Class Charge


  • public class Charge
    extends java.lang.Object
    • Constructor Summary

      Constructors 
      Constructor Description
      Charge​(Tables t, java.lang.String csv_pbci, java.lang.String csv_bci)  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int bci_binary_search​(int col, int val, int lo, int hi, boolean findlow)
      Binary search in the bci table.
      double get_bci_f​(int row, int col)  
      int get_bci_len()  
      int get_bci_n​(int row, int col)  
      double getFcadj​(int type)
      Returns the formal charge adjustment for a given atom type.
      double getPartial​(int bondt, int a1t, int a2t)
      Gets the partial charge of a bond type and its two atom types.
      double getPbci​(int type)  
      • Methods inherited from class java.lang.Object

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

      • Charge

        public Charge​(Tables t,
                      java.lang.String csv_pbci,
                      java.lang.String csv_bci)
    • Method Detail

      • getFcadj

        public double getFcadj​(int type)
        Returns the formal charge adjustment for a given atom type.
        Parameters:
        type - The MMFF atom type for an atom.
        Returns:
        The formal charge adjustment as a double.
      • getPbci

        public double getPbci​(int type)
      • getPartial

        public double getPartial​(int bondt,
                                 int a1t,
                                 int a2t)
        Gets the partial charge of a bond type and its two atom types.
        Parameters:
        bondt - The MMFF bond type.
        a1t - The MMFF atom type of atom 1.
        a2t - The MMFF atom type of atom 2.
        Returns:
        The partial charge.
      • bci_binary_search

        public int bci_binary_search​(int col,
                                     int val,
                                     int lo,
                                     int hi,
                                     boolean findlow)
        Binary search in the bci table. This is a wrapper function around 'binary_search' which just passes a SearchArray object for bci.
        Parameters:
        col - The column in the array to search, it should be an integer value.
        val - The value to be searched for.
        lo - The starting low index to begin searching from. This index is included in the search.
        hi - The ending high index to end searching in. This index is EXCLUDED in the search, with the value below it being searched.
        findlow - True if the binary search should find the lowest value if there are duplicates, False if the binary search should find the highest value if there are duplicates.
        Returns:
        The lowest/highest index to the value.
      • get_bci_f

        public double get_bci_f​(int row,
                                int col)
      • get_bci_n

        public int get_bci_n​(int row,
                             int col)
      • get_bci_len

        public int get_bci_len()