mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-05 22:04:27 +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
202 lines
7.2 KiB
C++
202 lines
7.2 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 "Params.h"
|
|
#include <cmath>
|
|
#include <ForceField/ForceField.h>
|
|
#include <RDGeneral/Invariant.h>
|
|
|
|
namespace ForceFields {
|
|
namespace MMFF {
|
|
namespace Utils {
|
|
double calcTorsionCosPhi(const RDGeom::Point3D &iPoint,
|
|
const RDGeom::Point3D &jPoint, const RDGeom::Point3D &kPoint,
|
|
const RDGeom::Point3D &lPoint)
|
|
{
|
|
RDGeom::Point3D r1 = iPoint - jPoint;
|
|
RDGeom::Point3D r2 = kPoint - jPoint;
|
|
RDGeom::Point3D r3 = jPoint - kPoint;
|
|
RDGeom::Point3D r4 = lPoint - kPoint;
|
|
RDGeom::Point3D t1 = r1.crossProduct(r2);
|
|
RDGeom::Point3D t2 = r3.crossProduct(r4);
|
|
double cosPhi = t1.dotProduct(t2) / (t1.length() * t2.length());
|
|
clipToOne(cosPhi);
|
|
|
|
return cosPhi;
|
|
}
|
|
|
|
boost::tuple<double, double, double>
|
|
calcTorsionForceConstant(const MMFFTor *mmffTorParams)
|
|
{
|
|
return boost::make_tuple(mmffTorParams->V1,
|
|
mmffTorParams->V2, mmffTorParams->V3);
|
|
}
|
|
|
|
double calcTorsionEnergy(const double V1,
|
|
const double V2, const double V3, const double cosPhi)
|
|
{
|
|
double cos2Phi = 2.0 * cosPhi * cosPhi - 1.0;
|
|
double cos3Phi = cosPhi * (2.0 * cos2Phi - 1.0);
|
|
|
|
return (0.5 * (V1 * (1.0 + cosPhi)
|
|
+ V2 * (1.0 - cos2Phi) + V3 * (1.0 + cos3Phi)));
|
|
}
|
|
|
|
void calcTorsionGrad(RDGeom::Point3D *r, RDGeom::Point3D *t,
|
|
double *d, double **g, double &sinTerm, double &cosPhi)
|
|
{
|
|
// -------
|
|
// dTheta/dx is trickier:
|
|
double dCos_dT[6] = {
|
|
1.0 / d[0] * (t[1].x - cosPhi * t[0].x),
|
|
1.0 / d[0] * (t[1].y - cosPhi * t[0].y),
|
|
1.0 / d[0] * (t[1].z - cosPhi * t[0].z),
|
|
1.0 / d[1] * (t[0].x - cosPhi * t[1].x),
|
|
1.0 / d[1] * (t[0].y - cosPhi * t[1].y),
|
|
1.0 / d[1] * (t[0].z - cosPhi * t[1].z)
|
|
};
|
|
|
|
g[0][0] += sinTerm * (dCos_dT[2] * r[1].y - dCos_dT[1] * r[1].z);
|
|
g[0][1] += sinTerm * (dCos_dT[0] * r[1].z - dCos_dT[2] * r[1].x);
|
|
g[0][2] += sinTerm * (dCos_dT[1] * r[1].x - dCos_dT[0] * r[1].y);
|
|
|
|
g[1][0] += sinTerm * (dCos_dT[1] * (r[1].z - r[0].z)
|
|
+ dCos_dT[2] * (r[0].y - r[1].y) + dCos_dT[4] * (-r[3].z) + dCos_dT[5] * (r[3].y));
|
|
g[1][1] += sinTerm * (dCos_dT[0] * (r[0].z - r[1].z)
|
|
+ dCos_dT[2] * (r[1].x - r[0].x) + dCos_dT[3] * (r[3].z) + dCos_dT[5] * (-r[3].x));
|
|
g[1][2] += sinTerm * (dCos_dT[0] * (r[1].y - r[0].y)
|
|
+ dCos_dT[1] * (r[0].x - r[1].x) + dCos_dT[3] * (-r[3].y) + dCos_dT[4] * (r[3].x));
|
|
|
|
g[2][0] += sinTerm * (dCos_dT[1] * (r[0].z) + dCos_dT[2] * (-r[0].y) +
|
|
dCos_dT[4] * (r[3].z - r[2].z) + dCos_dT[5] * (r[2].y - r[3].y));
|
|
g[2][1] += sinTerm * (dCos_dT[0] * (-r[0].z) + dCos_dT[2] * (r[0].x) +
|
|
dCos_dT[3] * (r[2].z - r[3].z) + dCos_dT[5] * (r[3].x - r[2].x));
|
|
g[2][2] += sinTerm * (dCos_dT[0] * (r[0].y) + dCos_dT[1] * (-r[0].x) +
