Package com.actelion.research.chem.phesa
Class DescriptorHandlerShape
- java.lang.Object
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- com.actelion.research.chem.phesa.DescriptorHandlerShape
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- All Implemented Interfaces:
DescriptorHandler<PheSAMolecule,StereoMolecule>
,ISimilarityCalculator<PheSAMolecule>
- Direct Known Subclasses:
DescriptorHandlerShapeOneConf
public class DescriptorHandlerShape extends java.lang.Object implements DescriptorHandler<PheSAMolecule,StereoMolecule>
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Field Summary
Fields Modifier and Type Field Description static PheSAMolecule
FAILED_OBJECT
protected boolean
flexible
protected int
maxConfs
protected double
ppWeight
static int
SIZE_CUTOFF
protected ThreadMaster
threadMaster
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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 DescriptorHandlerShape()
DescriptorHandlerShape(boolean useSingleBaseConformation)
DescriptorHandlerShape(boolean useSingleBaseConformation, double ppWeight)
DescriptorHandlerShape(boolean useSingleBaseConformation, int maxConfs, double ppWeight)
DescriptorHandlerShape(double ppWeight)
DescriptorHandlerShape(int maxConfs, double ppWeight)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
calculationFailed(PheSAMolecule o)
PheSAMolecule
createDescriptor(ConformerSet confSet)
PheSAMolecule
createDescriptor(StereoMolecule mol)
the ShapeDescriptor consists of a whole ensemble of MolecularVolumes (MolecularGaussians), obtained from a conformational search algorithmPheSAMolecule
decode(byte[] arr)
PheSAMolecule
decode(java.lang.String s)
java.lang.String
encode(PheSAMolecule o)
static DescriptorHandlerShape
getDefaultInstance()
DescriptorInfo
getInfo()
double
getPpWeight()
java.util.List<Transformation>
getPreProcessTransformations()
StereoMolecule[]
getPreviousAlignment()
double[]
getPreviousPheSAResult()
additional output: element 0: total similarity (identical to getSimilarity(...)) element 1: pharmacophore similarity element 2: contribution to similarity that originates from additional volumes (incl/excl)float
getSimilarity(PheSAMolecule query, PheSAMolecule base)
calculates the Shape- and/or Pharmacophore similarity of a query molecule with a base moleculeDescriptorHandlerShape
getThreadSafeCopy()
java.lang.String
getVersion()
void
init()
boolean
isFlexible()
void
setFlexible(boolean flexible)
void
setMaxConfs(int maxConfs)
void
setPreviousAlignment(StereoMolecule[] previousAlignment)
void
setPreviousPheSAResult(double[] previousPhesaResult)
void
setThreadMaster(ThreadMaster tm)
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Field Detail
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SIZE_CUTOFF
public static final int SIZE_CUTOFF
- See Also:
- Constant Field Values
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FAILED_OBJECT
public static final PheSAMolecule FAILED_OBJECT
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maxConfs
protected int maxConfs
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ppWeight
protected double ppWeight
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flexible
protected boolean flexible
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threadMaster
protected ThreadMaster threadMaster
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Constructor Detail
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DescriptorHandlerShape
public DescriptorHandlerShape()
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DescriptorHandlerShape
public DescriptorHandlerShape(boolean useSingleBaseConformation)
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DescriptorHandlerShape
public DescriptorHandlerShape(boolean useSingleBaseConformation, double ppWeight)
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DescriptorHandlerShape
public DescriptorHandlerShape(int maxConfs, double ppWeight)
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DescriptorHandlerShape
public DescriptorHandlerShape(double ppWeight)
- Parameters:
ppWeight
- similarity weight for the pharmacophore in total similarity.
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DescriptorHandlerShape
public DescriptorHandlerShape(boolean useSingleBaseConformation, int maxConfs, double ppWeight)
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Method Detail
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setThreadMaster
public void setThreadMaster(ThreadMaster tm)
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getPreProcessTransformations
public java.util.List<Transformation> getPreProcessTransformations()
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createDescriptor
public PheSAMolecule createDescriptor(ConformerSet confSet)
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init
public void init()
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createDescriptor
public PheSAMolecule createDescriptor(StereoMolecule mol)
the ShapeDescriptor consists of a whole ensemble of MolecularVolumes (MolecularGaussians), obtained from a conformational search algorithm- Specified by:
createDescriptor
in interfaceDescriptorHandler<PheSAMolecule,StereoMolecule>
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getSimilarity
public float getSimilarity(PheSAMolecule query, PheSAMolecule base)
calculates the Shape- and/or Pharmacophore similarity of a query molecule with a base molecule- Specified by:
getSimilarity
in interfaceISimilarityCalculator<PheSAMolecule>
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getPreviousAlignment
public StereoMolecule[] getPreviousAlignment()
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getPreviousPheSAResult
public double[] getPreviousPheSAResult()
additional output: element 0: total similarity (identical to getSimilarity(...)) element 1: pharmacophore similarity element 2: contribution to similarity that originates from additional volumes (incl/excl)- Returns:
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setPreviousAlignment
public void setPreviousAlignment(StereoMolecule[] previousAlignment)
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setPreviousPheSAResult
public void setPreviousPheSAResult(double[] previousPhesaResult)
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getVersion
public java.lang.String getVersion()
- Specified by:
getVersion
in interfaceDescriptorHandler<PheSAMolecule,StereoMolecule>
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getInfo
public DescriptorInfo getInfo()
- Specified by:
getInfo
in interfaceDescriptorHandler<PheSAMolecule,StereoMolecule>
- Specified by:
getInfo
in interfaceISimilarityCalculator<PheSAMolecule>
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encode
public java.lang.String encode(PheSAMolecule o)
- Specified by:
encode
in interfaceDescriptorHandler<PheSAMolecule,StereoMolecule>
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decode
public PheSAMolecule decode(java.lang.String s)
- Specified by:
decode
in interfaceDescriptorHandler<PheSAMolecule,StereoMolecule>
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decode
public PheSAMolecule decode(byte[] arr)
- Specified by:
decode
in interfaceDescriptorHandler<PheSAMolecule,StereoMolecule>
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calculationFailed
public boolean calculationFailed(PheSAMolecule o)
- Specified by:
calculationFailed
in interfaceDescriptorHandler<PheSAMolecule,StereoMolecule>
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getThreadSafeCopy
public DescriptorHandlerShape getThreadSafeCopy()
- Specified by:
getThreadSafeCopy
in interfaceDescriptorHandler<PheSAMolecule,StereoMolecule>
- Specified by:
getThreadSafeCopy
in interfaceISimilarityCalculator<PheSAMolecule>
- Returns:
- a deep copy for parallel computing.
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getDefaultInstance
public static DescriptorHandlerShape getDefaultInstance()
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setMaxConfs
public void setMaxConfs(int maxConfs)
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setFlexible
public void setFlexible(boolean flexible)
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isFlexible
public boolean isFlexible()
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getPpWeight
public double getPpWeight()
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