Class Tables


  • public final class Tables
    extends java.lang.Object
    A collection of tables with the official parameters of the MMFF94/MMFF94s force field variants.
    • Constructor Summary

      Constructors 
      Constructor Description
      Tables​(java.lang.String csv_angle, java.lang.String csv_atom, java.lang.String csv_bci, java.lang.String csv_bndk, java.lang.String csv_bond, java.lang.String csv_covrad, java.lang.String csv_dfsb, java.lang.String csv_def, java.lang.String csv_hblaurie, java.lang.String csv_oop, java.lang.String csv_pbci, java.lang.String csv_stbn, java.lang.String csv_torsion, java.lang.String csv_vdws)
      Construct a new Tables object.
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static Tables newMMFF94​(java.lang.String tableSet)
      Returns a new MMFF94 table.
      • Methods inherited from class java.lang.Object

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

      • Tables

        public Tables​(java.lang.String csv_angle,
                      java.lang.String csv_atom,
                      java.lang.String csv_bci,
                      java.lang.String csv_bndk,
                      java.lang.String csv_bond,
                      java.lang.String csv_covrad,
                      java.lang.String csv_dfsb,
                      java.lang.String csv_def,
                      java.lang.String csv_hblaurie,
                      java.lang.String csv_oop,
                      java.lang.String csv_pbci,
                      java.lang.String csv_stbn,
                      java.lang.String csv_torsion,
                      java.lang.String csv_vdws)
        Construct a new Tables object. Takes several string paths to CSV files to be used for the different parameter tables.
        Parameters:
        csv_angle - Path to the angles parameter table. The angle table holds ideal angle and force constant values.
        csv_atom - Path to the atoms parameter table. This table specifies the chemical, topological and geometrical properties associated with each of the MMFF atom types.
        csv_bci - Path to the bond charge increments table. This table is used for the MMFF partial charge computation.
        csv_bndk - Path to the bond length and default force constants table. Used as fallback values if bond parameters are not found in csv_bond.
        csv_bond - Path to the bond parameters table. Holds the ideal length and force constants for bonds between MMFF atom typed atoms.
        csv_covrad - Path to the CovRad CSV table.
        csv_dfsb - Path to the Dfsb CSV table. Holds the default stretch bend parameters.
        csv_def - Path to the default types table. Holds fallback MMFF types for atoms. Used to help find matches for energy terms in their parameter tables.
        csv_hblaurie - Path to the HerschbachLaurie table. Parameters table for Badger's rule.
        csv_oop - Path to the out of plane parameters table. Holds the force constant parameter.
        csv_pbci - Path to the partial bond charge increments and formal charge adjustments table.
        csv_stbn - Path to the stretch bend parameters table. Holds the force constants for both i-j-k and k-j-i atom configurations.
        csv_torsion - Path to the torsional parameters table. Holds the three force constants for given MMFF atom types.
        csv_vdws - Path to the van der Waals parameters table.
    • Method Detail

      • newMMFF94

        public static Tables newMMFF94​(java.lang.String tableSet)
        Returns a new MMFF94 table. The paths provided here are correct when running the project using ant/eclipse or from the same directory as build.xml and the README.