Package com.actelion.research.chem.forcefield.mmff.table

Class Bond

  • All Implemented Interfaces:
    Searchable
    public final class Bond
extends java.lang.Object
implements Searchable
    Bond table, corresponds to the MMFFBOND.PAR parameters table provided in the MMFF literature. This table holds parameters for bond stretching interactions.

    • Constructor Summary

      Constructors 
      Constructor Description
      Bond​(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.
      double kb​(int index)
      Returns the 'kb' value at the given index from the Bond table.
      double kb​(MMFFMolecule mol, int atom1, int atom2)
      Returns 'kb' given a molecule and two atoms in that molecule that form a bond.
      int length()
      This function should return the total number of rows in a searchable table.
      double r0​(int index)
      Returns the 'r0' value at the given index from the Bond table.
      double r0​(MMFFMolecule mol, int atom1, int atom2)
      Returns 'r0' given a molecule and two atoms in that molecule that form a bond.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • Bond

        public Bond​(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.

      • r0

        public double r0​(int index)
        Returns the 'r0' value at the given index from the Bond table.
        Parameters:
        index - The table index for the row.
        Returns:
        'r0' for that index.

      • kb

        public double kb​(int index)
        Returns the 'kb' value at the given index from the Bond table.
        Parameters:
        index - The table index for the row.
        Returns:
        'kb' for that index.

      • r0

        public double r0​(MMFFMolecule mol,
                 int atom1,
                 int atom2)
        Returns 'r0' given a molecule and two atoms in that molecule that form a bond.
        Parameters:
        mol - The molecule containing the bond.
        atom1 - The first atom of the bond.
        atom2 - The second atom of the bond.
        Returns:
        'r0' for that bond.

      • kb

        public double kb​(MMFFMolecule mol,
                 int atom1,
                 int atom2)
        Returns 'kb' given a molecule and two atoms in that molecule that form a bond.
        Parameters:
        mol - The molecule containing the bond.
        atom1 - The first atom of the bond.
        atom2 - The second atom of the bond.
        Returns:
        'kb' for that bond.