QueryAtom |
class |
SymbolAndChargeQueryAtom |
class |
SymbolChargeIDQueryAtom |
class |
SymbolQueryAtom |
class |
SymbolSetQueryAtom
A QueryAtom that matches all symbols in this container.
|
Modifier and Type | Class and Description |
---|---|
class |
AliphaticAtom
This matcher any non-aromatic atom.
|
class |
AliphaticSymbolAtom
This smarts atom matches aliphatic atom with element symbol specified.
|
class |
AnyAtom
This matcher any Atom including explicit hydrogens.
|
class |
AromaticAtom
This matcher any aromatic atom.
|
class |
AromaticSymbolAtom
This class matches aromatic atom with element symbol specified.
|
class |
AtomicNumberAtom
This matches an atom using the atomic number.
|
class |
ChiralityAtom
This matches an atom with chirality property.
|
class |
ExplicitConnectionAtom
Match an atom with the defined degree.
|
class |
FormalChargeAtom
This matcher checks the formal charge of the Atom.
|
class |
HybridizationNumberAtom
This matcher checks the hybridization state of an atom.
|
class |
HydrogenAtom
This matches Hydrogen atoms.
|
class |
ImplicitHCountAtom
This matcher checks the number of implicit hydrogens of the Atom.
|
class |
LogicalOperatorAtom
This class matches a logical operator that connects two query atoms.
|
class |
MassAtom
This class matches an atom based on the atomic mass.
|
class |
NonCHHeavyAtom
This matcher any heavy atom that is not C or H.
|
class |
PeriodicGroupNumberAtom
This matcher checks the periodic group number of an atom.
|
class |
ReactionRoleQueryAtom
Matches atoms with a particular role in a reaction.
|
class |
RecursiveSmartsAtom
This matches recursive smarts atoms.
|
class |
RingIdentifierAtom
This encapsulates an atom with a ring identifier, with an optional ring
bond specified.
|
class |
RingMembershipAtom
This query is found in a specified number of ring.
|
class |
SmallestRingAtom
Match an atom in a specific size ring.
|
class |
SMARTSAtom
Abstract smarts atom.
|
class |
TotalConnectionAtom
This matches an atom using total number of connections - referred to in
SMARTS as the connectivity.
|
class |
TotalHCountAtom
SMARTS query atom for matching the total hydrogen count.
|
class |
TotalRingConnectionAtom
This matcher checks the number of ring connections of the checked Atom with
other Atom's.
|
class |
TotalValencyAtom
This matcher checks the valence of the Atom.
|
Modifier and Type | Method and Description |
---|---|
List<IAtomType> |
MMFF94BasedParameterSetReader.getAtomTypes() |
List<IAtomType> |
MM2BasedParameterSetReader.getAtomTypes() |
List<IAtomType> |
ForceFieldConfigurator.getAtomTypes()
Gets the atomTypes attribute of the ForceFieldConfigurator object
|
Modifier and Type | Method and Description |
---|---|
void |
ForceFieldConfigurator.setAtomTypes(List<IAtomType> atomtypes)
Sets the atomTypes attribute of the ForceFieldConfigurator object
|
Modifier and Type | Class and Description |
---|---|
class |
PharmacophoreAtom
A representation of a pharmacophore group.
|
class |
PharmacophoreQueryAtom
Represents a query pharmacophore group.
|
Modifier and Type | Class and Description |
---|---|
class |
PDBAtom
Represents the idea of an atom as used in PDB files.
|
Modifier and Type | Method and Description |
---|---|
boolean |
SmilesValencyChecker.couldMatchAtomType(IAtomContainer container,
IAtom atom,
IAtomType type)
Determines if the atom can be of type AtomType.
|
boolean |
SaturationChecker.couldMatchAtomType(IAtomContainer atomContainer,
IAtom atom,
IAtomType atomType)
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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
ValidationReport |
ValidatorEngine.validateAtomType(IAtomType subject) |
ValidationReport |
IValidator.validateAtomType(IAtomType subject) |
ValidationReport |
AbstractValidator.validateAtomType(IAtomType subject) |
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