Package com.actelion.research.chem.phesa

Class DescriptorHandlerShape

java.lang.Object

com.actelion.research.chem.phesa.DescriptorHandlerShape

All Implemented Interfaces:

DescriptorHandler<PheSAMolecule,StereoMolecule>, ISimilarityCalculator<PheSAMolecule>

Direct Known Subclasses:

DescriptorHandlerShapeOneConf

public class DescriptorHandlerShape
extends java.lang.Object
implements DescriptorHandler<PheSAMolecule,StereoMolecule>

Field Summary

Fields

Modifier and Type	Field	Description
static PheSAMolecule	FAILED_OBJECT
protected boolean	flexible
protected int	maxConfs
protected double	ppWeight

Fields inherited from interface com.actelion.research.chem.descriptor.DescriptorHandler

FAILED_BYTES, FAILED_STRING

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)

Method Summary

Modifier and Type	Method	Description
boolean	calculationFailed(PheSAMolecule o)
PheSAMolecule	createDescriptor(ConformerSet fullSet)
PheSAMolecule	createDescriptor(StereoMolecule mol)	the ShapeDescriptor consists of a whole ensemble of MolecularVolumes (MolecularGaussians), obtained from a conformational search algorithm
PheSAMolecule	decode(byte[] arr)
PheSAMolecule	decode(java.lang.String s)
java.lang.String	encode(PheSAMolecule o)
static DescriptorHandlerShape	getDefaultInstance()
DescriptorInfo	getInfo()
double	getPpWeight()
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 molecule
DescriptorHandlerShape	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)

Methods inherited from class java.lang.Object

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

Field Detail

FAILED_OBJECT

public static final PheSAMolecule FAILED_OBJECT

maxConfs

protected int maxConfs

ppWeight

protected double ppWeight

flexible

protected boolean flexible

Constructor Detail

DescriptorHandlerShape

public DescriptorHandlerShape()

DescriptorHandlerShape

public DescriptorHandlerShape(boolean useSingleBaseConformation)

DescriptorHandlerShape

public DescriptorHandlerShape(boolean useSingleBaseConformation,
                              double ppWeight)

DescriptorHandlerShape

public DescriptorHandlerShape(int maxConfs,
                              double ppWeight)

DescriptorHandlerShape

public DescriptorHandlerShape(double ppWeight)

Parameters:

ppWeight - similarity weight for the pharmacophore in total similarity.

DescriptorHandlerShape

public DescriptorHandlerShape(boolean useSingleBaseConformation,
                              int maxConfs,
                              double ppWeight)

Method Detail

createDescriptor

public PheSAMolecule createDescriptor(ConformerSet fullSet)

init

public void init()

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 interface DescriptorHandler<PheSAMolecule,StereoMolecule>

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 interface ISimilarityCalculator<PheSAMolecule>

getPreviousAlignment

public StereoMolecule[] getPreviousAlignment()

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:

setPreviousAlignment

public void setPreviousAlignment(StereoMolecule[] previousAlignment)

setPreviousPheSAResult

public void setPreviousPheSAResult(double[] previousPhesaResult)

getVersion

public java.lang.String getVersion()

Specified by:

getVersion in interface DescriptorHandler<PheSAMolecule,StereoMolecule>

getInfo

public DescriptorInfo getInfo()

Specified by:

getInfo in interface DescriptorHandler<PheSAMolecule,StereoMolecule>

Specified by:

getInfo in interface ISimilarityCalculator<PheSAMolecule>

encode

public java.lang.String encode(PheSAMolecule o)

Specified by:

encode in interface DescriptorHandler<PheSAMolecule,StereoMolecule>

decode

public PheSAMolecule decode(java.lang.String s)

Specified by:

decode in interface DescriptorHandler<PheSAMolecule,StereoMolecule>

decode

public PheSAMolecule decode(byte[] arr)

Specified by:

decode in interface DescriptorHandler<PheSAMolecule,StereoMolecule>

calculationFailed

public boolean calculationFailed(PheSAMolecule o)

Specified by:

calculationFailed in interface DescriptorHandler<PheSAMolecule,StereoMolecule>

getThreadSafeCopy

public DescriptorHandlerShape getThreadSafeCopy()

Specified by:

getThreadSafeCopy in interface DescriptorHandler<PheSAMolecule,StereoMolecule>

Specified by:

getThreadSafeCopy in interface ISimilarityCalculator<PheSAMolecule>

Returns:

a deep copy for parallel computing.

getDefaultInstance

public static DescriptorHandlerShape getDefaultInstance()

setMaxConfs

public void setMaxConfs(int maxConfs)

setFlexible

public void setFlexible(boolean flexible)

isFlexible

public boolean isFlexible()

getPpWeight

public double getPpWeight()