Class VFlibMCSHandler
java.lang.Object
org.openscience.cdk.smsd.interfaces.AbstractMCSAlgorithm
org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
- 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 class should be used to find MCS between query
graph and target graph.
First the algorithm runs VF lib
VFMCSMapper
and reports MCS between
run query and target graphs. Then these solutions are extended
using McGregor McGregor
algorithm where ever required.- 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.void
searchMCS
(boolean bondTypeMatch) Deprecated.Initialise the MCS 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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VFlibMCSHandler
public VFlibMCSHandler()Deprecated.Constructor for an extended VF Algorithm for the MCS search
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Method Details
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searchMCS
public void searchMCS(boolean bondTypeMatch) Deprecated.Initialise the MCS search algorithm. Each MCS algorithm should contain this method.- Specified by:
searchMCS
in classAbstractMCSAlgorithm
- Parameters:
bondTypeMatch
-
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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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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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