Class OutOfPlane

  • All Implemented Interfaces:
    EnergyTerm

    public class OutOfPlane
    extends java.lang.Object
    implements EnergyTerm
    Out of plane energy term class. This energy term represents the out of plane energy associated with four atoms: A1 / A2--AC \ A3 Where AC is the central atom and A1, A2 and A3 are each connected to AC.
    • Constructor Summary

      Constructors 
      Constructor Description
      OutOfPlane​(Tables table, MMFFMolecule mol, int ac, int a1, int a2, int a3)
      Construct a new out of plane energy term.
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean equals​(int ac, int a1, int a2, int a3)
      Checks if this OutOfPlane's atoms are the same as a given set of 4 atoms, it checks all possible permutations of a1, a2 and a3.
      boolean exactly​(int ac, int a1, int a2, int a3)
      Checks if this OutOfPlane term is exactly equal to a given set of four atoms.
      static java.util.List<OutOfPlane> findIn​(MMFFMolecule mol)  
      static java.util.List<OutOfPlane> findIn​(Tables t, MMFFMolecule mol)
      Finds all out of plane angles in the current molecule.
      double getEnergy​(double[] pos)
      Calculates the out of plane energy.
      void getGradient​(double[] pos, double[] grad)
      Calculates the gradient and adds it to the gradients array.
      double getKoop()  
      • Methods inherited from class java.lang.Object

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

      • OutOfPlane

        public OutOfPlane​(Tables table,
                          MMFFMolecule mol,
                          int ac,
                          int a1,
                          int a2,
                          int a3)
        Construct a new out of plane 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.
        a3 - Index of atom 3 in mol.
    • Method Detail

      • getKoop

        public double getKoop()
      • getEnergy

        public double getEnergy​(double[] pos)
        Calculates the out of plane 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.
      • equals

        public boolean equals​(int ac,
                              int a1,
                              int a2,
                              int a3)
        Checks if this OutOfPlane's atoms are the same as a given set of 4 atoms, it checks all possible permutations of a1, a2 and a3.
        Parameters:
        ac - The central atom.
        a1 - Neighbouring atom 1.
        a2 - Neighbouring atom 2.
        a3 - Neighbouring atom 3.
        Returns:
        True if this OutOfPlane has the same permutation of neighbouring atoms as those provided.
      • exactly

        public boolean exactly​(int ac,
                               int a1,
                               int a2,
                               int a3)
        Checks if this OutOfPlane term is exactly equal to a given set of four atoms.
        Parameters:
        ac - The central atom.
        a1 - Neighbouring atom 1.
        a2 - Neighbouring atom 2.
        a3 - Neighbouring atom 3.
        Returns:
        True if the out of plane atoms are the same as the provided atoms.
      • findIn

        public static java.util.List<OutOfPlane> findIn​(Tables t,
                                                        MMFFMolecule mol)
        Finds all out of plane angles in the current molecule.
        Parameters:
        t - The tables parameter object.
        mol - The molecule to search in.
        Returns:
        An array of OutOfPlane angles.