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
|
//
// Copyright (C) 2024 Niels Maeder 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 "AngleConstraints.h"
#include "ForceField.h"
#include <cmath>
#include <RDGeneral/Invariant.h>
#ifndef M_PI
#define M_PI 3.14159265358979323846
#endif
namespace ForceFields {
constexpr double RAD2DEG = 180.0 / M_PI;
AngleConstraintContribs::AngleConstraintContribs(ForceField *owner) {
PRECONDITION(owner, "bad owner");
dp_forceField = owner;
}
void AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2,
unsigned int idx3, double minAngleDeg,
double maxAngleDeg,
double forceConst) {
RANGE_CHECK(0.0, minAngleDeg, 180.0);
RANGE_CHECK(0.0, maxAngleDeg, 180.0);
URANGE_CHECK(idx1, dp_forceField->positions().size());
URANGE_CHECK(idx2, dp_forceField->positions().size());
URANGE_CHECK(idx3, dp_forceField->positions().size());
PRECONDITION(maxAngleDeg >= minAngleDeg,
"minAngleDeg must be <= maxAngleDeg");
d_contribs.emplace_back(idx1, idx2, idx3, minAngleDeg, maxAngleDeg,
forceConst);
}
void AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2,
unsigned int idx3, bool relative,
double minAngleDeg, double maxAngleDeg,
double forceConst) {
const RDGeom::PointPtrVect &pos = dp_forceField->positions();
URANGE_CHECK(idx1, pos.size());
URANGE_CHECK(idx2, pos.size());
URANGE_CHECK(idx3, pos.size());
PRECONDITION(maxAngleDeg >= minAngleDeg,
"minAngleDeg must be <= maxAngleDeg");
if (relative) {
const RDGeom::Point3D &p1 = *((RDGeom::Point3D *)pos[idx1]);
const RDGeom::Point3D &p2 = *((RDGeom::Point3D *)pos[idx2]);
const RDGeom::Point3D &p3 = *((RDGeom::Point3D *)pos[idx3]);
const RDGeom::Point3D r[2] = {p1 - p2, p3 - p2};
const double rLengthSq[2] = {std::max(1.0e-5, r[0].lengthSq()),
std::max(1.0e-5, r[1].lengthSq())};
double cosTheta = r[0].dotProduct(r[1]) / sqrt(rLengthSq[0] * rLengthSq[1]);
cosTheta = std::clamp(cosTheta, -1.0, 1.0);
const double angle = RAD2DEG * acos(cosTheta);
minAngleDeg += angle;
maxAngleDeg += angle;
}
RANGE_CHECK(0.0, minAngleDeg, 180.0);
RANGE_CHECK(0.0, maxAngleDeg, 180.0);
d_contribs.emplace_back(idx1, idx2, idx3, minAngleDeg, maxAngleDeg,
forceConst);
}
double AngleConstraintContribs::computeAngleTerm(
const double &angle, const AngleConstraintContribsParams &contrib) const {
double angleTerm = 0.0;
if (angle < contrib.minAngle) {
angleTerm = angle - contrib.minAngle;
} else if (angle > contrib.maxAngle) {
angleTerm = angle - contrib.maxAngle;
}
return angleTerm;
}
double AngleConstraintContribs::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
double accum = 0.0;
for (const auto &contrib : d_contribs) {
const RDGeom::Point3D p1(pos[3 * contrib.idx1], pos[3 * contrib.idx1 + 1],
pos[3 * contrib.idx1 + 2]);
const RDGeom::Point3D p2(pos[3 * contrib.idx2], pos[3 * contrib.idx2 + 1],
pos[3 * contrib.idx2 + 2]);
const RDGeom::Point3D p3(pos[3 * contrib.idx3], pos[3 * contrib.idx3 + 1],
pos[3 * contrib.idx3 + 2]);
const RDGeom::Point3D r[2] = {p1 - p2, p3 - p2};
const double rLengthSq[2] = {std::max(1.0e-5, r[0].lengthSq()),
std::max(1.0e-5, r[1].lengthSq())};
double cosTheta = r[0].dotProduct(r[1]) / sqrt(rLengthSq[0] * rLengthSq[1]);
cosTheta = std::clamp(cosTheta, -1.0, 1.0);
const double angle = RAD2DEG * acos(cosTheta);
const double angleTerm = computeAngleTerm(angle, contrib);
accum += contrib.forceConstant * angleTerm * angleTerm;
}
return accum;
}
void AngleConstraintContribs::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
for (const auto &contrib : d_contribs) {
const RDGeom::Point3D p1(pos[3 * contrib.idx1], pos[3 * contrib.idx1 + 1],
pos[3 * contrib.idx1 + 2]);
const RDGeom::Point3D p2(pos[3 * contrib.idx2], pos[3 * contrib.idx2 + 1],
pos[3 * contrib.idx2 + 2]);
const RDGeom::Point3D p3(pos[3 * contrib.idx3], pos[3 * contrib.idx3 + 1],
pos[3 * contrib.idx3 + 2]);
const RDGeom::Point3D r[2] = {p1 - p2, p3 - p2};
const double rLengthSq[2] = {std::max(1.0e-5, r[0].lengthSq()),
std::max(1.0e-5, r[1].lengthSq())};
double cosTheta = r[0].dotProduct(r[1]) / sqrt(rLengthSq[0] * rLengthSq[1]);
cosTheta = std::clamp(cosTheta, -1.0, 1.0);
const double angle = RAD2DEG * acos(cosTheta);
const double angleTerm = computeAngleTerm(angle, contrib);
const double dE_dTheta = 2.0 * RAD2DEG * contrib.forceConstant * angleTerm;
const RDGeom::Point3D rp = r[1].crossProduct(r[0]);
const double prefactor = dE_dTheta / std::max(1.0e-5, rp.length());
const double t[2] = {-prefactor / rLengthSq[0], prefactor / rLengthSq[1]};
RDGeom::Point3D dedp[3];
dedp[0] = r[0].crossProduct(rp) * t[0];
dedp[2] = r[1].crossProduct(rp) * t[1];
dedp[1] = -dedp[0] - dedp[2];
double *g[3] = {&(grad[3 * contrib.idx1]), &(grad[3 * contrib.idx2]),
&(grad[3 * contrib.idx3])};
for (unsigned int i = 0; i < 3; ++i) {
g[i][0] += dedp[i].x;
g[i][1] += dedp[i].y;
g[i][2] += dedp[i].z;
}
}
}
} // namespace ForceFields
|
