Package org.openscience.cdk.smsd.interfaces

Interface IMCSBase

All Known Implementing Classes:

CDKMCSHandler, CDKSubGraphHandler, MCSPlusHandler, SingleMappingHandler, VFlibMCSHandler, VFlibSubStructureHandler, VFlibTurboHandler

@Deprecated
public interface 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.

Interface that holds basic core interface for all MCS algorithm.

Author:

Syed Asad Rahman <asad@ebi.ac.uk>

Source code:

main

Belongs to CDK module:

smsd

Method Summary

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.
void	set(IQueryAtomContainer source, IAtomContainer target)	Deprecated. Initialise the query and target molecule.
void	set(MolHandler source, MolHandler target)	Deprecated. Initialise the query and target molecule.

Method Detail

set

void set(MolHandler source,
         MolHandler target)
  throws CDKException

Deprecated.

Initialise the query and target molecule.

Parameters:

source - source molecule

target - target molecule

Throws:

CDKException

set

void set(IQueryAtomContainer source,
         IAtomContainer target)
  throws CDKException

Deprecated.

Initialise the query and target molecule.

Parameters:

source - source molecule

target - target molecule

Throws:

CDKException

getAllAtomMapping

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

Returns:

All possible MCS atom Mappings

getAllMapping

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

Returns:

All possible MCS Mapping Index

getFirstAtomMapping

Map<IAtom,IAtom> getFirstAtomMapping()

Deprecated.

Returns one of the best matches with atoms mapped.

Returns:

Best Atom Mapping

getFirstMapping

Map<Integer,Integer> getFirstMapping()

Deprecated.

Returns one of the best matches with atom indexes mapped.

Returns:

Best Mapping Index