Examples of org.jmol.minimize.MinBond

org.jmol.minimize.MinBond

    List calc;


    DistanceCalc distanceCalc = new DistanceCalc();
    calc = calculations[CALC_DISTANCE] = new ArrayList();
    for (int i = 0; i < bondCount; i++) {
      MinBond bond = bonds[i];
      double bondOrder = bond.atomIndexes[2];
      if (bond.isAromatic)
        bondOrder = 1.5;
      if (bond.isAmide)
        bondOrder = 1.41;

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        c1 = -4.0 * c2 * cosT0;
        c0 = c2 * (2.0 * cosT0 * cosT0 + 1.0);
      }


      // Precompute the force constant
      MinBond bond = a.getBondTo(ib);
      double bondorder = bond.atomIndexes[2];
      if (bond.isAromatic)
        bondorder = 1.5;
      if (bond.isAmide)
        bondorder = 1.41;

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      double V = 0;
      a = atoms[ia = t[0]];
      b = atoms[ib = t[1]];
      c = atoms[ic = t[2]];
      d = atoms[id = t[3]];
      MinBond bc = c.getBondTo(ib);
      double bondOrder = bc.atomIndexes[2];
      if (bc.isAromatic)
        bondOrder = 1.5;
      if (bc.isAmide)
        bondOrder = 1.41;

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      for (int j = 0; j < 3; j++)
        if (!Util.isFinite(atom.coord[j]))
          return true;
    }
    for (int i = 0; i < bondCount; i++) {
      MinBond bond = bonds[i];
      if (Util.distance2(atoms[bond.atomIndexes[0]].coord,
          atoms[bond.atomIndexes[1]].coord) > 900.0)
        return true;
    }
    return false;

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Related Classes of org.jmol.minimize.MinBond

org.jmol.minimize.forcefield.CalculationsUFF

org.jmol.minimize.forcefield.CalculationsUFF$AngleCalc

org.jmol.minimize.forcefield.CalculationsUFF$TorsionCalc

org.jmol.minimize.forcefield.ForceField

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