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// $Id$
//
// 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 "AngleConstraint.h"
#include "Params.h"
#include <cmath>
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
namespace ForceFields {
namespace MMFF {
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(!(minAngleDeg > maxAngleDeg),
"minAngleDeg must be <= maxAngleDeg");
RDKit::ForceFieldsHelper::normalizeAngleDeg(minAngleDeg);
RDKit::ForceFieldsHelper::normalizeAngleDeg(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(!(minAngleDeg > maxAngleDeg),
"minAngleDeg must be <= maxAngleDeg");
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;
RDKit::ForceFieldsHelper::normalizeAngleDeg(minAngleDeg);
RDKit::ForceFieldsHelper::normalizeAngleDeg(maxAngleDeg);
d_minAngleDeg = minAngleDeg;
d_maxAngleDeg = maxAngleDeg;
d_forceConstant = forceConst;
}
double AngleConstraintContrib::computeAngleTerm(double angle) const {
double angleTerm = 0.0;
if (angle < d_minAngleDeg) {
angleTerm = angle - d_minAngleDeg;
} else if (angle > d_maxAngleDeg) {
angleTerm = angle - d_maxAngleDeg;
}
return angleTerm;
}
double AngleConstraintContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
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 r[2] = {p1 - p2, p3 - p2};
double rLengthSq[2] = {(std::max)(1.0e-5, r[0].lengthSq()),
(std::max)(1.0e-5, r[1].lengthSq())};
double cosTheta = r[0].dotProduct(r[1]) / sqrt(rLengthSq[0] * rLengthSq[1]);
clipToOne(cosTheta);
double angle = RAD2DEG * acos(cosTheta);
double angleTerm = computeAngleTerm(angle);
double res = 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");
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, p3 - p2};
double rLengthSq[2] = {(std::max)(1.0e-5, r[0].lengthSq()),
(std::max)(1.0e-5, r[1].lengthSq())};
double cosTheta = r[0].dotProduct(r[1]) / sqrt(rLengthSq[0] * rLengthSq[1]);
clipToOne(cosTheta);
double angle = RAD2DEG * acos(cosTheta);
double angleTerm = computeAngleTerm(angle);
double dE_dTheta = 2.0 * RAD2DEG * d_forceConstant * angleTerm;
RDGeom::Point3D rp = r[1].crossProduct(r[0]);
double prefactor = dE_dTheta / (std::max)(1.0e-5, rp.length());
double t[2] = {-prefactor / rLengthSq[0], prefactor / rLengthSq[1]};
RDGeom::Point3D dedp[3];
dedp[0] = r[0].crossProduct(rp) * t[0];
dedp[2] = r[1].crossProduct(rp) * t[1];
dedp[1] = -dedp[0] - dedp[2];
for (unsigned int i = 0; i < 3; ++i) {
g[i][0] += dedp[i].x;
g[i][1] += dedp[i].y;
g[i][2] += dedp[i].z;
}
}
} // namespace MMFF
} // namespace ForceFields
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