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

Class Atom

  • All Implemented Interfaces:
    Searchable
    public final class Atom
extends java.lang.Object
implements Searchable
    Atom table, corresponds to the MMFFPROP.PAR parameters table provided in the MMFF literature. This table specifies the chemical, topological and geometrical properties associated with each of the MMFF atom types.

    • Constructor Summary

      Constructors 
      Constructor Description
      Atom​(Tables t, java.lang.String csvpath)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean arom​(int type)
      Returns the Arom bool of an atom given its MMFF type.
      int aspec​(int type)
      Returns the ASPEC type of an atom given its MMFF type.
      int crd​(int type)
      Returns the CRD type of an atom given its MMFF type.
      int get​(int row, int col)
      This should get an integer value given a column and row.
      int length()
      This function should return the total number of rows in a searchable table.
      boolean linear​(int type)
      Returns the linear bool of an atom given its MMFF type.
      int mltb​(int type)
      Returns the MLTB type of an atom given its MMFF type.
      int pilp​(int type)
      Returns the PILP type of an atom given its MMFF type.
      boolean sbmb​(int type)
      Returns the SBMB type of an atom given its MMFF type.
      int val​(int type)
      Returns the VAL type of an atom given its MMFF type.

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • Atom

        public Atom​(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.

      • aspec

        public int aspec​(int type)
        Returns the ASPEC type of an atom given its MMFF type.
        Parameters:
        type - The MMFF atom type of the atom.
        Returns:
        The ASPEC value for the atom.

      • crd

        public int crd​(int type)
        Returns the CRD type of an atom given its MMFF type.
        Parameters:
        type - The MMFF atom type of the atom.
        Returns:
        The CRD value for the atom.

      • val

        public int val​(int type)
        Returns the VAL type of an atom given its MMFF type.
        Parameters:
        type - The MMFF atom type of the atom.
        Returns:
        The VAL type for the atom.

      • pilp

        public int pilp​(int type)
        Returns the PILP type of an atom given its MMFF type.
        Parameters:
        type - The MMFF atom type of the atom.
        Returns:
        The PILP type for the atom.

      • mltb

        public int mltb​(int type)
        Returns the MLTB type of an atom given its MMFF type.
        Parameters:
        type - The MMFF atom type of the atom.
        Returns:
        The MLTB type for the atom.

      • arom

        public boolean arom​(int type)
        Returns the Arom bool of an atom given its MMFF type.
        Parameters:
        type - The MMFF atom type of the atom.
        Returns:
        The Arom bool for the atom.

      • linear

        public boolean linear​(int type)
        Returns the linear bool of an atom given its MMFF type.
        Parameters:
        type - The MMFF atom type of the atom.
        Returns:
        The Linear bool for the atom.

      • sbmb

        public boolean sbmb​(int type)
        Returns the SBMB type of an atom given its MMFF type.
        Parameters:
        type - The MMFF atom type of the atom.
        Returns:
        The SBMB boolean for the atom.