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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 "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);
}
}
}
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