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.MMFFMolecule;
  import com.actelion.research.chem.forcefield.mmff.PeriodicTable;
  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 final class Dfsb implements Searchable {
      private final Object[][] table;
  
      public Dfsb(Tables t, String csvpath) {
          table = Csv.readFile(csvpath);
      }
  
      @Override
      public int get(int row, int col) {
          return ((Number) table[row][col]).intValue();
      }
  
      @Override
      public int length() {
          return table.length;
      }
  
      /**
       * Returns the index that a given set of three atoms have in the Dfsb
       * table.
       *  @param mol The molecule containing the atoms.
       *  @param a1 Atom 1.
       *  @param a2 Atom 2.
       *  @param a3 Atom 3.
       *  @return The row index in the table.
       */
      public int index(MMFFMolecule mol, int a1, int a2, int a3) {
          int a1r = PeriodicTable.row(mol.getAtomicNo(a1));
          int a2r = PeriodicTable.row(mol.getAtomicNo(a2));
          int a3r = PeriodicTable.row(mol.getAtomicNo(a3));
  
          if (a1r > a3r)
              a1r = Search.s(a3r, a3r = a1r);
  
          return Search.binary(new int[]{1,0,2},
                  new int[]{a2r,a1r,a3r}, this);
      }
  
      /**
       * Returns the equivalent 'kb' value for a given set of three atoms.
       *  @param mol The molecule containing the atoms.
       *  @param a1 Atom 1.
       *  @param a2 Atom 2.
       *  @param a3 Atom 3.
       *  @return Returns the 'kb' value or 0 if no entry was found.
       */
      public double kb(MMFFMolecule mol, int a1, int a2, int a3) {
          int a1r = PeriodicTable.row(mol.getAtomicNo(a1));
          int a3r = PeriodicTable.row(mol.getAtomicNo(a3));
          int at = a1r > a3r ? 4 : 3;
          int idx = index(mol, a1, a2, a3);
  
          return idx >= 0 ? ((Number) table[idx][at]).doubleValue() : 0.0;
      }
  }
  