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
|
//
// Created by Santosh Putta, Nov 2006
//
#include <RDGeneral/export.h>
#ifndef __RD_FOURTHDIMCONTRIB_H__
#define __RD_FOURTHDIMCONTRIB_H__
#include <RDGeneral/Invariant.h>
#include <ForceField/Contrib.h>
#include <ForceField/ForceField.h>
namespace DistGeom {
//! A term used in penalizing chirality violations
//!
class RDKIT_DISTGEOMETRY_EXPORT FourthDimContrib
: public ForceFields::ForceFieldContrib {
public:
FourthDimContrib() {}
//! Constructor
/*!
\param owner pointer to the owning ForceField
\param idx the index of the atom to be considered
\param weight (optional) the weight to be used for this contrib
*/
FourthDimContrib(ForceFields::ForceField *owner, unsigned int idx,
double weight)
: d_idx(idx), d_weight(weight) {
PRECONDITION(owner, "bad force field");
PRECONDITION(owner->dimension() == 4, "force field has wrong dimension");
dp_forceField = owner;
}
//! return the contribution of this contrib to the energy of a given state
double getEnergy(double *pos) const override {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(dp_forceField->dimension() == 4,
"force field has wrong dimension");
PRECONDITION(pos, "bad vector");
unsigned int pid = d_idx * dp_forceField->dimension() + 3;
return d_weight * pos[pid] * pos[pid];
}
//! calculate the contribution of this contrib to the gradient at a given
/// state
void getGrad(double *pos, double *grad) const override {
PRECONDITION(dp_forceField, "no owner");
PRECONDITION(dp_forceField->dimension() == 4,
"force field has wrong dimension");
PRECONDITION(pos, "bad vector");
unsigned int pid = d_idx * dp_forceField->dimension() + 3;
grad[pid] += d_weight * pos[pid];
}
FourthDimContrib *copy() const override {
return new FourthDimContrib(*this);
}
private:
unsigned int d_idx{0};
double d_weight{0.0};
};
} // namespace DistGeom
#endif
|
