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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 "TorsionAngle.h"
#include "TorsionConstraint.h"
#include "Params.h"
#include <cmath>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/math/special_functions/round.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
namespace ForceFields {
namespace UFF {
void _pretreatDihedrals(double &minDihedralDeg, double &maxDihedralDeg) {
if (minDihedralDeg < 0.0) minDihedralDeg += 360.0;
if (maxDihedralDeg < 0.0) maxDihedralDeg += 360.0;
minDihedralDeg = fmod(minDihedralDeg, 360.0);
maxDihedralDeg = fmod(maxDihedralDeg, 360.0);
if (maxDihedralDeg < minDihedralDeg) maxDihedralDeg += 360.0;
}
TorsionConstraintContrib::TorsionConstraintContrib(
ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3,
unsigned int idx4, double minDihedralDeg, double maxDihedralDeg,
double forceConst) {
PRECONDITION(owner, "bad owner");
URANGE_CHECK(idx1, owner->positions().size());
URANGE_CHECK(idx2, owner->positions().size());
URANGE_CHECK(idx3, owner->positions().size());
URANGE_CHECK(idx4, owner->positions().size());
PRECONDITION((!(maxDihedralDeg < minDihedralDeg)) &&
((maxDihedralDeg - minDihedralDeg) < 360.0),
"bad bounds");
_pretreatDihedrals(minDihedralDeg, maxDihedralDeg);
dp_forceField = owner;
d_at1Idx = idx1;
d_at2Idx = idx2;
d_at3Idx = idx3;
d_at4Idx = idx4;
d_minDihedralDeg = minDihedralDeg;
d_maxDihedralDeg = maxDihedralDeg;
d_forceConstant = forceConst;
}
TorsionConstraintContrib::TorsionConstraintContrib(
ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3,
unsigned int idx4, bool relative, double minDihedralDeg,
double maxDihedralDeg, 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());
URANGE_CHECK(idx4, pos.size());
PRECONDITION((!(maxDihedralDeg < minDihedralDeg)) &&
((maxDihedralDeg - minDihedralDeg) < 360.0),
"bad bounds");
double dihedral = 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]);
RDGeom::Point3D p4 = *((RDGeom::Point3D *)pos[idx4]);
RDGeom::Point3D r12 = p2 - p1;
RDGeom::Point3D r23 = p3 - p2;
RDGeom::Point3D r34 = p4 - p3;
RDGeom::Point3D n123 = r12.crossProduct(r23);
double nIJKSqLength = n123.lengthSq();
RDGeom::Point3D n234 = r23.crossProduct(r34);
double nJKLSqLength = n234.lengthSq();
RDGeom::Point3D m = n123.crossProduct(r23);
// we want a signed dihedral, that's why we use atan2 instead of acos
dihedral =
RAD2DEG *
(-atan2(m.dotProduct(n234) / sqrt(nJKLSqLength * m.lengthSq()),
n123.dotProduct(n234) / sqrt(nIJKSqLength * nJKLSqLength)));
}
dp_forceField = owner;
d_at1Idx = idx1;
d_at2Idx = idx2;
d_at3Idx = idx3;
d_at4Idx = idx4;
minDihedralDeg += dihedral;
maxDihedralDeg += dihedral;
_pretreatDihedrals(minDihedralDeg, maxDihedralDeg);
d_minDihedralDeg = minDihedralDeg;
d_maxDihedralDeg = maxDihedralDeg;
d_forceConstant = forceConst;
}
double TorsionConstraintContrib::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 p4(pos[3 * d_at4Idx], pos[3 * d_at4Idx + 1],
pos[3 * d_at4Idx + 2]);
RDGeom::Point3D r1 = p2 - p1;
RDGeom::Point3D r2 = p3 - p2;
RDGeom::Point3D r4 = p4 - p3;
RDGeom::Point3D n123 = r1.crossProduct(r2);
double n123SqLength = n123.lengthSq();
RDGeom::Point3D n234 = r2.crossProduct(r4);
double n234SqLength = n234.lengthSq();
RDGeom::Point3D m = n123.crossProduct(r2);
// we want a signed dihedral, that's why we use atan2 instead of acos
double dihedral =
RAD2DEG *
(-atan2(m.dotProduct(n234) / sqrt(n234SqLength * m.lengthSq()),
n123.dotProduct(n234) / sqrt(n123SqLength * n234SqLength)));
if (dihedral < 0.0) dihedral += 360.0;
double dihedralTerm = 0.0;
if (dihedral < d_minDihedralDeg) {
dihedralTerm = dihedral - d_minDihedralDeg;
} else if (dihedral > d_maxDihedralDeg) {
dihedralTerm = dihedral - d_maxDihedralDeg;
}
double const c = 0.5 * DEG2RAD * DEG2RAD;
double res = c * d_forceConstant * dihedralTerm * dihedralTerm;
return res;
}
void TorsionConstraintContrib::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]);
RDGeom::Point3D p4(pos[3 * d_at4Idx], pos[3 * d_at4Idx + 1],
pos[3 * d_at4Idx + 2]);
double *g[4] = {&(grad[3 * d_at1Idx]), &(grad[3 * d_at2Idx]),
&(grad[3 * d_at3Idx]), &(grad[3 * d_at4Idx])};
RDGeom::Point3D r[4] = {p1 - p2, p3 - p2, p2 - p3, p4 - p3};
RDGeom::Point3D t[2] = {r[0].crossProduct(r[1]), r[2].crossProduct(r[3])};
double d[2] = {t[0].length(), t[1].length()};
if (isDoubleZero(d[0]) || isDoubleZero(d[1])) {
return;
}
t[0] /= d[0];
t[1] /= d[1];
double cosPhi = t[0].dotProduct(t[1]);
clipToOne(cosPhi);
double sinPhiSq = 1.0 - cosPhi * cosPhi;
double sinPhi = ((sinPhiSq > 0.0) ? sqrt(sinPhiSq) : 0.0);
// dE/dPhi is independent of cartesians:
RDGeom::Point3D n123 = (-r[0]).crossProduct(r[1]);
double n123SqLength = n123.lengthSq();
RDGeom::Point3D n234 = r[1].crossProduct(r[3]);
double n234SqLength = n234.lengthSq();
RDGeom::Point3D m = n123.crossProduct(r[1]);
// we want a signed dihedral, that's why we use atan2 instead of acos
double dihedral =
RAD2DEG *
(-atan2(m.dotProduct(n234) / sqrt(n234SqLength * m.lengthSq()),
n123.dotProduct(n234) / sqrt(n123SqLength * n234SqLength)));
if (dihedral < 0.0) dihedral += 360.0;
// double dihedral = RAD2DEG * acos(cosPhi);
double dihedralTerm = 0.0;
if (dihedral < d_minDihedralDeg) {
dihedralTerm = dihedral - d_minDihedralDeg;
} else if (dihedral > d_maxDihedralDeg) {
dihedralTerm = dihedral - d_maxDihedralDeg;
}
if (dihedral > 180.0) dihedralTerm = -dihedralTerm;
double dE_dPhi = DEG2RAD * d_forceConstant * dihedralTerm;
// FIX: use a tolerance here
// this is hacky, but it's per the
// recommendation from Niketic and Rasmussen:
double sinTerm =
-dE_dPhi * (isDoubleZero(sinPhi) ? (1.0 / cosPhi) : (1.0 / sinPhi));
Utils::calcTorsionGrad(r, t, d, g, sinTerm, cosPhi);
}
}
}
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