org.openscience.cdk.smsd.interfaces

Class AbstractMCS

java.lang.Object

org.openscience.cdk.smsd.interfaces.AbstractMCS

Direct Known Subclasses:

Isomorphism

Deprecated.

SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.

@Deprecated
public abstract class AbstractMCS
extends Object

Interface for all MCS algorithms.

Author:

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

Source code:

master

Belongs to CDK module:

smsd

Constructor Summary

Constructors

Constructor and Description
AbstractMCS() Deprecated.

Method Summary

Modifier and Type	Method and Description
abstract 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.
abstract 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.
abstract double	getBondInSensitiveTimeOut() Deprecated. get timeout in mins for bond insensitive searches
abstract double	getBondSensitiveTimeOut() Deprecated. get timeout in mins for bond sensitive searches
abstract Double	getEnergyScore(int key) Deprecated. Returns summation energy score of the disorder if the MCS is removed from the target and query graph.
abstract double	getEuclideanDistance() Deprecated. Returns Euclidean Distance between query and target molecule.
abstract Map<IAtom,IAtom>	getFirstAtomMapping() Deprecated. Returns one of the best matches with atoms mapped.
abstract Map<Integer,Integer>	getFirstMapping() Deprecated. Returns one of the best matches with atom indexes mapped.
abstract Integer	getFragmentSize(int key) Deprecated. Returns number of fragment generated in the solution space, if the MCS is removed from the target and query graph.
abstract IAtomContainer	getProductMolecule() Deprecated. Returns modified target molecule on which mapping was performed.
abstract IAtomContainer	getReactantMolecule() Deprecated. Returns modified query molecule on which mapping was performed.
abstract Integer	getStereoScore(int key) Deprecated. Returns a number which denotes the quality of the mcs.
abstract double	getTanimotoSimilarity() Deprecated. Returns Tanimoto similarity between query and target molecules (Score is between 0-min and 1-max).
abstract void	init(IAtomContainer source, IAtomContainer target, boolean removeHydrogen, boolean cleanAndConfigureMolecule) Deprecated. initialize query and target molecules.
abstract void	init(IQueryAtomContainer source, IAtomContainer target) Deprecated. initialize query and target molecules.
abstract boolean	isStereoMisMatch() Deprecated. Returns true if mols have different stereo chemistry else false if no stereo mismatch.
abstract boolean	isSubgraph() Deprecated. Checks if query is a subgraph of the target.
abstract void	setBondInSensitiveTimeOut(double bondInSensitiveTimeOut) Deprecated. set timeout in mins (default 1.00 min) for bond insensitive searches
abstract void	setBondSensitiveTimeOut(double bondSensitiveTimeOut) Deprecated. set timeout in mins (default 0.10 min) for bond sensitive searches
abstract void	setChemFilters(boolean stereoFilter, boolean fragmentFilter, boolean energyFilter) Deprecated. initialize query and target molecules.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AbstractMCS

public AbstractMCS()

Deprecated.

Method Detail

init

public abstract void init(IAtomContainer source,
                          IAtomContainer target,
                          boolean removeHydrogen,
                          boolean cleanAndConfigureMolecule)
                   throws CDKException

Deprecated.

initialize query and target molecules.

Parameters:

source - query mol

target - target mol

removeHydrogen - true if remove H (implicit) before mapping

cleanAndConfigureMolecule - eg: percieveAtomTypesAndConfigureAtoms, detect aromaticity etc

Throws:

CDKException

init

public abstract void init(IQueryAtomContainer source,
                          IAtomContainer target)
                   throws CDKException

Deprecated.

initialize query and target molecules. Note: Here its assumed that hydrogens are implicit and user has called these two methods percieveAtomTypesAndConfigureAtoms and CDKAromicityDetector before initializing calling this method.

Parameters:

source - query mol

target - target mol

Throws:

CDKException

setChemFilters

public abstract void setChemFilters(boolean stereoFilter,
                                    boolean fragmentFilter,
                                    boolean energyFilter)

Deprecated.

initialize query and target molecules.

