Package com.actelion.research.chem.descriptor.flexophore.completegraphmatcher

Class ObjectiveFlexophoreHardMatchUncovered

java.lang.Object

com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveFlexophoreHardMatchUncovered

All Implemented Interfaces:

IObjectiveCompleteGraph<IMolDistHist>

public class ObjectiveFlexophoreHardMatchUncovered
extends java.lang.Object
implements IObjectiveCompleteGraph<IMolDistHist>

ObjectiveFlexophoreHardMatchUncovered The weighting of the coverage is hard. Which means that uncovered nodes are strongly change the final similarity score. look in getScoreUncoveredNearestNodesBase(SolutionCompleteGraph solution) and getScoreUncoveredNearestNodesQuery(SolutionCompleteGraph solution). Use is subject to license terms.

Author:

Modest von Korff Oct 2, 2012 MvK: Start implementation Mar 3. 2016 MvK: updates. Lowered thresh for histogram similarity. Mar 31. 2020 MvK: fraction of carbon is considered in pharmacophore node similarity.

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	INFO
static int	MAX_NUM_NODES_FLEXOPHORE
static double	THRESH_HISTOGRAM_SIMILARITY
static java.lang.String	VERSION

Constructor Summary

Constructors

Constructor	Description
ObjectiveFlexophoreHardMatchUncovered(int versionInteractionTable, int modePPNodeSimilarity, double threshSimilarityNodeHardMatch, double threshHistogramSimilarity)

Method Summary

Modifier and Type	Method	Description
boolean	areNodesMapping(int indexNodeQuery, int indexNodeBase)	Dynamic calculation of similarity threshold.
IMolDistHist	getBase()
IMolDistHist	getQuery()
float	getSimilarity(SolutionCompleteGraph solution)
double	getSimilarityNodes(PPNode query, PPNode base)
boolean	isValidSolution(SolutionCompleteGraph solution)	If a single histogram is not matching the solution is invalid.
void	setBase(IMolDistHist iMolDistHistBase)
void	setMatchingInfoInQueryAndBase(SolutionCompleteGraph solution)	Sets the color information for the visualization of the Flexophore PPPoints.
void	setQuery(IMolDistHist iMolDistHistQuery)
void	setVerbose(boolean v)
java.lang.String	toString()
java.lang.String	toStringParameter()
java.lang.String	toStringRecentSimilarityResults()

Methods inherited from class java.lang.Object

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

Field Detail

VERSION

public static final java.lang.String VERSION

See Also:

Constant Field Values

INFO

public static final java.lang.String INFO

See Also:

Constant Field Values

MAX_NUM_NODES_FLEXOPHORE

public static final int MAX_NUM_NODES_FLEXOPHORE

See Also:

Constant Field Values

THRESH_HISTOGRAM_SIMILARITY

public static final double THRESH_HISTOGRAM_SIMILARITY

See Also:

Constant Field Values

Constructor Detail

ObjectiveFlexophoreHardMatchUncovered

public ObjectiveFlexophoreHardMatchUncovered(int versionInteractionTable,
                                             int modePPNodeSimilarity,
                                             double threshSimilarityNodeHardMatch,
                                             double threshHistogramSimilarity)

Method Detail

toStringParameter

public java.lang.String toStringParameter()

setVerbose

public void setVerbose(boolean v)

Specified by:

setVerbose in interface IObjectiveCompleteGraph<IMolDistHist>

isValidSolution

public boolean isValidSolution(SolutionCompleteGraph solution)

If a single histogram is not matching the solution is invalid. If at least one node is not matching the solution is invalid.

Specified by:

isValidSolution in interface IObjectiveCompleteGraph<IMolDistHist>

areNodesMapping

public boolean areNodesMapping(int indexNodeQuery,
                               int indexNodeBase)

Dynamic calculation of similarity threshold. Depends on the number of interaction types in the nodes.

Specified by:

areNodesMapping in interface IObjectiveCompleteGraph<IMolDistHist>

Parameters:

indexNodeQuery -

indexNodeBase -

Returns:

getSimilarity

public float getSimilarity(SolutionCompleteGraph solution)

Specified by:

getSimilarity in interface IObjectiveCompleteGraph<IMolDistHist>

setMatchingInfoInQueryAndBase

public void setMatchingInfoInQueryAndBase(SolutionCompleteGraph solution)

Sets the color information for the visualization of the Flexophore PPPoints. Call before visualization. Method sets identical info values for corresponding nodes.

Parameters:

solution -

getBase

public IMolDistHist getBase()

Specified by:

getBase in interface IObjectiveCompleteGraph<IMolDistHist>

getQuery

public IMolDistHist getQuery()

Specified by:

getQuery in interface IObjectiveCompleteGraph<IMolDistHist>

setBase

public void setBase(IMolDistHist iMolDistHistBase)

Specified by:

setBase in interface IObjectiveCompleteGraph<IMolDistHist>

setQuery

public void setQuery(IMolDistHist iMolDistHistQuery)

Specified by:

setQuery in interface IObjectiveCompleteGraph<IMolDistHist>

getSimilarityNodes

public double getSimilarityNodes(PPNode query,
                                 PPNode base)

toStringRecentSimilarityResults

public java.lang.String toStringRecentSimilarityResults()

Returns:

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object