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

Class ObjectiveBlurFlexophoreHardMatchUncovered

java.lang.Object

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

All Implemented Interfaces:

IObjectiveCompleteGraph<IMolDistHist>

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

ObjectiveBlurFlexophoreHardMatchUncovered The weighting of the coverage is hard. Which means that uncovered nodes 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 double	THRESH_HISTOGRAM_SIMILARITY
static java.lang.String	VERSION

Constructor Summary

Constructors

Constructor	Description
ObjectiveBlurFlexophoreHardMatchUncovered()
ObjectiveBlurFlexophoreHardMatchUncovered(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()
long	getDeltaNanoBaseBlur()
long	getDeltaNanoQueryBlur()
long	getDeltaNanoSimilarity()
IMolDistHist	getQuery()
float	getSimilarity(SolutionCompleteGraph solution)
float	getSimilarityHistogram(int indexNode1Query, int indexNode2Query, int indexNode1Base, int indexNode2Base)
float	getSimilarityNodes(int indexNodeQuery, int indexNodeBase)
double	getSimilarityNodes(IPPNode query, IPPNode base)
boolean	isModeQuery()
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	setModeQuery(boolean modeQuery)
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

THRESH_HISTOGRAM_SIMILARITY

public static final double THRESH_HISTOGRAM_SIMILARITY

See Also:

Constant Field Values

Constructor Detail

ObjectiveBlurFlexophoreHardMatchUncovered

public ObjectiveBlurFlexophoreHardMatchUncovered()

ObjectiveBlurFlexophoreHardMatchUncovered

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

Method Detail

setModeQuery

public void setModeQuery(boolean modeQuery)

isModeQuery

public boolean isModeQuery()

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>

getDeltaNanoQueryBlur

public long getDeltaNanoQueryBlur()

getDeltaNanoBaseBlur

public long getDeltaNanoBaseBlur()

getDeltaNanoSimilarity

public long getDeltaNanoSimilarity()

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.

Specified by:

setMatchingInfoInQueryAndBase in interface IObjectiveCompleteGraph<IMolDistHist>

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 float getSimilarityNodes(int indexNodeQuery,
                                int indexNodeBase)

getSimilarityHistogram

public float getSimilarityHistogram(int indexNode1Query,
                                    int indexNode2Query,
                                    int indexNode1Base,
                                    int indexNode2Base)

Specified by:

getSimilarityHistogram in interface IObjectiveCompleteGraph<IMolDistHist>

getSimilarityNodes

public double getSimilarityNodes(IPPNode query,
                                 IPPNode base)

Specified by:

getSimilarityNodes in interface IObjectiveCompleteGraph<IMolDistHist>

toStringRecentSimilarityResults

public java.lang.String toStringRecentSimilarityResults()

Returns:

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object