Class VFlibSubStructureHandler
java.lang.Object
org.openscience.cdk.smsd.interfaces.AbstractSubGraph
org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
- All Implemented Interfaces:
IMCSBase
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent
version of SMSD is available at http://github.com/asad/smsd.
This is an ultra fast method to report if query
is a substructure for target molecule. If this case is true
then it returns only all mapping.
This is much faster than
VFlibMCSHandler
class
as it only reports first match and backtracks.
This class should only be used to report if a query
graph is a substructure of the target graph.- Author:
- Syed Asad Rahman <asad@ebi.ac.uk>
- Source code:
- main
- Belongs to CDK module:
- smsd
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Constructor Summary
ConstructorsConstructorDescriptionDeprecated.Constructor for an extended VF Algorithm for the MCS search -
Method Summary
Modifier and TypeMethodDescriptionDeprecated.Returns all plausible mappings between query and target molecules.Deprecated.Returns all plausible mappings between query and target molecules.Deprecated.Returns one of the best matches with atoms mapped.Deprecated.Returns one of the best matches with atom indexes mapped.boolean
Deprecated.boolean
isSubgraph
(boolean shouldMatchBonds) Deprecated.Initialise the Subgraph search algorithm.void
set
(IQueryAtomContainer source, IAtomContainer target) Deprecated.Initialise the query and target molecule.void
set
(MolHandler reactant, MolHandler product) Deprecated.Initialise the query and target molecule.void
setBondMatchFlag
(boolean shouldMatchBonds) Deprecated.
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Constructor Details
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VFlibSubStructureHandler
public VFlibSubStructureHandler()Deprecated.Constructor for an extended VF Algorithm for the MCS search
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Method Details
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set
Deprecated.Initialise the query and target molecule. Set the VFLib MCS software -
set
Deprecated.Initialise the query and target molecule. -
getAllAtomMapping
Deprecated.Returns all plausible mappings between query and target molecules. Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e. map.getKey() for the query and map.getValue() for the target molecule- Specified by:
getAllAtomMapping
in interfaceIMCSBase
- Returns:
- All possible MCS atom Mappings
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getAllMapping
Deprecated.Returns all plausible mappings between query and target molecules. Each map in the list has atom-atom equivalence index of the mappings between query and target molecule i.e. map.getKey() for the query and map.getValue() for the target molecule- Specified by:
getAllMapping
in interfaceIMCSBase
- Returns:
- All possible MCS Mapping Index
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getFirstAtomMapping
Deprecated.Returns one of the best matches with atoms mapped.- Specified by:
getFirstAtomMapping
in interfaceIMCSBase
- Returns:
- Best Atom Mapping
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getFirstMapping
Deprecated.Returns one of the best matches with atom indexes mapped.- Specified by:
getFirstMapping
in interfaceIMCSBase
- Returns:
- Best Mapping Index
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isSubgraph
public boolean isSubgraph(boolean shouldMatchBonds) Deprecated.Description copied from class:AbstractSubGraph
Initialise the Subgraph search algorithm. Each Subgraph algorithm should contain this method.- Specified by:
isSubgraph
in classAbstractSubGraph
- Returns:
- true if Query/reactant is a subgraph of Target/product else false
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isBondMatchFlag
public boolean isBondMatchFlag()Deprecated.- Returns:
- the shouldMatchBonds
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setBondMatchFlag
public void setBondMatchFlag(boolean shouldMatchBonds) Deprecated.- Parameters:
shouldMatchBonds
- the shouldMatchBonds to set
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