1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
|
//
// Copyright (C) 2013-2024 Paolo Tosco and other RDKit contributors
//
// @@ 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 "ForceField.h"
#include "TorsionConstraint.h"
#include <RDGeneral/BoostStartInclude.h>
#include <RDGeneral/BoostEndInclude.h>
#include <RDGeneral/Invariant.h>
#include <boost/math/special_functions/round.hpp>
#include <cmath>
#ifndef M_PI
#define M_PI 3.14159265358979323846
#endif
namespace ForceFields {
constexpr double RAD2DEG = 180.0 / M_PI;
inline void checkPrecondition(const ForceField *owner, unsigned int idx1,
unsigned int idx2, unsigned int idx3,
unsigned int idx4, double minDihedralDeg,
double maxDihedralDeg) {
PRECONDITION(owner, "bad owner");
PRECONDITION(!(minDihedralDeg > maxDihedralDeg),
"minDihedralDeg must be <= maxDihedralDeg");
URANGE_CHECK(idx1, owner->positions().size());
URANGE_CHECK(idx2, owner->positions().size());
URANGE_CHECK(idx3, owner->positions().size());
URANGE_CHECK(idx4, owner->positions().size());
}
double TorsionConstraintContrib::computeDihedralTerm(double dihedral) const {
double dihedralTarget = dihedral;
if (!(dihedral > d_minDihedralDeg && dihedral < d_maxDihedralDeg) &&
!(dihedral > d_minDihedralDeg && d_minDihedralDeg > d_maxDihedralDeg) &&
!(dihedral < d_maxDihedralDeg && d_minDihedralDeg > d_maxDihedralDeg)) {
double dihedralMinTarget = dihedral - d_minDihedralDeg;
RDKit::ForceFieldsHelper::normalizeAngleDeg(dihedralMinTarget);
double dihedralMaxTarget = dihedral - d_maxDihedralDeg;
RDKit::ForceFieldsHelper::normalizeAngleDeg(dihedralMaxTarget);
if (fabs(dihedralMinTarget) < fabs(dihedralMaxTarget)) {
dihedralTarget = d_minDihedralDeg;
} else {
dihedralTarget = d_maxDihedralDeg;
}
}
double dihedralTerm = dihedral - dihedralTarget;
RDKit::ForceFieldsHelper::normalizeAngleDeg(dihedralTerm);
return dihedralTerm;
}
void TorsionConstraintContrib::setParameters(
ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3,
unsigned int idx4, double minDihedralDeg, double maxDihedralDeg,
double forceConst) {
dp_forceField = owner;
d_at1Idx = idx1;
d_at2Idx = idx2;
d_at3Idx = idx3;
d_at4Idx = idx4;
RDKit::ForceFieldsHelper::normalizeAngleDeg(minDihedralDeg);
RDKit::ForceFieldsHelper::normalizeAngleDeg(maxDihedralDeg);
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, double minDihedralDeg, double maxDihedralDeg,
double forceConst) {
checkPrecondition(owner, idx1, idx2, idx3, idx4, minDihedralDeg,
maxDihedralDeg);
setParameters(owner, idx1, idx2, idx3, idx4, minDihedralDeg, maxDihedralDeg,
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) {
checkPrecondition(owner, idx1, idx2, idx3, idx4, minDihedralDeg,
maxDihedralDeg);
if (relative) {
double dihedral;
RDKit::ForceFieldsHelper::computeDihedral(owner->positions(), idx1, idx2,
idx3, idx4, &dihedral);
dihedral *= RAD2DEG;
minDihedralDeg += dihedral;
maxDihedralDeg += dihedral;
}
setParameters(owner, idx1, idx2, idx3, idx4, minDihedralDeg, maxDihedralDeg,
forceConst);
}
double TorsionConstraintContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
double dihedral;
RDKit::ForceFieldsHelper::computeDihedral(pos, d_at1Idx, d_at2Idx, d_at3Idx,
d_at4Idx, &dihedral);
dihedral *= RAD2DEG;
double dihedralTerm = computeDihedralTerm(dihedral);
double res = 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");
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 dihedral;
RDKit::ForceFieldsHelper::computeDihedral(
pos, d_at1Idx, d_at2Idx, d_at3Idx, d_at4Idx, &dihedral, nullptr, r, t, d);
dihedral *= RAD2DEG;
double dihedralTerm = computeDihedralTerm(dihedral);
double dE_dPhi = 2.0 * RAD2DEG * d_forceConstant * dihedralTerm;
double d23 = dp_forceField->distance(d_at2Idx, d_at3Idx, pos);
RDGeom::Point3D r31(pos[3 * d_at3Idx] - pos[3 * d_at1Idx],
pos[3 * d_at3Idx + 1] - pos[3 * d_at1Idx + 1],
pos[3 * d_at3Idx + 2] - pos[3 * d_at1Idx + 2]);
RDGeom::Point3D r42(pos[3 * d_at4Idx] - pos[3 * d_at2Idx],
pos[3 * d_at4Idx + 1] - pos[3 * d_at2Idx + 1],
pos[3 * d_at4Idx + 2] - pos[3 * d_at2Idx + 2]);
double prefactor = dE_dPhi / d23;
RDGeom::Point3D tt[2] = {r[0].crossProduct(r[1]), r[2].crossProduct(r[3])};
RDGeom::Point3D dedt[2] = {
tt[0].crossProduct(r[2]) / tt[0].lengthSq() * prefactor,
tt[1].crossProduct(r[1]) / tt[1].lengthSq() * prefactor};
RDGeom::Point3D dedp[4] = {
r[2].crossProduct(dedt[0]),
r31.crossProduct(dedt[0]) - r[3].crossProduct(dedt[1]),
r[0].crossProduct(dedt[0]) + r42.crossProduct(dedt[1]),
r[2].crossProduct(dedt[1])};
for (unsigned int i = 0; i < 4; ++i) {
g[i][0] += dedp[i].x;
g[i][1] += dedp[i].y;
g[i][2] += dedp[i].z;
}
}
} // namespace ForceFields
|
