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;
  
  import com.actelion.research.util.DoubleFormat;
  
  import java.util.ArrayList;
  import java.util.List;
  
  /**
   * Bond stretching energy term class. This energy term represents the
   * bond stretching energy associated with two bonded atoms A1--A2.
   */
  public class BondStretch implements EnergyTerm {
      private final MMFFMolecule mol;
      public final int a1;
      public final int a2;
      public final double kb; // Force constant.
      public final double r0; // Ideal bond length.
  
      /**
       * Creates a new bond stretch given a force field and a bond. This is
       * a wrapper constructor.
       *  @param table The tables parameter object.
       *  @param mol The molecule.
       *  @param bond The bond index.
       */
      public BondStretch(Tables table, MMFFMolecule mol, int bond) {
          this(table, mol, mol.getBondAtom(0, bond), mol.getBondAtom(1, bond));
      }
  
      /**
       * Creates a new bond stretch given a force field and two bonded
       * atoms.
       *  @param table The tables parameter object.
       *  @param mol The molecule.
       *  @param a1 Atom 1 index.
       *  @param a2 Atom 2 index.
       */
      public BondStretch(Tables table, MMFFMolecule mol, int a1, int a2) {
          this.mol = mol;
          this.a1 = a1;
          this.a2 = a2;
  
          r0 = table.bond.r0(mol, a1, a2);
          kb = table.bond.kb(mol, a1, a2);
      }
  
      /**
       * Calculates the bond stretch energy.
       *  @param pos The atoms current positions array.
       *  @return The energy.
       */
      public double getEnergy(double[] pos) {
          return getEnergy(pos, null, null, false);
      }
  
      /**
       * Calculates the bond stretch energy.
       *  @param pos The atoms current positions array.
       *  @return The energy.
       */
      public double getEnergy(double[] pos, StringBuilder detail, String detailID, boolean skipHydrogen) {
          if (skipHydrogen && (mol.getAtomicNo(a1) == 1 || mol.getAtomicNo(a2) == 1))
              return 0.0;
  
          final double c1 = 143.9325;
          final double cs = -2.0;
          final double c3 = 7.0 / 12.0;
          final double dist = new Vector3(pos,a1).distance(new Vector3(pos,a2));
          final double diff = (dist - r0)*(dist - r0);
  
          double e = (0.5*c1*kb*diff * (1.0 + cs*(dist - r0) + c3*cs*cs*diff));
  
          if (detail != null)
              detail.append(detailID+"\tbondStretch\t"+DoubleFormat.toString(dist)+"\t"
                      +DoubleFormat.toString(r0)+"\t"+a1+","+a2+"\t"+ DoubleFormat.toString(e)+"\n");
  
          return e;
      }
  
      /**
       * Calculates the gradient and adds it to the gradients array.
       *  @param pos The atoms current positions array.
       *  @param grad the atoms current gradients array.
       */
      public void getGradient(double[] pos, double[] grad) {
          final double cs = -2.0;
          final double c1 = Constants.MDYNE_A_TO_KCAL_MOL;
          final double c3 = 7.0/12.0;
          final double dist = new Vector3(pos,a1).distance(new Vector3(pos,a2));
  
          double distTerm = dist - r0;
          double dE_dr = c1*kb*distTerm *
              (1.0 + 1.5*cs*distTerm + 2.0*c3*cs*cs*distTerm*distTerm);
  
          if (dist > 0.0) {
              for (int i=0; i<3; i++) {
                  grad[3*a1 + i] += dE_dr*(pos[3*a1 + i] - pos[3*a2 + i])/dist;
                  grad[3*a2 + i] -= dE_dr*(pos[3*a1 + i] - pos[3*a2 + i])/dist;
              }
          }
      }
  
      /**
       * Finds all bond stretch energy terms in the current molecule.
       *  @param t The tables parameter object.
       *  @param mol The molecule.
       *  @return The bond stretch energy terms for this molecule.
       */
      public static List<BondStretch> findIn(Tables t, MMFFMolecule mol) {
          List<BondStretch> bstretches = new ArrayList<BondStretch>();
  
          for (int b=0; b<mol.getAllBonds(); b++)
              bstretches.add(new BondStretch(t, mol, b));
  
          return bstretches;
      }
  }
  