Modifier and Type | Class and Description |
---|---|
class |
QueryAtomContainer |
Modifier and Type | Method and Description |
---|---|
IQueryAtomContainer |
QueryAtomContainer.clone()
Clones this AtomContainer object and its content.
|
Constructor and Description |
---|
RecursiveSmartsAtom(IQueryAtomContainer query)
Deprecated.
Creates a new instance
|
Modifier and Type | Class and Description |
---|---|
class |
PharmacophoreQuery
Represents a colleciton of pharmacophore groups and constraints.
|
Modifier and Type | Method and Description |
---|---|
void |
Isomorphism.init(IQueryAtomContainer reactant,
IAtomContainer product)
Deprecated.
|
Constructor and Description |
---|
DefaultMCSPlusAtomMatcher(IQueryAtom smartQueryAtom,
IQueryAtomContainer container)
Deprecated.
Constructor
|
DefaultVFAtomMatcher(IQueryAtom smartQueryAtom,
IQueryAtomContainer container)
Deprecated.
Constructor
|
Modifier and Type | Method and Description |
---|---|
protected void |
QueryProcessor.process(IQueryAtomContainer query,
IAtomContainer target,
List<Integer> unmappedAtomsMolA,
List<Integer> mappedAtoms,
int counter)
Deprecated.
|
Constructor and Description |
---|
McGregor(IQueryAtomContainer source,
IAtomContainer target,
List<List<Integer>> mappings)
Deprecated.
Constructor for the McGregor algorithm.
|
Modifier and Type | Method and Description |
---|---|
void |
MCSPlusHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
Initialise the query and target molecule.
|
Modifier and Type | Method and Description |
---|---|
void |
CDKSubGraphHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
Initialise the query and target molecule.
|
void |
CDKMCSHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
Initialise the query and target molecule.
|
Modifier and Type | Method and Description |
---|---|
protected List<Map<IAtom,IAtom>> |
SingleMapping.getOverLaps(IQueryAtomContainer source,
IAtomContainer target,
boolean removeHydrogen)
Deprecated.
Returns single mapping solutions.
|
void |
SingleMappingHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
Initialise the query and target molecule.
|
Modifier and Type | Method and Description |
---|---|
void |
VFlibSubStructureHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
Initialise the query and target molecule.
|
void |
VFlibTurboHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
Initialise the query and target molecule.
|
void |
VFlibMCSHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
Initialise the query and target molecule.
|
Constructor and Description |
---|
QueryCompiler(IQueryAtomContainer molecule)
Deprecated.
Construct query object from the molecule
|
Modifier and Type | Method and Description |
---|---|
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.
|
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