Class EvaluableFlexibleOverlap
- java.lang.Object
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- com.actelion.research.chem.phesaflex.EvaluableFlexibleOverlap
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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)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description EvaluableFlexibleOverlap
clone()
PheSAAlignment
getAlignment()
double
getFGValue(double[] grad)
double
getFGValuePP(double[] grad)
double
getFGValueSelfPP(double[] grad, ShapeVolume molVol, boolean rigid)
double
getFGValueShape(double[] grad)
calculates the gradient of the overlap function with respect to the cartesian coordinates of the atomsdouble
getFGValueShapeSelf(double[] grad, ShapeVolume 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)
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Constructor Detail
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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)
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EvaluableFlexibleOverlap
public EvaluableFlexibleOverlap(EvaluableFlexibleOverlap e)
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Method Detail
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getState
public double[] getState(double[] v)
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setE0
public void setE0(double e0)
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getAlignment
public PheSAAlignment getAlignment()
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getFGValue
public double getFGValue(double[] grad)
- Specified by:
getFGValue
in interfaceEvaluable
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getFGValueShape
public double getFGValueShape(double[] grad)
calculates the gradient of the overlap function with respect to the cartesian coordinates of the atoms
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getFGValuePP
public double getFGValuePP(double[] grad)
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getFGValueShapeSelf
public double getFGValueShapeSelf(double[] grad, ShapeVolume molGauss, boolean rigid)
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getGradientContribution
public double getGradientContribution(Gaussian3D refAt, Gaussian3D fitAt, double[] grad, boolean rigid)
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getFGValueSelfPP
public double getFGValueSelfPP(double[] grad, ShapeVolume molVol, boolean rigid)
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clone
public EvaluableFlexibleOverlap clone()
- Overrides:
clone
in classjava.lang.Object
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