Class 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 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)
    • 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
      • 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,
                                          ShapeVolume molGauss,
                                          boolean rigid)
      • getGradientContribution

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

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