Parameters:

stereoFilter - set true to rank the solutions as per stereo matches

fragmentFilter - set true to return matches with minimum fragments

energyFilter - set true to return matches with minimum bond changes based on the bond breaking energy

getEnergyScore

public abstract Double getEnergyScore(int key)

Deprecated.

Returns summation energy score of the disorder if the MCS is removed from the target and query graph. Amongst the solutions, a solution with lowest energy score is preferred.

Parameters:

key - Index of the mapping solution

Returns:

Total bond breaking energy required to remove the mapped part

getFragmentSize

public abstract Integer getFragmentSize(int key)

Deprecated.

Returns number of fragment generated in the solution space, if the MCS is removed from the target and query graph. Amongst the solutions, a solution with lowest fragment size is preferred.

Parameters:

key - Index of the mapping solution

Returns:

Fragment count(s) generated after removing the mapped parts

getProductMolecule

public abstract IAtomContainer getProductMolecule()

Deprecated.

Returns modified target molecule on which mapping was performed.

Returns:

return modified product Molecule

getReactantMolecule

public abstract IAtomContainer getReactantMolecule()

Deprecated.

Returns modified query molecule on which mapping was performed.

Returns:

return modified reactant Molecule

getStereoScore

public abstract Integer getStereoScore(int key)

Deprecated.

Returns a number which denotes the quality of the mcs. A solution with highest stereo score is preferred over other scores.

Parameters:

key - Index of the mapping solution

Returns:

true if no stereo mismatch occurs else false if stereo mismatch occurs

isStereoMisMatch

public abstract boolean isStereoMisMatch()

Deprecated.

Returns true if mols have different stereo chemistry else false if no stereo mismatch.

Returns:

true if mols have different stereo chemistry else false if no stereo mismatch. true if stereo mismatch occurs else true if stereo mismatch occurs.

isSubgraph

public abstract boolean isSubgraph()

Deprecated.

Checks if query is a subgraph of the target. Returns true if query is a subgraph of target else false

Returns:

true if query molecule is a subgraph of the target molecule

getTanimotoSimilarity

public abstract double getTanimotoSimilarity()
                                      throws IOException

Deprecated.

Returns Tanimoto similarity between query and target molecules (Score is between 0-min and 1-max).

Returns:

Tanimoto Similarity between 0 and 1

Throws:

IOException

getEuclideanDistance

public abstract double getEuclideanDistance()
                                     throws IOException

Deprecated.

Returns Euclidean Distance between query and target molecule.

Returns:

Euclidean Distance (lower the score, better the match)

Throws:

IOException

getAllAtomMapping

public abstract 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

public abstract 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

public abstract Map<IAtom,IAtom> getFirstAtomMapping()

Deprecated.

Returns one of the best matches with atoms mapped.

Returns:

Best Atom Mapping

getFirstMapping

public abstract Map<Integer,Integer> getFirstMapping()

Deprecated.

Returns one of the best matches with atom indexes mapped.

Returns:

Best Mapping Index

getBondSensitiveTimeOut

public abstract double getBondSensitiveTimeOut()

Deprecated.

get timeout in mins for bond sensitive searches

Returns:

the bondSensitive TimeOut

setBondSensitiveTimeOut

public abstract void setBondSensitiveTimeOut(double bondSensitiveTimeOut)

Deprecated.

set timeout in mins (default 0.10 min) for bond sensitive searches

Parameters:

bondSensitiveTimeOut - the bond Sensitive Timeout in mins (default 0.30 min)

getBondInSensitiveTimeOut

public abstract double getBondInSensitiveTimeOut()

Deprecated.

get timeout in mins for bond insensitive searches

Returns:

the bondInSensitive TimeOut

setBondInSensitiveTimeOut

public abstract void setBondInSensitiveTimeOut(double bondInSensitiveTimeOut)

Deprecated.

set timeout in mins (default 1.00 min) for bond insensitive searches

Parameters:

bondInSensitiveTimeOut - the bond insensitive