|
|
dCos_dT[3] * (r[3].y - r[2].y) + dCos_dT[4] * (r[2].x - r[3].x));
|
|
|
|
g[3][0] += sinTerm * (dCos_dT[4] * r[2].z - dCos_dT[5] * r[2].y);
|
|
g[3][1] += sinTerm * (dCos_dT[5] * r[2].x - dCos_dT[3] * r[2].z);
|
|
g[3][2] += sinTerm * (dCos_dT[3] * r[2].y - dCos_dT[4] * r[2].x);
|
|
}
|
|
}
|
|
|
|
|
|
TorsionAngleContrib::TorsionAngleContrib(ForceField *owner,
|
|
unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4,
|
|
const MMFFTor *mmffTorParams)
|
|
{
|
|
PRECONDITION(owner, "bad owner");
|
|
PRECONDITION((idx1 != idx2) && (idx1 != idx3) && (idx1 != idx4)
|
|
&& (idx2 != idx3) && (idx2 != idx4) && (idx3 != idx4), "degenerate points");
|
|
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);
|
|
|
|
dp_forceField = owner;
|
|
d_at1Idx = idx1;
|
|
d_at2Idx = idx2;
|
|
d_at3Idx = idx3;
|
|
d_at4Idx = idx4;
|
|
d_V1 = mmffTorParams->V1;
|
|
d_V2 = mmffTorParams->V2;
|
|
d_V3 = mmffTorParams->V3;
|
|
}
|
|
|
|
|
|
double TorsionAngleContrib::getEnergy(double *pos) const
|
|
{
|
|
PRECONDITION(dp_forceField, "no owner");
|
|
PRECONDITION(pos, "bad vector");
|
|
|
|
RDGeom::Point3D iPoint(pos[3 * d_at1Idx],
|
|
pos[3 * d_at1Idx + 1], pos[3 * d_at1Idx + 2]);
|
|
RDGeom::Point3D jPoint(pos[3 * d_at2Idx],
|
|
pos[3 * d_at2Idx + 1], pos[3 * d_at2Idx + 2]);
|
|
RDGeom::Point3D kPoint(pos[3 * d_at3Idx],
|
|
pos[3 * d_at3Idx + 1], pos[3 * d_at3Idx + 2]);
|
|
RDGeom::Point3D lPoint(pos[3 * d_at4Idx],
|
|
pos[3 * d_at4Idx + 1], pos[3 * d_at4Idx + 2]);
|
|
|
|
return Utils::calcTorsionEnergy(d_V1, d_V2, d_V3,
|
|
Utils::calcTorsionCosPhi(iPoint, jPoint, kPoint, lPoint));
|
|
}
|
|
|
|
void TorsionAngleContrib::getGrad(double *pos, double *grad) const
|
|
{
|
|
PRECONDITION(dp_forceField,"no owner");
|
|
PRECONDITION(pos,"bad vector");
|
|
PRECONDITION(grad,"bad vector");
|
|
|
|
RDGeom::Point3D iPoint(pos[3 * d_at1Idx],
|
|
pos[3 * d_at1Idx + 1], pos[3 * d_at1Idx + 2]);
|
|
RDGeom::Point3D jPoint(pos[3 * d_at2Idx],
|
|
pos[3 * d_at2Idx + 1], pos[3 * d_at2Idx + 2]);
|
|
RDGeom::Point3D kPoint(pos[3 * d_at3Idx],
|
|
pos[3 * d_at3Idx + 1], pos[3 * d_at3Idx + 2]);
|
|
RDGeom::Point3D lPoint(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] = {
|
|
iPoint - jPoint,
|
|
kPoint - jPoint,
|
|
jPoint - kPoint,
|
|
lPoint - kPoint
|
|
};
|
|
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);
|
|
double sin2Phi = 2.0 * sinPhi * cosPhi;
|
|
double sin3Phi = 3.0 * sinPhi - 4.0 * sinPhi * sinPhiSq;
|
|
// dE/dPhi is independent of cartesians:
|
|
double dE_dPhi = 0.5 * (-(d_V1) * sinPhi + 2.0
|
|
* d_V2 * sin2Phi - 3.0 * d_V3 * sin3Phi);
|
|
#if 0
|
|
if(dE_dPhi!=dE_dPhi){
|
|
std::cout << "\tNaN in Torsion("<<d_at1Idx<<","<<d_at2Idx<<","<<d_at3Idx<<","<<d_at4Idx<<")"<< std::endl;
|
|
std::cout << "sin: " << sinPhi << std::endl;
|
|
std::cout << "cos: " << cosPhi << std::endl;
|
|
}
|
|
|
|
#endif
|
|
// 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);
|
|
}
|
|
}
|
|
}
|