rdkit/Code/ForceField/MMFF/StretchBend.cpp

// $Id$
//
//  Copyright (C) 2013 Paolo Tosco
//
//  Copyright (C) 2004-2006 Rational Discovery LLC
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include "StretchBend.h"
#include "AngleBend.h"
#include "BondStretch.h"
#include "Params.h"
#include <cmath>
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/utils.h>


namespace ForceFields {
  namespace MMFF {
    namespace Utils {

      std::pair<double, double> calcStbnForceConstants(const MMFFStbn *mmffStbnParams)
      {
        PRECONDITION(mmffStbnParams, "stretch-bend parameters not found");
        
        return std::make_pair(mmffStbnParams->kbaIJK, mmffStbnParams->kbaKJI);
      }

      std::pair<double, double> calcStretchBendEnergy
        (const double deltaDist1, const double deltaDist2,
        const double deltaTheta, const std::pair<double, double> forceConstants)
      {
        double factor = MDYNE_A_TO_KCAL_MOL * DEG2RAD * deltaTheta;
        
        return std::make_pair(factor * forceConstants.first * deltaDist1,
          factor * forceConstants.second * deltaDist2);
      }
    } // end of namespace Utils
    
    StretchBendContrib::StretchBendContrib(ForceField *owner,
      const unsigned int idx1, const unsigned int idx2, const unsigned int idx3,
      const MMFFStbn *mmffStbnParams,const MMFFAngle *mmffAngleParams,
      const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2)
    {
      PRECONDITION(owner, "bad owner");
      PRECONDITION(((idx1 != idx2) && (idx2 != idx3) && (idx1 != idx3)), "degenerate points");
      RANGE_CHECK(0, idx1, owner->positions().size() - 1);
      RANGE_CHECK(0, idx2, owner->positions().size() - 1);
      RANGE_CHECK(0, idx3, owner->positions().size() - 1);
        
      dp_forceField = owner;
      d_at1Idx = idx1;
      d_at2Idx = idx2;
      d_at3Idx = idx3;
      d_restLen1 = Utils::calcBondRestLength(mmffBondParams1);
      d_restLen2 = Utils::calcBondRestLength(mmffBondParams2);
      d_theta0 = Utils::calcAngleRestValue(mmffAngleParams);
      d_forceConstants = Utils::calcStbnForceConstants(mmffStbnParams);
    }

    double StretchBendContrib::getEnergy(double *pos) const
    {
      PRECONDITION(dp_forceField,"no owner");
      PRECONDITION(pos,"bad vector");
      double dist1 = dp_forceField->distance(d_at1Idx, d_at2Idx,pos);
      double dist2 = dp_forceField->distance(d_at2Idx, d_at3Idx,pos);
      
      RDGeom::Point3D p1(pos[3 * d_at1Idx],
			  pos[3 * d_at1Idx + 1],
			  pos[3 * d_at1Idx + 2]);
      RDGeom::Point3D p2(pos[3 * d_at2Idx],
			  pos[3 * d_at2Idx + 1],
			  pos[3 * d_at2Idx + 2]);
      RDGeom::Point3D p3(pos[3 * d_at3Idx],
			  pos[3 * d_at3Idx + 1],
			  pos[3 * d_at3Idx + 2]);
      
      std::pair<double, double> stretchBendEnergies =
        Utils::calcStretchBendEnergy(dist1 - d_restLen1,
        dist2 - d_restLen2, RAD2DEG * acos(Utils::calcCosTheta
        (p1, p2, p3, dist1, dist2)) - d_theta0, d_forceConstants);
      
      return (stretchBendEnergies.first + stretchBendEnergies.second);
    }

    void StretchBendContrib::getGrad(double *pos, double *grad) const
    {
      PRECONDITION(dp_forceField, "no owner");
      PRECONDITION(pos, "bad vector");
      PRECONDITION(grad, "bad vector");
      double dist1 = dp_forceField->distance(d_at1Idx, d_at2Idx, pos);
      double dist2 = dp_forceField->distance(d_at2Idx, d_at3Idx, pos);

      RDGeom::Point3D p1(pos[3 * d_at1Idx],
        pos[3 * d_at1Idx + 1], pos[3 * d_at1Idx + 2]);
      RDGeom::Point3D p2(pos[3 * d_at2Idx],
        pos[3 * d_at2Idx + 1], pos[3 * d_at2Idx + 2]);
      RDGeom::Point3D p3(pos[3 * d_at3Idx],
        pos[3 * d_at3Idx + 1], pos[3 * d_at3Idx + 2]);
      double *g1 = &(grad[3 * d_at1Idx]);
      double *g2 = &(grad[3 * d_at2Idx]);
      double *g3 = &(grad[3 * d_at3Idx]);

      RDGeom::Point3D p12 = (p1 - p2) / dist1;
      RDGeom::Point3D p32 = (p3 - p2) / dist2;
      double const c5 = MDYNE_A_TO_KCAL_MOL * DEG2RAD;
      double cosTheta = p12.dotProduct(p32);
      clipToOne(cosTheta);
      double sinThetaSq = 1.0 - cosTheta * cosTheta;
      double sinTheta = std::max(((sinThetaSq > 0.0) ? sqrt(sinThetaSq) : 0.0), 1.0e-8);
      double angleTerm = RAD2DEG * acos(cosTheta) - d_theta0;
      double distTerm = RAD2DEG * (d_forceConstants.first * (dist1 - d_restLen1)
        + d_forceConstants.second * (dist2 - d_restLen2));
      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);

      g1[0] += c5 * (p12.x * d_forceConstants.first
        * angleTerm + dCos_dS1 / (-sinTheta) * distTerm);
      g1[1] += c5 * (p12.y * d_forceConstants.first
        * angleTerm + dCos_dS2 / (-sinTheta) * distTerm);
      g1[2] += c5 * (p12.z * d_forceConstants.first
        * angleTerm + dCos_dS3 / (-sinTheta) * distTerm);

      g2[0] += c5 * ((-p12.x * d_forceConstants.first
        - p32.x * d_forceConstants.second) * angleTerm
        + (-dCos_dS1 - dCos_dS4) / (-sinTheta) * distTerm);
      g2[1] += c5 * ((-p12.y * d_forceConstants.first
        - p32.y * d_forceConstants.second) * angleTerm
        + (-dCos_dS2 - dCos_dS5) / (-sinTheta) * distTerm);
      g2[2] += c5 * ((-p12.z * d_forceConstants.first
        - p32.z * d_forceConstants.second) * angleTerm
        + (-dCos_dS3 - dCos_dS6) / (-sinTheta) * distTerm);
    
      g3[0] += c5 * (p32.x * d_forceConstants.second
        * angleTerm + dCos_dS4 / (-sinTheta) * distTerm);
      g3[1] += c5 * (p32.y * d_forceConstants.second
        * angleTerm + dCos_dS5 / (-sinTheta) * distTerm);
      g3[2] += c5 * (p32.z * d_forceConstants.second
        * angleTerm + dCos_dS6 / (-sinTheta) * distTerm);
    }
  }
}