mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-06 22:39:55 +08:00
ba4a48ce05
- fixed a bug in Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp which caused misassignment of atom types in CYGUAN01 upon shuffling the order of atoms in the validation SDF files - added checks for acos and asin function parameters to be within a (-1, 1) range
213 lines
7.7 KiB
C++
213 lines
7.7 KiB
C++
// $Id$
|
|
//
|
|
// 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 <boost/math/special_functions/round.hpp>
|
|
#include <ForceField/ForceField.h>
|
|
#include <RDGeneral/Invariant.h>
|
|
|
|
namespace ForceFields {
|
|
namespace MMFF {
|
|
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");
|
|
RANGE_CHECK(0, idx1, owner->positions().size() - 1);
|
|
RANGE_CHECK(0, idx2, owner->positions().size() - 1);
|
|
RANGE_CHECK(0, idx3, owner->positions().size() - 1);
|
|
RANGE_CHECK(0, idx4, owner->positions().size() - 1);
|
|
_pretreatAngles(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();
|
|
RANGE_CHECK(0, idx1, pos.size() - 1);
|
|
RANGE_CHECK(0, idx2, pos.size() - 1);
|
|
RANGE_CHECK(0, idx3, pos.size() - 1);
|
|
RANGE_CHECK(0, idx4, pos.size() - 1);
|
|
|
|
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;
|
|
_pretreatAngles(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 = p1 - p2;
|
|
RDGeom::Point3D r2 = p3 - p2;
|
|
RDGeom::Point3D r3 = p2 - p3;
|
|
RDGeom::Point3D r4 = p4 - p3;
|
|
RDGeom::Point3D t1 = r1.crossProduct(r2);
|
|
RDGeom::Point3D t2 = r3.crossProduct(r4);
|
|
double d1 = std::max(t1.length(), 0.0);
|
|
double d2 = std::max(t2.length(), 0.0);
|
|
t1 /= d1;
|
|
t2 /= d2;
|
|
|
|
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)));
|
|
double ave = 0.5 * (d_minDihedralDeg + d_maxDihedralDeg);
|
|
dihedral += 360.0 * boost::math::round((ave - 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)));
|
|
//double dihedral = RAD2DEG * acos(cosPhi);
|
|
double ave = 0.5 * (d_minDihedralDeg + d_maxDihedralDeg);
|
|
dihedral += 360.0 * boost::math::round((ave - 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 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);
|
|
}
|
|
}
|
|
}
|