Class VanDerWaals

  • All Implemented Interfaces:
    EnergyTerm

    public class VanDerWaals
    extends java.lang.Object
    implements EnergyTerm
    Nonbonded van der Waals energy term class. This energy term represents the van der Waals interaction between two atoms A1..A2 which are in a 1,X (X > 3) relationship. A cutoff (default: 100.0 angstrom) can be set to skip computation of van der Waals interactions between atoms separated by distances larger than the cutoff.
    • Constructor Summary

      Constructors 
      Constructor Description
      VanDerWaals​(Tables table, MMFFMolecule mol, int a1, int a2)
      Construct a new van der Waals energy term.
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      static java.util.List<VanDerWaals> findIn​(Tables table, MMFFMolecule mol, Separation sep, double nonbondedCutoff)
      Finds all van der Waals energy terms in the current molecule.
      double getEnergy​(double[] pos)
      Calculates the van der Waals energy.
      void getGradient​(double[] pos, double[] grad)
      Calculates the gradient and adds it to the gradients array.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Field Detail

      • a1t

        public final int a1t
      • a2t

        public final int a2t
      • rstar_ij

        public final double rstar_ij
      • well_depth

        public final double well_depth
      • a1

        public final int a1
      • a2

        public final int a2
      • da1

        public final char da1
      • da2

        public final char da2
    • Constructor Detail

      • VanDerWaals

        public VanDerWaals​(Tables table,
                           MMFFMolecule mol,
                           int a1,
                           int a2)
        Construct a new van der Waals energy term.
        Parameters:
        table - The tables parameter object.
        mol - The molecule.
        a1 - Index of atom 1 in mol.
        a2 - Index of atom 2 (the central atom) in mol.
    • Method Detail

      • getEnergy

        public double getEnergy​(double[] pos)
        Calculates the van der Waals energy.
        Specified by:
        getEnergy in interface EnergyTerm
        Parameters:
        pos - The atoms current positions array.
        Returns:
        The energy.
      • getGradient

        public void getGradient​(double[] pos,
                                double[] grad)
        Calculates the gradient and adds it to the gradients array.
        Specified by:
        getGradient in interface EnergyTerm
        Parameters:
        pos - The atoms current positions array.
        grad - the atoms current gradients array.
      • findIn

        public static java.util.List<VanDerWaals> findIn​(Tables table,
                                                         MMFFMolecule mol,
                                                         Separation sep,
                                                         double nonbondedCutoff)
        Finds all van der Waals energy terms in the current molecule.
        Parameters:
        table - The tables object.
        mol - The molecule to search for van der Waals forces.
        sep - The separations table for molecule mol.
        Returns:
        The van der Waals energy terms for this molecule.