mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
d315e246e1
* fix unsigned int to int comparison
* revert previous mistake
* declaration & init together, sinthetaSq in [0, 1]
* using std::swap
* use that sinThetaSq in [0,1]
* declare & init at same time
* use knowledge about target range
* use std::clamp
* use std::max
* numerically more stable trigonometrics
* numerically more stable trigonometrics
* numerically more stable trigonometrics
* range based for-loop
* actually do the assignement
* Update Code/ForceField/MMFF/Params.h
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* implemented suggested changes
* Revert "implemented suggested changes"
This reverts commit f56e8f0ab2.
* auto typing
* remove old comment
* revert to numerically more stable expression
* now correctly formatted
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
278 lines
10 KiB
C++
278 lines
10 KiB
C++
// $Id$
|
|
//
|
|
// 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 UFF {
|
|
namespace Utils {
|
|
double calculateCosTorsion(const RDGeom::Point3D &p1, const RDGeom::Point3D &p2,
|
|
const RDGeom::Point3D &p3,
|
|
const RDGeom::Point3D &p4) {
|
|
RDGeom::Point3D r1 = p1 - p2, r2 = p3 - p2, r3 = p2 - p3, r4 = p4 - p3;
|
|
RDGeom::Point3D t1 = r1.crossProduct(r2);
|
|
RDGeom::Point3D t2 = r3.crossProduct(r4);
|
|
double d1 = t1.length(), d2 = t2.length();
|
|
double cosPhi = t1.dotProduct(t2) / (d1 * d2);
|
|
clipToOne(cosPhi);
|
|
return cosPhi;
|
|
}
|
|
|
|
// used locally
|
|
bool isInGroup6(int num) {
|
|
return (num == 8 || num == 16 || num == 34 || num == 52 || num == 84);
|
|
}
|
|
|
|
// used locally, implement equation 17 of the UFF paper.
|
|
double equation17(double bondOrder23, const AtomicParams *at2Params,
|
|
const AtomicParams *at3Params) {
|
|
return 5. * sqrt(at2Params->U1 * at3Params->U1) *
|
|
(1. + 4.18 * log(bondOrder23));
|
|
}
|
|
|
|
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);
|
|
}
|
|
} // namespace Utils
|
|
|
|
TorsionAngleContrib::TorsionAngleContrib(
|
|
ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3,
|
|
unsigned int idx4, double bondOrder23, int atNum2, int atNum3,
|
|
RDKit::Atom::HybridizationType hyb2, RDKit::Atom::HybridizationType hyb3,
|
|
const AtomicParams *at2Params, const AtomicParams *at3Params,
|
|
bool endAtomIsSP2) {
|
|
PRECONDITION(owner, "bad owner");
|
|
PRECONDITION(at2Params, "bad params pointer");
|
|
PRECONDITION(at3Params, "bad params pointer");
|
|
PRECONDITION((idx1 != idx2 && idx1 != idx3 && idx1 != idx4 && idx2 != idx3 &&
|
|
idx2 != idx4 && idx3 != idx4),
|
|
"degenerate points");
|
|
URANGE_CHECK(idx1, owner->positions().size());
|
|
URANGE_CHECK(idx2, owner->positions().size());
|
|
URANGE_CHECK(idx3, owner->positions().size());
|
|
