content: /*
  * Copyright (c) 1997 - 2016
  * Actelion Pharmaceuticals Ltd.
  * Gewerbestrasse 16
  * CH-4123 Allschwil, Switzerland
  *
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
  *
  * 1. Redistributions of source code must retain the above copyright notice, this
  *    list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
  * 3. Neither the name of the the copyright holder nor the
  *    names of its contributors may be used to endorse or promote products
  *    derived from this software without specific prior written permission.
  *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
  * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
  * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
  * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
  * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
  * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
  * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *
  */
  
  package com.actelion.research.chem.forcefield.mmff.table;
  
  import com.actelion.research.chem.forcefield.mmff.Csv;
  import com.actelion.research.chem.forcefield.mmff.Search;
  import com.actelion.research.chem.forcefield.mmff.Searchable;
  import com.actelion.research.chem.forcefield.mmff.Tables;
  
  public class Charge {
      private final Object[][] pbci;
      private final Object[][] bci;
  
      public Charge(Tables t, String csv_pbci, String csv_bci) {
          pbci = Csv.readFile(csv_pbci);
          bci = Csv.readFile(csv_bci);
      }
  
      /**
       * Returns the formal charge adjustment for a given atom type.
       *  @param type The MMFF atom type for an atom.
       *  @return The formal charge adjustment as a double.
       */
      public double getFcadj(int type) {
          return ((Number) pbci[type-1][2]).doubleValue();
      }
  
      public double getPbci(int type) {
          return ((Number) pbci[type-1][1]).doubleValue();
      }
  
      /**
       * Gets the partial charge of a bond type and its two atom types.
       *  @param bondt The MMFF bond type.
       *  @param a1t The MMFF atom type of atom 1.
       *  @param a2t The MMFF atom type of atom 2.
       *  @return The partial charge.
       */
      public double getPartial(int bondt, int a1t, int a2t) {
          double sign = a1t > a2t ? 1.0 : -1.0;
  
          int atl = a1t > a2t ? a2t : a1t;
          int ath = a1t > a2t ? a1t : a2t;
  
          int a1lo = bci_binary_search(1, atl, 0, bci.length, true);
          int a1hi = bci_binary_search(1, atl, 0, bci.length, false);
  
          // Couldn't find the first atom type.
          if (a1lo == -1 || a1hi == -1)
              return getPbci(a1t) - getPbci(a2t);
  
          int a2lo = bci_binary_search(2, ath, a1lo, a1hi+1, true);
          int a2hi = bci_binary_search(2, ath, a1lo, a1hi+1, false);
  
          // couldn't find the second atom type.
          if (a2lo == -1 || a2hi == -1)
              return getPbci(a1t) - getPbci(a2t);
  
          if (bondt == 0 && get_bci_n(a2lo, 0) == 0)
              return sign * get_bci_f(a2lo, 3);
          else if (bondt == 1 && get_bci_n(a2hi, 0) == 1)
              return sign * get_bci_f(a2hi, 3);
  
          // Couldn't find the bond type.
          return getPbci(a1t) - getPbci(a2t);
      }
  
      /**
       * Binary search in the bci table. This is a wrapper function around
       * 'binary_search' which just passes a SearchArray object for bci.
       *  @param col The column in the array to search, it should be an
       *      integer value.
       *  @param val The value to be searched for.
       *  @param lo The starting low index to begin searching from. This
       *      index is included in the search.
       *  @param hi The ending high index to end searching in. This index is
       *      EXCLUDED in the search, with the value below it being searched.
       *  @param 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.
       *  @return The lowest/highest index to the value.
       */
      public int bci_binary_search(int col, int val, int lo, int hi,
              boolean findlow) {
          return Search.binary(col, val, lo, hi, findlow, new Searchable(){
              public int get(int row, int col) {
                  return ((Number) bci[row][col]).intValue();
              }
  
              public int length() {
                  return bci.length;
              }
          });
      }
  
      public double get_bci_f(int row, int col) {
          return ((Number) bci[row][col]).doubleValue();
      }
  
      public int get_bci_n(int row, int col) {
          return ((Number) bci[row][col]).intValue();
      }
  
      public int get_bci_len() {
          return bci.length;
      }
  }
  