Class DescriptorHandlerFlexophore
- java.lang.Object
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- com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore
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- All Implemented Interfaces:
DescriptorHandler
,IDescriptorHandlerFlexophore
,ISimilarityCalculator
public class DescriptorHandlerFlexophore extends java.lang.Object implements IDescriptorHandlerFlexophore
DescriptorHandlerFlexophoreCopyright: Actelion Ltd., Inc. All Rights Reserved This software is the proprietary information of Actelion Pharmaceuticals, Ltd. Use is subject to license terms.
- Author:
- Modest von Korff 29 Jan 2009 MvK: Start implementation 15 Oct 2012 MvK renamed DescriptorHandler3DMM2PPInteract-->DescriptorHandlerFlexophore 19 Apr 2013 MvK major changes in Flexophore encoding decoding 25 Apr 2013 MvK Flexophore version changed --> 3.0 07 May 2013 MvK bug fixes in encoding. Flexophore version changed --> 3.1 15 May 2013 MvK Bug fix for the objective function 03 May 2016 MvK versioning for interaction tables from Joel introduced. 10 Jun 2016 MvK DescriptorHandlerFlexophoreV4 --> DescriptorHandlerFlexophore, V4 becomes today the new Flexophore 18 Jun 2016 MvK New ConformationGenerator from TS for Flexophore creation. V 4.1 29 Jun 2016 MvK number of histogram bins and range increased in CGMult. V 4.2 15 Jul 2016 MvK if generation of conformer failed a new seed is injected and the generation is tried again. 11 Aug 2016 MvK number of bins increase from 50 to 80, histogram range increased from 25 to 40 Angstroem. --> V.4.3 30 Jan 2017 MvK minor bug fix. Two constants for the number of conformations. --> V.4.4. Compatible with V.4.3 April 2020 Version 5.0, new interaction tables from Joel Wahl, algorithmic changes. 20.05.2020 Changed definition of end-standing aliphatic groups. Center of gravity moved one bond to the outside. Aromatic rings are not aliphatic any more. Methyl groups connected to a ring are not considered. The next O or N must have a minimum distance of two bonds to the end standing atom.
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Field Summary
Fields Modifier and Type Field Description protected CreatorMolDistHistViz
creatorMolDistHistViz
static boolean
DEBUG
static MolDistHist
FAILED_OBJECT
protected static int
MAX_NUM_HEAVY_ATOMS
static int
MAX_NUM_SOLUTIONS
protected static int
MIN_NUM_ATOMS
static int
MODE_PPNODE_SIMILARITY_COMPARISON
static int
NUM_CONFORMATIONS
static java.lang.String
PARA_TAG_HISTOGRAM_SIMILARITY_THRESH
static java.lang.String
PARA_TAG_MODE_MATCH
static java.lang.String
PARA_TAG_MODE_SINGLE_CONFORMATION_QUERY
static java.lang.String
PARA_TAG_PPNODE_SIMILARITY_THRESH
protected java.lang.Exception
recentException
static java.lang.String
SEP_PARAMETER
static double
THRESH_HISTOGRAM_SIMILARITY
static double
THRESH_SIMILARITY_COMPARISON_NODE
static int
VERSION_INTERACTION_TABLES
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Fields inherited from interface com.actelion.research.chem.descriptor.DescriptorHandler
FAILED_BYTES, FAILED_STRING
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Constructor Summary
Constructors Constructor Description DescriptorHandlerFlexophore()
DescriptorHandlerFlexophore(int versionInteractionTable, int modePPNodeSimilarityComparison, double threshSimilarityHardMatch, double threshHistogramSimilarity, boolean singleConformationModeQuery)
DescriptorHandlerFlexophore(java.lang.String parameter)
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Method Summary
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Field Detail
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DEBUG
public static final boolean DEBUG
- See Also:
- Constant Field Values
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SEP_PARAMETER
public static final java.lang.String SEP_PARAMETER
- See Also:
- Constant Field Values
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PARA_TAG_PPNODE_SIMILARITY_THRESH
public static final java.lang.String PARA_TAG_PPNODE_SIMILARITY_THRESH
- See Also:
- Constant Field Values
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PARA_TAG_HISTOGRAM_SIMILARITY_THRESH
public static final java.lang.String PARA_TAG_HISTOGRAM_SIMILARITY_THRESH
- See Also:
- Constant Field Values
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PARA_TAG_MODE_MATCH
public static final java.lang.String PARA_TAG_MODE_MATCH
- See Also:
- Constant Field Values
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PARA_TAG_MODE_SINGLE_CONFORMATION_QUERY
public static final java.lang.String PARA_TAG_MODE_SINGLE_CONFORMATION_QUERY
- See Also:
- Constant Field Values
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MAX_NUM_HEAVY_ATOMS
protected static final int MAX_NUM_HEAVY_ATOMS
- See Also:
- Constant Field Values
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MIN_NUM_ATOMS
protected static final int MIN_NUM_ATOMS
- See Also:
- Constant Field Values
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NUM_CONFORMATIONS
public static final int NUM_CONFORMATIONS
- See Also:
- Constant Field Values
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MAX_NUM_SOLUTIONS
public static final int MAX_NUM_SOLUTIONS
- See Also:
- Constant Field Values
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FAILED_OBJECT
public static final MolDistHist FAILED_OBJECT
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VERSION_INTERACTION_TABLES
public static final int VERSION_INTERACTION_TABLES
- See Also:
- Constant Field Values
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MODE_PPNODE_SIMILARITY_COMPARISON
public static final int MODE_PPNODE_SIMILARITY_COMPARISON
- See Also:
- Constant Field Values
