Package com.actelion.research.chem.phesaflex

Class EvaluableFlexibleOverlap

java.lang.Object

com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap

All Implemented Interfaces:

Evaluable

public class EvaluableFlexibleOverlap
extends java.lang.Object
implements Evaluable

Author:

JW, Oktober 2019 functionality for optimizing PheSA overlap (Pharmacophore+Shape) allowing for molecular flexibility

Constructor Summary

Constructors

Constructor	Description
EvaluableFlexibleOverlap(PheSAAlignment shapeAlign, StereoMolecule refMol, StereoMolecule fitMol, double ppWeight, boolean[] isHydrogen, double[] v, java.util.Map<java.lang.String,java.lang.Object> ffOptions)
EvaluableFlexibleOverlap(EvaluableFlexibleOverlap e)

Method Summary

Modifier and Type	Method	Description
EvaluableFlexibleOverlap	clone()
PheSAAlignment	getAlignment()
double	getFGValue(double[] grad)
double	getFGValuePP(double[] grad)
double	getFGValueSelfPP(double[] grad, MolecularVolume molVol, boolean rigid)
double	getFGValueShape(double[] grad)	calculates the gradient of the overlap function with respect to the cartesian coordinates of the atoms
double	getFGValueShapeSelf(double[] grad, MolecularVolume molGauss, boolean rigid)
double	getGradientContribution(Gaussian3D refAt, Gaussian3D fitAt, double[] grad, boolean rigid)
double[]	getState()
double[]	getState(double[] v)
void	setE0(double e0)
void	setState(double[] v)

Methods inherited from class java.lang.Object

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

Constructor Detail

EvaluableFlexibleOverlap

public EvaluableFlexibleOverlap(PheSAAlignment shapeAlign,
                                StereoMolecule refMol,
                                StereoMolecule fitMol,
                                double ppWeight,
                                boolean[] isHydrogen,
                                double[] v,
                                java.util.Map<java.lang.String,java.lang.Object> ffOptions)

EvaluableFlexibleOverlap

public EvaluableFlexibleOverlap(EvaluableFlexibleOverlap e)

Method Detail

setState

public void setState(double[] v)

Specified by:

setState in interface Evaluable

getState

public double[] getState(double[] v)

setE0

public void setE0(double e0)

getState

public double[] getState()

Specified by:

getState in interface Evaluable

getAlignment

public PheSAAlignment getAlignment()

getFGValue

public double getFGValue(double[] grad)

Specified by:

getFGValue in interface Evaluable

getFGValueShape

public double getFGValueShape(double[] grad)

calculates the gradient of the overlap function with respect to the cartesian coordinates of the atoms

getFGValuePP

public double getFGValuePP(double[] grad)

getFGValueShapeSelf

public double getFGValueShapeSelf(double[] grad,
                                  MolecularVolume molGauss,
                                  boolean rigid)

getGradientContribution

public double getGradientContribution(Gaussian3D refAt,
                                      Gaussian3D fitAt,
                                      double[] grad,
                                      boolean rigid)

getFGValueSelfPP

public double getFGValueSelfPP(double[] grad,
                               MolecularVolume molVol,
                               boolean rigid)

clone

public EvaluableFlexibleOverlap clone()

Overrides:

clone in class java.lang.Object