content: /*
  * Copyright (c) 1997 - 2016
  * Actelion Pharmaceuticals Ltd.
  * Gewerbestrasse 16
  * CH-4123 Allschwil, Switzerland
  *
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  *    list of conditions and the following disclaimer.
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  *    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
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  package com.actelion.research.chem.forcefield.mmff;
  
  import com.actelion.research.util.DoubleFormat;
  
  import java.util.ArrayList;
  import java.util.List;
  
  /**
   * Stretch bending energy term class. This energy term represents the
   * bond stretching-angle bending energy associated with three bonded
   * atoms A1--A2--A3 with an angle at A2.
   */
  public class StretchBend implements EnergyTerm {
      public final MMFFMolecule mol;
      public final int a1;
      public final int a2; // Central atom.
      public final int a3;
  
      public final double theta0;
      public final double kba_ijk;
      public final double kba_kji;
      public final double r0i;
      public final double r0k;
  
      /**
       * Constructs a new stretch bend object. Note that it only represents
       * the stretch bend energy in the IJK direction. A separate stretch
       * bend object should be created to represent the KJI direction with
       * a1 and a3 swapped.
       *  @param mol The molecule containing the atoms.
       *  @param a1 Atom 1 (atom i).
       *  @param a2 Atom 2, the central atom (atom j).
       *  @param a3 Atom 3 (atom k).
       */
      public StretchBend(Tables table, MMFFMolecule mol, int a1, int a2, int a3) {
          this.mol = mol;
          this.a1 = a1;
          this.a2 = a2;
          this.a3 = a3;
  
          theta0 = table.angle.theta(mol, a1, a2, a3);
          r0i = table.bond.r0(mol, a1, a2);
          r0k = table.bond.r0(mol, a3, a2);
          kba_ijk = table.stbn.kba(mol, a1, a2, a3);
          kba_kji = table.stbn.kba(mol, a3, a2, a1);
      }
  
      /**
       * Calculates the stretch bend energy.
       *  @param pos The atoms current positions array.
       *  @return The energy.
       */
      @Override
      public double getEnergy(double[] pos) {
          return getEnergy(pos, null, null, false);
      }
  
      /**
       * Calculates the stretch bend energy.
       *  @param pos The atoms current positions array.
       *  @return The energy.
       */
      @Override
      public double getEnergy(double[] pos, StringBuilder detail, String detailID, boolean skipHydrogen) {
          if (skipHydrogen && (mol.getAtomicNo(a1) == 1 || mol.getAtomicNo(a3) == 1))
              return 0.0;
  
          double dist1 = new Vector3(pos, a2, a1).length();
          double dist2 = new Vector3(pos, a2, a3).length();
          double theta = new Vector3(pos,a2,a1).angle(new Vector3(pos,a2,a3));
          double factor = Constants.MDYNE_A_TO_KCAL_MOL * Constants.DEG2RAD
              * (Math.toDegrees(theta) - theta0);
  
          double e = factor*(dist1 - r0i)*kba_ijk + factor*(dist2 - r0k)*kba_kji;
  
          if (detail != null)
              detail.append(detailID+"\tstretchBend\t"
                      +DoubleFormat.toString(dist1)+","+DoubleFormat.toString(dist2)+","
                      +DoubleFormat.toString(Math.toDegrees(theta))+"\t"
                      +DoubleFormat.toString(r0i)+","+DoubleFormat.toString(r0k)+","
                      +DoubleFormat.toString(theta0)+"\t"
                      +a1+","+a2+","+a3+"\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.
       */
      @Override
      public void getGradient(double[] pos, double[] grad) {
          double dist1 = new Vector3(pos, a2, a1).length();
          double dist2 = new Vector3(pos, a2, a3).length();
  
          Vector3 p12 = new Vector3(pos, a2, a1).normalise();
          Vector3 p32 = new Vector3(pos, a2, a3).normalise();
  
          final double c5 = Constants.MDYNE_A_TO_KCAL_MOL * Constants.DEG2RAD;
          double cosTheta = p12.dot(p32);
          double sinThetaSq = 1.0 - cosTheta*cosTheta;
          double sinTheta = Math.max(sinThetaSq > 0.0
                  ? Math.sqrt(sinThetaSq) : 0.0, 1.0e-8);
          double angleTerm = Constants.RAD2DEG * Math.acos(cosTheta) - theta0;
          double distTerm = Constants.RAD2DEG
                  * (kba_ijk * (dist1 - r0i)
                  +  kba_kji * (dist2 - r0k));
  
