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
|
//
// Copyright (C) 2013-2025 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 <RDGeneral/export.h>
#ifndef RD_MMFFTORSIONANGLE_H
#define RD_MMFFTORSIONANGLE_H
#include <ForceField/Contrib.h>
#include <tuple>
#include <vector>
namespace RDGeom {
class Point3D;
}
namespace ForceFields {
namespace MMFF {
class MMFFTor;
//! the torsion term for MMFF
class RDKIT_FORCEFIELD_EXPORT TorsionAngleContrib : public ForceFieldContrib {
public:
TorsionAngleContrib() {}
//! Constructor
TorsionAngleContrib(ForceField *owner);
/*!
Adds a torsion term to the force field contrib.
The torsion is between atom1 - atom2 - atom3 - atom4
(i.e the angle between bond atom1-atom2 and bond atom3-atom4
while looking down bond atom2-atom3)
\param idx1 index of atom1 in the ForceField's positions
\param idx2 index of atom2 in the ForceField's positions
\param idx3 index of atom3 in the ForceField's positions
\param idx4 index of atom4 in the ForceField's positions
\param torsionType MMFF type of the torsional bond between atoms 2 and 3
*/
void addTerm(unsigned int idx1, unsigned int idx2, unsigned int idx3,
unsigned int idx4, const MMFFTor *mmffTorParams);
double getEnergy(double *pos) const override;
void getGrad(double *pos, double *grad) const override;
TorsionAngleContrib *copy() const override {
return new TorsionAngleContrib(*this);
}
private:
std::vector<int16_t> d_at1Idx;
std::vector<int16_t> d_at2Idx;
std::vector<int16_t> d_at3Idx;
std::vector<int16_t> d_at4Idx;
std::vector<double> d_V1;
std::vector<double> d_V2;
std::vector<double> d_V3;
};
namespace Utils {
//! calculates and returns the cosine of a torsion angle
RDKIT_FORCEFIELD_EXPORT double calcTorsionCosPhi(const RDGeom::Point3D &iPoint,
const RDGeom::Point3D &jPoint,
const RDGeom::Point3D &kPoint,
const RDGeom::Point3D &lPoint);
//! returns the 3-tuple of a torsion angle force constants
RDKIT_FORCEFIELD_EXPORT std::tuple<double, double, double>
calcTorsionForceConstant(const MMFFTor *mmffTorParams);
//! calculates and returns the torsional MMFF energy
RDKIT_FORCEFIELD_EXPORT double calcTorsionEnergy(const double V1,
const double V2,
const double V3,
const double cosPhi);
RDKIT_FORCEFIELD_EXPORT void calcTorsionGrad(RDGeom::Point3D *r,
RDGeom::Point3D *t, double *d,
double **g, double &sinTerm,
double &cosPhi);
} // namespace Utils
} // namespace MMFF
} // namespace ForceFields
#endif
|