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THRESH_SIMILARITY_COMPARISON_NODE
public static final double THRESH_SIMILARITY_COMPARISON_NODE
- See Also:
- Constant Field Values
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THRESH_HISTOGRAM_SIMILARITY
public static final double THRESH_HISTOGRAM_SIMILARITY
- See Also:
- Constant Field Values
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creatorMolDistHistViz
protected CreatorMolDistHistViz creatorMolDistHistViz
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recentException
protected java.lang.Exception recentException
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Constructor Detail
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DescriptorHandlerFlexophore
public DescriptorHandlerFlexophore(java.lang.String parameter)
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DescriptorHandlerFlexophore
public DescriptorHandlerFlexophore()
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DescriptorHandlerFlexophore
public DescriptorHandlerFlexophore(int versionInteractionTable, int modePPNodeSimilarityComparison, double threshSimilarityHardMatch, double threshHistogramSimilarity, boolean singleConformationModeQuery)
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Method Detail
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setModeQuery
public void setModeQuery(boolean modeQuery)
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setThreadMaster
public void setThreadMaster(ThreadMaster threadMaster)
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isSingleConformationModeQuery
public boolean isSingleConformationModeQuery()
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setSingleConformationModeQuery
public void setSingleConformationModeQuery(boolean singleConformationModeQuery)
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getNewCompleteGraphMatcher
public CompleteGraphMatcher<IMolDistHist> getNewCompleteGraphMatcher()
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getObjectiveCompleteGraph
public ObjectiveBlurFlexophoreHardMatchUncovered getObjectiveCompleteGraph()
- Specified by:
getObjectiveCompleteGraph
in interfaceIDescriptorHandlerFlexophore
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getInfo
public DescriptorInfo getInfo()
- Specified by:
getInfo
in interfaceDescriptorHandler
- Specified by:
getInfo
in interfaceISimilarityCalculator
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getVersion
public java.lang.String getVersion()
- Specified by:
getVersion
in interfaceDescriptorHandler
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toStringParameter
public java.lang.String toStringParameter()
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getDefaultInstance
public static DescriptorHandlerFlexophore getDefaultInstance()
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encode
public java.lang.String encode(java.lang.Object o)
- Specified by:
encode
in interfaceDescriptorHandler
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decode
public MolDistHist decode(byte[] bytes)
- Specified by:
decode
in interfaceDescriptorHandler
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decode
public MolDistHist decode(java.lang.String s)
- Specified by:
decode
in interfaceDescriptorHandler
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createDescriptorSingleConf
public MolDistHist createDescriptorSingleConf(StereoMolecule mol)
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createDescriptorSingleConf
public MolDistHist createDescriptorSingleConf(ConformerSet conformerSet)
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createVisualDescriptorSingleConf
public MolDistHistViz createVisualDescriptorSingleConf(ConformerSet conformerSet)
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createDescriptor
public MolDistHist createDescriptor(java.lang.Object mol)
- Specified by:
createDescriptor
in interfaceDescriptorHandler
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createVisualDescriptor
public MolDistHistViz createVisualDescriptor(StereoMolecule fragBiggest)
This descriptor contains the molecule used for construction. The descriptor also contains information about corresponding atoms in the molecule.- Specified by:
createVisualDescriptor
in interfaceIDescriptorHandlerFlexophore
- Parameters:
fragBiggest
-- Returns:
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getRecentException
public java.lang.Exception getRecentException()
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getSimilarity
public float getSimilarity(java.lang.Object query, java.lang.Object base)
- Specified by:
getSimilarity
in interfaceISimilarityCalculator
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getBestMatch
public ModelSolutionSimilarity getBestMatch(MolDistHistViz mdhvBase, MolDistHistViz mdhvQuery)
- Specified by:
getBestMatch
in interfaceIDescriptorHandlerFlexophore
- Parameters:
mdhvBase
-mdhvQuery
-- Returns:
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normalizeValue
public static float normalizeValue(double value)
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calculationFailed
public boolean calculationFailed(java.lang.Object o)
- Specified by:
calculationFailed
in interfaceDescriptorHandler
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getThreadSafeCopy
public DescriptorHandlerFlexophore getThreadSafeCopy()
- Specified by:
getThreadSafeCopy
in interfaceDescriptorHandler
- Specified by:
getThreadSafeCopy
in interfaceISimilarityCalculator
- Returns:
- a deep copy for parallel computing.
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setObjectiveQueryBiased
public void setObjectiveQueryBiased(boolean enable)
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