Class Angle

  • All Implemented Interfaces:
    Searchable

    public final class Angle
    extends java.lang.Object
    implements Searchable
    Angle table, corresponds to the MMFFANG.PAR parameters table provided in the MMFF literature. This table provides parameters for angle bending interactions. This table is loaded from a CSV file as it is too large to hard code in to the class file.
    • Constructor Summary

      Constructors 
      Constructor Description
      Angle​(Tables t, java.lang.String csvpath)  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int get​(int row, int col)
      This should get an integer value given a column and row.
      int index​(MMFFMolecule mol, int a1, int a2, int a3)
      Returns the index of a row for a given molecule and three connected atoms which form an angle.
      double ka​(int index)
      Returns 'ka' the force constant for a given index in the table.
      double ka​(MMFFMolecule mol, int a1, int a2, int a3)
      Returns 'ka' given a molecule and three connected atoms which form an angle.
      int length()
      This function should return the total number of rows in a searchable table.
      double theta​(int index)
      Returns 'theta0' the equilibrium angle for a given index in the table.
      double theta​(MMFFMolecule mol, int a1, int a2, int a3)
      Returns 'theta0' the ideal angle given a molecule and three connected atoms which form an angle.
      • Methods inherited from class java.lang.Object

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

      • Angle

        public Angle​(Tables t,
                     java.lang.String csvpath)
    • Method Detail

      • get

        public int get​(int row,
                       int col)
        Description copied from interface: Searchable
        This should get an integer value given a column and row. The binary search function only searches columns containing integers for a value.
        Specified by:
        get in interface Searchable
        Parameters:
        row - The row in the table.
        col - The column in the row to return.
        Returns:
        The value at 'col' in 'row'.
      • length

        public int length()
        Description copied from interface: Searchable
        This function should return the total number of rows in a searchable table. This is normally just the length of the array.
        Specified by:
        length in interface Searchable
        Returns:
        The number of elements that can be searched.
      • ka

        public double ka​(int index)
        Returns 'ka' the force constant for a given index in the table.
        Parameters:
        index - The row index in the table.
        Returns:
        The force constant.
      • theta

        public double theta​(int index)
        Returns 'theta0' the equilibrium angle for a given index in the table.
        Parameters:
        index - The row index in the table.
        Returns:
        The force constant.
      • index

        public int index​(MMFFMolecule mol,
                         int a1,
                         int a2,
                         int a3)
        Returns the index of a row for a given molecule and three connected atoms which form an angle.
        Parameters:
        mol - The molecule that the atoms are in.
        a1 - Atom 1.
        a2 - Atom 2 (the central atom).
        a3 - Atom 3.
        Returns:
        The index in the angle table, or -1 if no suitable entry was found.
      • theta

        public double theta​(MMFFMolecule mol,
                            int a1,
                            int a2,
                            int a3)
        Returns 'theta0' the ideal angle given a molecule and three connected atoms which form an angle.
        Parameters:
        mol - The molecule that the atoms are in.
        a1 - Atom 1.
        a2 - Atom 2 (the central atom).
        a3 - Atom 3.
        Returns:
        The value of 'theta' from the angle table or calculated empirically.
      • ka

        public double ka​(MMFFMolecule mol,
                         int a1,
                         int a2,
                         int a3)
        Returns 'ka' given a molecule and three connected atoms which form an angle.
        Parameters:
        mol - The molecule that the atoms are in.
        a1 - Atom 1.
        a2 - Atom 2 (the central atom).
        a3 - Atom 3.
        Returns:
        The value of 'ka' from the angle table or calculated empirically.