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
159
160
161
162
163
164
165
|
// $Id$
//
// 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 "AngleBend.h"
#include "AngleConstraint.h"
#include "Params.h"
#include <cmath>
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
namespace ForceFields {
namespace MMFF {
void _pretreatAngles(double &minAngleDeg, double &maxAngleDeg) {
minAngleDeg = fmod(minAngleDeg, 360.0);
maxAngleDeg = fmod(maxAngleDeg, 360.0);
if (minAngleDeg > 180.0) minAngleDeg -= 360.0;
if (maxAngleDeg > 180.0) maxAngleDeg -= 360.0;
if ((minAngleDeg < 0.0) && (!(maxAngleDeg < 0.0))) {
maxAngleDeg = std::max(fabs(maxAngleDeg), fabs(minAngleDeg));
minAngleDeg = 0.0;
}
minAngleDeg = fabs(minAngleDeg);
maxAngleDeg = fabs(maxAngleDeg);
if (minAngleDeg > maxAngleDeg) {
double t = minAngleDeg;
minAngleDeg = maxAngleDeg;
maxAngleDeg = t;
}
}
AngleConstraintContrib::AngleConstraintContrib(
ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3,
double minAngleDeg, double maxAngleDeg, double forceConst) {
PRECONDITION(owner, "bad owner");
URANGE_CHECK(idx1, owner->positions().size());
URANGE_CHECK(idx2, owner->positions().size());
URANGE_CHECK(idx3, owner->positions().size());
PRECONDITION(maxAngleDeg >= minAngleDeg, "allowedDeltaDeg must be >= 0.0");
_pretreatAngles(minAngleDeg, maxAngleDeg);
dp_forceField = owner;
d_at1Idx = idx1;
d_at2Idx = idx2;
d_at3Idx = idx3;
d_minAngleDeg = minAngleDeg;
d_maxAngleDeg = maxAngleDeg;
d_forceConstant = forceConst;
}
AngleConstraintContrib::AngleConstraintContrib(
ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3,
bool relative, double minAngleDeg, double maxAngleDeg, double forceConst) {
PRECONDITION(owner, "bad owner");
const RDGeom::PointPtrVect &pos = owner->positions();
URANGE_CHECK(idx1, pos.size());
URANGE_CHECK(idx2, pos.size());
URANGE_CHECK(idx3, pos.size());
PRECONDITION(maxAngleDeg >= minAngleDeg, "allowedDeltaDeg must be >= 0.0");
double angle = 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]);
double dist1 = (p1 - p2).length();
double dist2 = (p3 - p2).length();
RDGeom::Point3D p12 = (p1 - p2) / dist1;
RDGeom::Point3D p32 = (p3 - p2) / dist2;
double cosTheta = p12.dotProduct(p32);
clipToOne(cosTheta);
angle = RAD2DEG * acos(cosTheta);
}
dp_forceField = owner;
d_at1Idx = idx1;
d_at2Idx = idx2;
d_at3Idx = idx3;
minAngleDeg += angle;
maxAngleDeg += angle;
_pretreatAngles(minAngleDeg, maxAngleDeg);
d_minAngleDeg = minAngleDeg;
d_maxAngleDeg = maxAngleDeg;
d_forceConstant = forceConst;
}
double AngleConstraintContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
double dist1 = dp_forceField->distance(d_at1Idx, d_at2Idx, pos);
double dist2 = dp_forceField->distance(d_at2Idx, d_at3Idx, pos);
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 p12 = (p1 - p2) / dist1;
RDGeom::Point3D p32 = (p3 - p2) / dist2;
double cosTheta = p12.dotProduct(p32);
clipToOne(cosTheta);
double angle = RAD2DEG * acos(cosTheta);
double angleTerm = 0.0;
if (angle < d_minAngleDeg) {
angleTerm = angle - d_minAngleDeg;
} else if (angle > d_maxAngleDeg) {
angleTerm = angle - d_maxAngleDeg;
}
double const c = 0.5 * DEG2RAD * DEG2RAD;
double res = c * d_forceConstant * angleTerm * angleTerm;
return res;
}
void AngleConstraintContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
double dist[2] = {dp_forceField->distance(d_at1Idx, d_at2Idx, pos),
dp_forceField->distance(d_at2Idx, d_at3Idx, pos)};
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]);
double *g[3] = {&(grad[3 * d_at1Idx]), &(grad[3 * d_at2Idx]),
&(grad[3 * d_at3Idx])};
RDGeom::Point3D r[2] = {(p1 - p2) / dist[0], (p3 - p2) / dist[1]};
double cosTheta = r[0].dotProduct(r[1]);
clipToOne(cosTheta);
double sinThetaSq = 1.0 - cosTheta * cosTheta;
double sinTheta =
std::max(((sinThetaSq > 0.0) ? sqrt(sinThetaSq) : 0.0), 1.0e-8);
// use the chain rule:
// dE/dx = dE/dTheta * dTheta/dx
// dE/dTheta is independent of cartesians:
double angle = RAD2DEG * acos(cosTheta);
double angleTerm = 0.0;
if (angle < d_minAngleDeg) {
angleTerm = angle - d_minAngleDeg;
} else if (angle > d_maxAngleDeg) {
angleTerm = angle - d_maxAngleDeg;
}
double dE_dTheta = DEG2RAD * d_forceConstant * angleTerm;
Utils::calcAngleBendGrad(r, dist, g, dE_dTheta, cosTheta, sinTheta);
}
}
}
|