URANGE_CHECK(idx4, owner->positions().size());
|
|
|
|
dp_forceField = owner;
|
|
d_at1Idx = idx1;
|
|
d_at2Idx = idx2;
|
|
d_at3Idx = idx3;
|
|
d_at4Idx = idx4;
|
|
|
|
calcTorsionParams(bondOrder23, atNum2, atNum3, hyb2, hyb3, at2Params,
|
|
at3Params, endAtomIsSP2);
|
|
}
|
|
|
|
void TorsionAngleContrib::calcTorsionParams(double bondOrder23, int atNum2,
|
|
int atNum3,
|
|
RDKit::Atom::HybridizationType hyb2,
|
|
RDKit::Atom::HybridizationType hyb3,
|
|
const AtomicParams *at2Params,
|
|
const AtomicParams *at3Params,
|
|
bool endAtomIsSP2) {
|
|
PRECONDITION((hyb2 == RDKit::Atom::SP2 || hyb2 == RDKit::Atom::SP3) &&
|
|
(hyb3 == RDKit::Atom::SP2 || hyb3 == RDKit::Atom::SP3),
|
|
"bad hybridizations");
|
|
|
|
if (hyb2 == RDKit::Atom::SP3 && hyb3 == RDKit::Atom::SP3) {
|
|
// general case:
|
|
d_forceConstant = sqrt(at2Params->V1 * at3Params->V1);
|
|
d_order = 3;
|
|
d_cosTerm = -1; // phi0=60
|
|
|
|
// special case for single bonds between group 6 elements:
|
|
if (bondOrder23 == 1.0 && Utils::isInGroup6(atNum2) &&
|
|
Utils::isInGroup6(atNum3)) {
|
|
double V2 = 6.8, V3 = 6.8;
|
|
if (atNum2 == 8) {
|
|
V2 = 2.0;
|
|
}
|
|
if (atNum3 == 8) {
|
|
V3 = 2.0;
|
|
}
|
|
d_forceConstant = sqrt(V2 * V3);
|
|
d_order = 2;
|
|
d_cosTerm = -1; // phi0=90
|
|
}
|
|
} else if (hyb2 == RDKit::Atom::SP2 && hyb3 == RDKit::Atom::SP2) {
|
|
d_forceConstant = Utils::equation17(bondOrder23, at2Params, at3Params);
|
|
d_order = 2;
|
|
// FIX: is this angle term right?
|
|
d_cosTerm = 1.0; // phi0= 180
|
|
} else {
|
|
// SP2 - SP3, this is, by default, independent of atom type in UFF:
|
|
d_forceConstant = 1.0;
|
|
d_order = 6;
|
|
d_cosTerm = 1.0; // phi0 = 0
|
|
if (bondOrder23 == 1.0) {
|
|
// special case between group 6 sp3 and non-group 6 sp2:
|
|
if ((hyb2 == RDKit::Atom::SP3 && Utils::isInGroup6(atNum2) &&
|
|
!Utils::isInGroup6(atNum3)) ||
|
|
(hyb3 == RDKit::Atom::SP3 && Utils::isInGroup6(atNum3) &&
|
|
!Utils::isInGroup6(atNum2))) {
|
|
d_forceConstant = Utils::equation17(bondOrder23, at2Params, at3Params);
|
|
d_order = 2;
|
|
d_cosTerm = -1; // phi0 = 90;
|
|
}
|
|
|
|
// special case for sp3 - sp2 - sp2
|
|
// (i.e. the sp2 has another sp2 neighbor, like propene)
|
|
else if (endAtomIsSP2) {
|
|
d_forceConstant = 2.0;
|
|
d_order = 3;
|
|
d_cosTerm = -1; // phi0 = 180;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
double TorsionAngleContrib::getEnergy(double *pos) const {
|
|
PRECONDITION(dp_forceField, "no owner");
|
|
PRECONDITION(pos, "bad vector");
|
|
PRECONDITION(d_order == 2 || d_order == 3 || d_order == 6, "bad order");
|
|
|
|
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 cosPhi = Utils::calculateCosTorsion(p1, p2, p3, p4);
|
|
double sinPhiSq = 1 - cosPhi * cosPhi;
|
|
|
|
