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.Tables;
  
  /**
   * Bond table, corresponds to the MMFFBOND.PAR parameters table provided
   * in the MMFF literature. This table holds parameters for bond stretching
   * interactions.
   */
  public final class Bond implements com.actelion.research.chem.forcefield.mmff.Searchable {
      private final Object[][] table;
      private final Tables t;
  
      public Bond(Tables t, String csvpath) {
          table = Csv.readFile(csvpath);
          this.t = t;
      }
  
      @Override
      public int get(int row, int col) {
          return ((Number) table[row][col]).intValue();
      }
  
      @Override
      public int length() {
          return table.length;
      }
  
      /**
       * Returns the 'r0' value at the given index from the Bond table.
       *  @param index The table index for the row.
       *  @return 'r0' for that index.
       */
      public double r0(int index) {
          return ((Number) table[index][4]).doubleValue();
      }
  
      /**
       * Returns the 'kb' value at the given index from the Bond table.
       *  @param index The table index for the row.
       *  @return 'kb' for that index.
       */
      public double kb(int index) {
          return ((Number) table[index][3]).doubleValue();
      }
  
      /**
       * Returns 'r0' given a molecule and two atoms in that molecule that
       * form a bond.
       *  @param mol The molecule containing the bond.
       *  @param atom1 The first atom of the bond.
       *  @param atom2 The second atom of the bond.
       *  @return 'r0' for that bond.
       */
      public double r0(MMFFMolecule mol, int atom1, int atom2) {
          int bondt = com.actelion.research.chem.forcefield.mmff.type.Bond.getType(t, mol, mol.getBond(atom1, atom2));
          int a1t = mol.getAtomType(atom1);
          int a2t = mol.getAtomType(atom2);
  
          // Ensure that atom types are in ascending order.
          if (a1t > a2t)
              a1t = com.actelion.research.chem.forcefield.mmff.Search.s(a2t, a2t = a1t);
  
          // Search the bond tabke for the atom types and bond type.
          int index = com.actelion.research.chem.forcefield.mmff.Search.binary(new int[]{1,2,0},
                  new int[]{a1t, a2t, bondt}, this);
  
          if (index >= 0)
              // Return r0 if it is in the table.
              return r0(index);
          else {
              int a1no = mol.getAtomicNo(atom1);
              int a2no = mol.getAtomicNo(atom2);
  
              if (a1no > a2no)
                  a1no = com.actelion.research.chem.forcefield.mmff.Search.s(a2no, a2no = a1no);
  
              int a1cri = com.actelion.research.chem.forcefield.mmff.Search.binary(0, a1no, t.covrad);
              int a2cri = com.actelion.research.chem.forcefield.mmff.Search.binary(0, a2no, t.covrad);
  
              double r0_i = t.covrad.r0(a1cri);
              double r0_j = t.covrad.r0(a2cri);
              double chi_i = t.covrad.chi(a1cri);
              double chi_j = t.covrad.chi(a2cri);
              double c = a1no == 1 || a2no == 1 ? 0.050 : 0.085;
  
              return r0_i + r0_j - c*Math.pow(Math.abs(chi_i - chi_j), 1.4);
          }
      }
  
      /**
       * Returns 'kb' given a molecule and two atoms in that molecule that
       * form a bond.
       *  @param mol The molecule containing the bond.
       *  @param atom1 The first atom of the bond.
       *  @param atom2 The second atom of the bond.
       *  @return 'kb' for that bond.
       */
      public double kb(MMFFMolecule mol, int atom1,
                       int atom2) {
          int bondt = com.actelion.research.chem.forcefield.mmff.type.Bond.getType(t, mol, mol.getBond(atom1, atom2));
          int a1t = mol.getAtomType(atom1);
          int a2t = mol.getAtomType(atom2);
  
          // Ensure that atom types are in ascending order.
          if (a1t > a2t)
              a1t = com.actelion.research.chem.forcefield.mmff.Search.s(a2t, a2t = a1t);
  
          // Search the bond tabke for the atom types and bond type.
          int index = com.actelion.research.chem.forcefield.mmff.Search.binary(new int[]{1,2,0},
                  new int[]{a1t, a2t, bondt}, this);
  
          if (index >= 0) {
              // Return r0 if it is in the table.
              return kb(index);
          } else {
              int a1no = mol.getAtomicNo(atom1);
              int a2no = mol.getAtomicNo(atom2);
  
              if (a1no > a2no)
                  a1no = com.actelion.research.chem.forcefield.mmff.Search.s(a2no, a2no = a1no);
  
              double r0 = r0(mol, atom1, atom2);
  
              // Search Bndk.
              int bndk_idx = com.actelion.research.chem.forcefield.mmff.Search.binary(new int[]{0, 1},
                      new int[]{a1no, a2no}, t.bndk);
  
              if (bndk_idx >= 0) {
                  // Found a value in Bndk.
                  double coeff = Math.pow(t.bndk.r0(bndk_idx) / r0, 6);
                  return t.bndk.kb(bndk_idx) * coeff;
              } else {
                  // Fall back to HerschbachLaurie.
                  int bidx = com.actelion.research.chem.forcefield.mmff.Search.binary(new int[]{0,1},
                          new int[]{PeriodicTable.rowtm(a1no),
                              PeriodicTable.rowtm(a2no)},
                          t.hblaurie);
                  return Math.pow(10.0, -(r0 - t.hblaurie.fget(bidx, 2))
                          / t.hblaurie.fget(bidx, 3));
              }
          }
      }
  }
  