Package com.chemaxon.search.mcs.buildup

Class BuildupMcs

java.lang.Object

com.chemaxon.search.mcs.MaxCommonSubstructure

com.chemaxon.search.mcs.buildup.BuildupMcs

All Implemented Interfaces:

chemaxon.license.Licensable

@PublicApi
public final class BuildupMcs
extends MaxCommonSubstructure

Implements a heuristic MCS algorithm using the build-up method of Takeshi Kawabata.

For more information and the public API, see the base class MaxCommonSubstructure.

Field Summary

Fields inherited from class com.chemaxon.search.mcs.MaxCommonSubstructure

DEFAULT_RANDOM_SEED, LOG, matcher, queryMol, randomSeed, searchMode, searchOpts, targetMol, timeLimit

Constructor Summary

Constructors

Constructor	Description
BuildupMcs(McsSearchOptions searchOpts)	Creates a new BuildupMcs object with the given search options.

Method Summary

Modifier and Type	Method	Description
protected McsSearchResult	findMcs()	Finds the MCS and all related data (fragments and mappings).
int	getTopologyConstraint()	Gets the the maximum difference in topology the mapped part of the molecules can have.
void	setTopologyConstraint(int t)	Sets the maximum difference in topology the mapped part of the molecules can have.

Methods inherited from class com.chemaxon.search.mcs.MaxCommonSubstructure

calculateSimilarityUpperBound, calculateUpperBound, find, getQuery, getRandomSeed, getSearchMode, getSearchOptions, getTarget, getTimeLimit, hasNextResult, isLicensed, newInstance, newInstance, nextResult, setLicenseEnvironment, setMolecules, setQuery, setRandomSeed, setSearchMode, setTarget, setTimeLimit

Methods inherited from class java.lang.Object

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

Constructor Details

BuildupMcs

public BuildupMcs(McsSearchOptions searchOpts)

Creates a new BuildupMcs object with the given search options.

Parameters:

searchOpts - the search options

Method Details

setTopologyConstraint

public void setTopologyConstraint(int t)

Sets the maximum difference in topology the mapped part of the molecules can have.

Parameters:

t - the topology constraint.

getTopologyConstraint

public int getTopologyConstraint()

Gets the the maximum difference in topology the mapped part of the molecules can have.

Returns:

the topology constraint.

findMcs

protected McsSearchResult findMcs()

Description copied from class: MaxCommonSubstructure

Finds the MCS and all related data (fragments and mappings). Deriving classes must implement this method to calculate an (approximate) maximum common substructure after internal data structures are properly initialized.

For internal use only.

Specified by:

findMcs in class MaxCommonSubstructure