Class VFlibTurboHandler
- java.lang.Object
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- org.openscience.cdk.smsd.interfaces.AbstractSubGraph
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- org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
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- All Implemented Interfaces:
IMCSBase
@Deprecated public class VFlibTurboHandler extends AbstractSubGraph implements 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 one mapping. This is much faster thanVFlibMCSHandler
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
Constructors Constructor Description VFlibTurboHandler()
Deprecated.Constructor for an extended VF Algorithm for the MCS search
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description List<Map<IAtom,IAtom>>
getAllAtomMapping()
Deprecated.Returns all plausible mappings between query and target molecules.List<Map<Integer,Integer>>
getAllMapping()
Deprecated.Returns all plausible mappings between query and target molecules.Map<IAtom,IAtom>
getFirstAtomMapping()
Deprecated.Returns one of the best matches with atoms mapped.Map<Integer,Integer>
getFirstMapping()
Deprecated.Returns one of the best matches with atom indexes mapped.boolean
isBondMatchFlag()
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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Method Detail
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set
public void set(MolHandler reactant, MolHandler product)
Deprecated.Initialise the query and target molecule. Set the VFLib MCS software
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set
public void set(IQueryAtomContainer source, IAtomContainer target)
Deprecated.Initialise the query and target molecule.
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getAllAtomMapping
public List<Map<IAtom,IAtom>> 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
public List<Map<Integer,Integer>> 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
public Map<IAtom,IAtom> 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
public Map<Integer,Integer> 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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