          double dCos_dS1 = 1.0 / dist1 * (p32.x - cosTheta * p12.x);
          double dCos_dS2 = 1.0 / dist1 * (p32.y - cosTheta * p12.y);
          double dCos_dS3 = 1.0 / dist1 * (p32.z - cosTheta * p12.z);
  
          double dCos_dS4 = 1.0 / dist2 * (p12.x - cosTheta * p32.x);
          double dCos_dS5 = 1.0 / dist2 * (p12.y - cosTheta * p32.y);
          double dCos_dS6 = 1.0 / dist2 * (p12.z - cosTheta * p32.z);
  
          grad[3*a1+0] += c5 * (p12.x * kba_ijk
              * angleTerm + dCos_dS1 / (-sinTheta) * distTerm);
          grad[3*a1+1] += c5 * (p12.y * kba_ijk
              * angleTerm + dCos_dS2 / (-sinTheta) * distTerm);
          grad[3*a1+2] += c5 * (p12.z * kba_ijk
              * angleTerm + dCos_dS3 / (-sinTheta) * distTerm);
  
          grad[3*a2+0] += c5 * ((-p12.x * kba_ijk
              - p32.x * kba_kji) * angleTerm
              + (-dCos_dS1 - dCos_dS4) / (-sinTheta) * distTerm);
          grad[3*a2+1] += c5 * ((-p12.y * kba_ijk
              - p32.y * kba_kji) * angleTerm
              + (-dCos_dS2 - dCos_dS5) / (-sinTheta) * distTerm);
          grad[3*a2+2] += c5 * ((-p12.z * kba_ijk
              - p32.z * kba_kji) * angleTerm
              + (-dCos_dS3 - dCos_dS6) / (-sinTheta) * distTerm);
  
          grad[3*a3+0] += c5 * (p32.x * kba_kji
              * angleTerm + dCos_dS4 / (-sinTheta) * distTerm);
          grad[3*a3+1] += c5 * (p32.y * kba_kji
              * angleTerm + dCos_dS5 / (-sinTheta) * distTerm);
          grad[3*a3+2] += c5 * (p32.z * kba_kji
              * angleTerm + dCos_dS6 / (-sinTheta) * distTerm);
      }
  
      /**
       * Checks if a Stretch Bend is valid
       */
      public static boolean valid(Tables table, MMFFMolecule mol, int a1,
  								int a2, int a3) {
          int a2t = mol.getAtomType(a2);
  
          // Fail if the central atom is linear or the two neighbours are the
          // same atom.
          if (table.atom.linear(a2t) || a1 == a3)
              return false;
  
          // Fail if the three atoms do not form an angle.
          if (mol.getBond(a1, a2) == -1 || mol.getBond(a2, a3) == -1)
              return false;
  
          return true;
      }
  
  
      /**
       * Helper function that builds a list of StretchBends for a molecule.
       *  @param t The tables object.
       *  @param mol The molecule to generate angles for.
       *  @return An array of AngleBends.
       */
      public static List<StretchBend> findIn(Tables t, MMFFMolecule mol) {
          ArrayList<StretchBend> stbn = new ArrayList<StretchBend>();
  
          for (int atom=0; atom<mol.getAllAtoms(); atom++) {
              int atomt = mol.getAtomType(atom);
  
              if (mol.getAllConnAtoms(atom) <= 1 && t.atom.linear(atomt))
                  continue;
  
              for (int i=0; i<mol.getAllConnAtoms(atom); i++) {
                  int nbr_i = mol.getConnAtom(atom, i);
                  for (int k=0; k<mol.getAllConnAtoms(atom); k++) {
                      int nbr_k = mol.getConnAtom(atom, k);
  
                      // Only add half of the bends.
                      if (nbr_i > nbr_k)
                          continue;
  
                      if (StretchBend.valid(t, mol, nbr_i, atom, nbr_k)) {
                          StretchBend bend = new StretchBend(t, mol, nbr_i,
                                  atom, nbr_k);
  
                          // Don't bother adding any stretch bends whose kba
                          // would be 0.
                          if (Math.abs(bend.kba_ijk) > 0.0001
                                  || Math.abs(bend.kba_kji) > 0.0001) {
                              stbn.add(bend);
                          }
                      }
                  }
              }
          }
  
          return stbn;
      }
  }
  