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
|
// $Id$
//
// 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 "PositionConstraint.h"
#include <cmath>
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>
namespace ForceFields {
namespace MMFF {
PositionConstraintContrib::PositionConstraintContrib(ForceField *owner,
unsigned int idx,
double maxDispl,
double forceConst) {
PRECONDITION(owner, "bad owner");
const RDGeom::PointPtrVect &pos = owner->positions();
URANGE_CHECK(idx, pos.size());
dp_forceField = owner;
d_atIdx = idx;
d_maxDispl = maxDispl;
d_pos0 = *((RDGeom::Point3D *)pos[idx]);
d_forceConstant = forceConst;
}
double PositionConstraintContrib::getEnergy(double *pos) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
RDGeom::Point3D p(pos[3 * d_atIdx], pos[3 * d_atIdx + 1],
pos[3 * d_atIdx + 2]);
double dist = (p - d_pos0).length();
double distTerm = (dist > d_maxDispl) ? dist - d_maxDispl : 0.0;
double res = 0.5 * d_forceConstant * distTerm * distTerm;
return res;
}
void PositionConstraintContrib::getGrad(double *pos, double *grad) const {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(pos, "bad vector");
PRECONDITION(grad, "bad vector");
RDGeom::Point3D p(pos[3 * d_atIdx], pos[3 * d_atIdx + 1],
pos[3 * d_atIdx + 2]);
double dist = (p - d_pos0).length();
double preFactor = 0.0;
if (dist > d_maxDispl) {
preFactor = dist - d_maxDispl;
} else {
return;
}
preFactor *= d_forceConstant;
for (unsigned int i = 0; i < 3; ++i) {
double dGrad = preFactor * (p[i] - d_pos0[i]) / std::max(dist, 1.0e-8);
grad[3 * d_atIdx + i] += dGrad;
}
}
}
}
|
