Class Contact

    • Field Detail

      • atoms

        protected Atom[] atoms
      • ac

        private int ac
      • minData

        private float minData
      • maxData

        private float maxData
      • vZ

        private javajs.util.V3 vZ
      • vY

        private javajs.util.V3 vY
      • vX

        private javajs.util.V3 vX
      • pt1

        private javajs.util.P3 pt1
      • pt2

        private javajs.util.P3 pt2
    • Constructor Detail

      • Contact

        public Contact()
    • Method Detail

      • setProperty

        public void setProperty​(java.lang.String propertyName,
                                java.lang.Object value,
                                BS bs)
        Overrides:
        setProperty in class Isosurface
      • setContacts

        private void setContacts​(java.lang.Object[] value,
                                 boolean doEditCpList)
      • combineSurfaces

        private float combineSurfaces​(javajs.util.Lst<ContactPair> pairs,
                                      int contactType,
                                      int displayType,
                                      float[] parameters,
                                      java.lang.Object func,
                                      boolean isColorDensity,
                                      boolean colorByType)
        Parameters:
        pairs -
        contactType -
        displayType -
        parameters -
        func -
        isColorDensity -
        colorByType -
        Returns:
        volume
      • setColorByScore

        private int setColorByScore​(float score,
                                    int nV)
      • getPairs

        private javajs.util.Lst<ContactPair> getPairs​(BS bsA,
                                                      BS bsB,
                                                      RadiusData rd,
                                                      int intramolecularMode,
                                                      boolean doEditCpList)
        Parameters:
        bsA -
        bsB -
        rd -
        intramolecularMode -
        doEditCpList -
        Returns:
        a list of pairs of atoms to process
      • isWithinFourBonds

        private boolean isWithinFourBonds​(Atom atomA,
                                          Atom atomB)
      • checkCp

        private static int checkCp​(ContactPair cp1,
                                   ContactPair cp2,
                                   int i1,
                                   int i2)
        Parameters:
        cp1 -
        cp2 -
        i1 -
        i2 -
        Returns:
        0 (no clash); 1 (remove #1); 2 (remove #2)
      • newSurface

        private void newSurface​(int displayType,
                                ContactPair cp,
                                BS bs1,
                                BS bs2,
                                RadiusData rd,
                                float[] parameters,
                                java.lang.Object func,
                                boolean isColorDensity,
                                VolumeData volumeData,
                                float sasurfaceRadius)
      • setVolumeData

        private void setVolumeData​(int type,
                                   VolumeData volumeData,
                                   ContactPair cp,
                                   float resolution,
                                   int nPairs)
      • mergeMesh

        private void mergeMesh​(MeshData md)
      • getVdwClashRadius

        private static void getVdwClashRadius​(ContactPair cp,
                                              double x0,
                                              double vdwA,
                                              double vdwB,
                                              double d)
        well, heh, heh... This calculates the VDW extension x at a given distance for a clashing pair that will produce a volume that is equivalent to the volume for the vdw contact at the point of touching (d0 = vdwA + vdwB) and the transition to clash. This will provide the surface that will surround the clash until the clash size is larger than it.
        Parameters:
        cp -
        x0 -
        vdwA -
        vdwB -
        d -