rdkit/Code/ForceField/UFF/AngleConstraint.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 "AngleBend.h"
#include "AngleConstraint.h"
#include "Params.h"
#include <cmath>
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>

namespace ForceFields {
namespace UFF {
void _pretreatAngles(double &minAngleDeg, double &maxAngleDeg) {
  minAngleDeg = fmod(minAngleDeg, 360.0);
  maxAngleDeg = fmod(maxAngleDeg, 360.0);
  if (minAngleDeg > 180.0) {
    minAngleDeg -= 360.0;
  }
  if (maxAngleDeg > 180.0) {
    maxAngleDeg -= 360.0;
  }
  if ((minAngleDeg < 0.0) && (!(maxAngleDeg < 0.0))) {
    maxAngleDeg = std::max(fabs(maxAngleDeg), fabs(minAngleDeg));
    minAngleDeg = 0.0;
  }
  minAngleDeg = fabs(minAngleDeg);
  maxAngleDeg = fabs(maxAngleDeg);
  if (minAngleDeg > maxAngleDeg) {
    double t = minAngleDeg;
    minAngleDeg = maxAngleDeg;
    maxAngleDeg = t;
  }
}

AngleConstraintContrib::AngleConstraintContrib(
    ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3,
    double minAngleDeg, double maxAngleDeg, double forceConst) {
  PRECONDITION(owner, "bad owner");
  URANGE_CHECK(idx1, owner->positions().size());
  URANGE_CHECK(idx2, owner->positions().size());
  URANGE_CHECK(idx3, owner->positions().size());
  PRECONDITION(maxAngleDeg >= minAngleDeg, "allowedDeltaDeg must be >= 0.0");
  _pretreatAngles(minAngleDeg, maxAngleDeg);

  dp_forceField = owner;
  d_at1Idx = idx1;
  d_at2Idx = idx2;
  d_at3Idx = idx3;
  d_minAngleDeg = minAngleDeg;
  d_maxAngleDeg = maxAngleDeg;
  d_forceConstant = forceConst;
}

AngleConstraintContrib::AngleConstraintContrib(
    ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3,
    bool relative, double minAngleDeg, double maxAngleDeg, double forceConst) {
  PRECONDITION(owner, "bad owner");
  const RDGeom::PointPtrVect &pos = owner->positions();
  URANGE_CHECK(idx1, pos.size());
  URANGE_CHECK(idx2, pos.size());
  URANGE_CHECK(idx3, pos.size());
  PRECONDITION(maxAngleDeg >= minAngleDeg, "allowedDeltaDeg must be >= 0.0");

  double angle = 0.0;
  if (relative) {
    RDGeom::Point3D p1 = *((RDGeom::Point3D *)pos[idx1]);
    RDGeom::Point3D p2 = *((RDGeom::Point3D *)pos[idx2]);
    RDGeom::Point3D p3 = *((RDGeom::Point3D *)pos[idx3]);
    double dist1 = (p1 - p2).length();
    double dist2 = (p3 - p2).length();
    RDGeom::Point3D p12 = (p1 - p2) / dist1;
    RDGeom::Point3D p32 = (p3 - p2) / dist2;
    double cosTheta = p12.dotProduct(p32);
    clipToOne(cosTheta);
    angle = RAD2DEG * acos(cosTheta);
  }
  dp_forceField = owner;
  d_at1Idx = idx1;
  d_at2Idx = idx2;
  d_at3Idx = idx3;
  minAngleDeg += angle;
  maxAngleDeg += angle;
  _pretreatAngles(minAngleDeg, maxAngleDeg);
  d_minAngleDeg = minAngleDeg;
  d_maxAngleDeg = maxAngleDeg;
  d_forceConstant = forceConst;
}

double AngleConstraintContrib::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]);

  RDGeom::Point3D p12 = (p1 - p2) / dist1;
  RDGeom::Point3D p32 = (p3 - p2) / dist2;
  double cosTheta = p12.dotProduct(p32);
  clipToOne(cosTheta);
  double angle = RAD2DEG * acos(cosTheta);
  double angleTerm = 0.0;
  if (angle < d_minAngleDeg) {
    angleTerm = angle - d_minAngleDeg;
  } else if (angle > d_maxAngleDeg) {
    angleTerm = angle - d_maxAngleDeg;
  }
  double const c = 0.5 * DEG2RAD * DEG2RAD;
  double res = c * d_forceConstant * angleTerm * angleTerm;

  return res;
}

void AngleConstraintContrib::getGrad(double *pos, double *grad) const {
  PRECONDITION(dp_forceField, "no owner");
  PRECONDITION(pos, "bad vector");
  PRECONDITION(grad, "bad vector");

  double dist[2] = {dp_forceField->distance(d_at1Idx, d_at2Idx, pos),
                    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 *g[3] = {&(grad[3 * d_at1Idx]), &(grad[3 * d_at2Idx]),
                  &(grad[3 * d_at3Idx])};
  RDGeom::Point3D r[2] = {(p1 - p2) / dist[0], (p3 - p2) / dist[1]};
  double cosTheta = r[0].dotProduct(r[1]);
  clipToOne(cosTheta);
  double sinThetaSq = 1.0 - cosTheta * cosTheta;
  double sinTheta =
      std::max(((sinThetaSq > 0.0) ? sqrt(sinThetaSq) : 0.0), 1.0e-8);

  // use the chain rule:
  // dE/dx = dE/dTheta * dTheta/dx

  // dE/dTheta is independent of cartesians:
  double angle = RAD2DEG * acos(cosTheta);
  double angleTerm = 0.0;
  if (angle < d_minAngleDeg) {
    angleTerm = angle - d_minAngleDeg;
  } else if (angle > d_maxAngleDeg) {
    angleTerm = angle - d_maxAngleDeg;
  }

  double dE_dTheta = DEG2RAD * d_forceConstant * angleTerm;

  Utils::calcAngleBendGrad(r, dist, g, dE_dTheta, cosTheta, sinTheta);
}
}
}