// E(phi) = V/2 * (1 - cos(n*phi_0)*cos(n*phi))
|
|
double cosNPhi = 0.0;
|
|
switch (d_order) {
|
|
case 2:
|
|
// cos(2x) = 1 - 2sin^2(x)
|
|
cosNPhi = 1 - 2 * sinPhiSq;
|
|
break;
|
|
case 3:
|
|
// cos(3x) = cos^3(x) - 3*cos(x)*sin^2(x) = 4cos^3(x) -3cos(x)
|
|
cosNPhi = cosPhi * (cosPhi * cosPhi - 3. * sinPhiSq);
|
|
break;
|
|
case 6:
|
|
// cos(6x) = 1 - 32*sin^6(x) + 48*sin^4(x) - 18*sin^2(x)
|
|
cosNPhi =
|
|
1 + sinPhiSq * (-32. * sinPhiSq * sinPhiSq + 48. * sinPhiSq - 18.);
|
|
break;
|
|
}
|
|
double res = d_forceConstant / 2.0 * (1. - d_cosTerm * cosNPhi);
|
|
// std::cout << " torsion(" << d_at1Idx << "," << d_at2Idx << "," << d_at3Idx
|
|
// << "," << d_at4Idx << "): " << cosPhi << "(" << acos(cosPhi) << ")" << " ->
|
|
// " << res << std::endl;
|
|
// if(d_at2Idx==5&&d_at3Idx==6) std::cerr << " torsion(" << d_at1Idx << "," <<
|
|
// d_at2Idx << "," << d_at3Idx << "," << d_at4Idx << "): " << cosPhi << "(" <<
|
|
// acos(cosPhi) << ")" << " -> " << res << std::endl;
|
|
return res;
|
|
}
|
|
|
|
void TorsionAngleContrib::getGrad(double *pos, double *grad) const {
|
|
PRECONDITION(dp_forceField, "no owner");
|
|
PRECONDITION(pos, "bad vector");
|
|
PRECONDITION(grad, "bad vector");
|
|
|
|
double *g[4] = {&(grad[3 * d_at1Idx]), &(grad[3 * d_at2Idx]),
|
|
&(grad[3 * d_at3Idx]), &(grad[3 * d_at4Idx])};
|
|
|
|
RDGeom::Point3D r[4];
|
|
RDGeom::Point3D t[2];
|
|
double d[2];
|
|
double cosPhi;
|
|
RDKit::ForceFieldsHelper::computeDihedral(
|
|
pos, d_at1Idx, d_at2Idx, d_at3Idx, d_at4Idx, nullptr, &cosPhi, r, t, d);
|
|
double sinPhiSq = 1.0 - cosPhi * cosPhi;
|
|
double sinPhi = ((sinPhiSq > 0.0) ? sqrt(sinPhiSq) : 0.0);
|
|
|
|
// dE/dPhi is independent of cartesians:
|
|
double dE_dPhi = getThetaDeriv(cosPhi, sinPhi);
|
|
#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
|
|
|
|
double sinTerm =
|
|
dE_dPhi * (isDoubleZero(sinPhi) ? (1.0 / cosPhi) : (1.0 / sinPhi));
|
|
|
|
Utils::calcTorsionGrad(r, t, d, g, sinTerm, cosPhi);
|
|
}
|
|
|
|
double TorsionAngleContrib::getThetaDeriv(double cosTheta,
|
|
double sinTheta) const {
|
|
PRECONDITION(d_order == 2 || d_order == 3 || d_order == 6, "bad order");
|
|
double sinThetaSq = sinTheta * sinTheta;
|
|
// cos(6x) = 1 - 32*sin^6(x) + 48*sin^4(x) - 18*sin^2(x)
|
|
|
|
double res = 0.0;
|
|
switch (d_order) {
|
|
case 2:
|
|
res = 2 * sinTheta * cosTheta;
|
|
break;
|
|
case 3:
|
|
// sin(3*x) = 3*sin(x) - 4*sin^3(x)
|
|
res = sinTheta * (3 - 4 * sinThetaSq);
|
|
break;
|
|
case 6:
|
|
// sin(6x) = cos(x) * [ 32*sin^5(x) - 32*sin^3(x) + 6*sin(x) ]
|
|
res = cosTheta * sinTheta * (32 * sinThetaSq * (sinThetaSq - 1) + 6);
|
|
break;
|
|
}
|
|
res *= d_forceConstant / 2.0 * d_cosTerm * -1 * d_order;
|
|
|
|
return res;
|
|
}
|
|
} // namespace UFF
|
|
} // namespace ForceFields
|