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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 "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 {
double calcAngleRestValue(const MMFFAngle *mmffAngleParams) {
PRECONDITION(mmffAngleParams, "angle parameters not found");
return mmffAngleParams->theta0;
}
double calcCosTheta(RDGeom::Point3D p1, RDGeom::Point3D p2, RDGeom::Point3D p3,
double dist1, double dist2) {
RDGeom::Point3D p12 = p1 - p2;
RDGeom::Point3D p32 = p3 - p2;
double cosTheta = p12.dotProduct(p32) / (dist1 * dist2);
clipToOne(cosTheta);
return cosTheta;
}
double calcAngleForceConstant(const MMFFAngle *mmffAngleParams) {
PRECONDITION(mmffAngleParams, "angle parameters not found");
return mmffAngleParams->ka;
}
double calcAngleBendEnergy(const double theta0, const double ka, bool isLinear,
const double cosTheta) {
double angle = RAD2DEG * acos(cosTheta) - theta0;
double const cb = -0.006981317;
double const c2 = MDYNE_A_TO_KCAL_MOL * DEG2RAD * DEG2RAD;
double res = 0.0;
if (isLinear) {
res = MDYNE_A_TO_KCAL_MOL * ka * (1.0 + cosTheta);
} else {
res = 0.5 * c2 * ka * angle * angle * (1.0 + cb * angle);
}
return res;
}
void calcAngleBendGrad(RDGeom::Point3D *r, double *dist, double **g,
double &dE_dTheta, double &cosTheta, double &sinTheta) {
// -------
// dTheta/dx is trickier:
double dCos_dS[6] = {1.0 / dist[0] * (r[1].x - cosTheta * r[0].x),
1.0 / dist[0] * (r[1].y - cosTheta * r[0].y),
1.0 / dist[0] * (r[1].z - cosTheta * r[0].z),
1.0 / dist[1] * (r[0].x - cosTheta * r[1].x),
1.0 / dist[1] * (r[0].y - cosTheta * r[1].y),
1.0 / dist[1] * (r[0].z - cosTheta * r[1].z)};
g[0][0] += dE_dTheta * dCos_dS[0] / (-sinTheta);
g[0][1] += dE_dTheta * dCos_dS[1] / (-sinTheta);
g[0][2] += dE_dTheta * dCos_dS[2] / (-sinTheta);
g[1][0] += dE_dTheta * (-dCos_dS[0] - dCos_dS[3]) / (-sinTheta);
g[1][1] += dE_dTheta * (-dCos_dS[1] - dCos_dS[4]) / (-sinTheta);
g[1][2] += dE_dTheta * (-dCos_dS[2] - dCos_dS[5]) / (-sinTheta);
g[2][0] += dE_dTheta * dCos_dS[3] / (-sinTheta);
g[2][1] += dE_dTheta * dCos_dS[4] / (-sinTheta);
g[2][2] += dE_dTheta * dCos_dS[5] / (-sinTheta);
}
} // end of namespace Utils
AngleBendContrib::AngleBendContrib(ForceField *owner, unsigned int idx1,
unsigned int idx2, unsigned int idx3,
const MMFFAngle *mmffAngleParams,
const MMFFProp *mmffPropParamsCentralAtom) {
PRECONDITION(owner, "bad owner");
PRECONDITION(((idx1 != idx2) && (idx2 != idx3) && (idx1 != idx3)),
"degenerate points");
URANGE_CHECK(idx1, owner->positions().size());
URANGE_CHECK(idx2, owner->positions().size());
URANGE_CHECK(idx3, owner->positions().size());
dp_forceField = owner;
d_at1Idx = idx1;
d_at2Idx = idx2;
d_at3Idx = idx3;
d_isLinear = (mmffPropParamsCentralAtom->linh ? true : false);
d_theta0 = mmffAngleParams->theta0;
d_ka = mmffAngleParams->ka;
}
double AngleBendContrib::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]);
return Utils::calcAngleBendEnergy(
d_theta0, d_ka, d_isLinear,
Utils::calcCosTheta(p1, p2, p3, dist1, dist2));
}
void AngleBendContrib::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 angleTerm = RAD2DEG * acos(cosTheta) - d_theta0;
double const cb = -0.006981317;
double const c2 = MDYNE_A_TO_KCAL_MOL * DEG2RAD * DEG2RAD;
double dE_dTheta = (d_isLinear ? -MDYNE_A_TO_KCAL_MOL * d_ka * sinTheta
: RAD2DEG * c2 * d_ka * angleTerm *
(1.0 + 1.5 * cb * angleTerm));
Utils::calcAngleBendGrad(r, dist, g, dE_dTheta, cosTheta, sinTheta);
}
}
}
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