RDKit: OopBend.h Source File

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OopBend.h
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1// Copyright (C) 2013-2025 Paolo Tosco and other RDKit contributors
2//
3// @@ All Rights Reserved @@
4// This file is part of the RDKit.
5// The contents are covered by the terms of the BSD license
6// which is included in the file license.txt, found at the root
7// of the RDKit source tree.
8//
9#include <RDGeneral/export.h>
10#ifndef __RD_MMFFOopBend_H__
11#define __RD_MMFFOopBend_H__
12
13#include <ForceField/Contrib.h>
14#include <Geometry/point.h>
15
16namespace ForceFields {
17namespace MMFF {
18class MMFFOop;
19
20//! the out-of-plane term for MMFF
21 class RDKIT_FORCEFIELD_EXPORT OopBendContrib : public ForceFieldContrib {
22 public:
23 OopBendContrib() {}
24 //! Constructor
25 OopBendContrib(ForceField *owner);
26 /*! Adds an out-of-plane term to the force field contrib.
27
28 The Wilson angle is between the vector formed by atom2-atom4
29 and the angle formed by atom1-atom2-atom3
30
31 \param idx1 index of atom1 in the ForceField's positions
32 \param idx2 index of atom2 in the ForceField's positions
33 \param idx3 index of atom3 in the ForceField's positions
34 \param idx4 index of atom4 in the ForceField's positions
35 */
36 void addTerm(unsigned int idx1, unsigned int idx2,
37 unsigned int idx3, unsigned int idx4,
38 const MMFFOop *mmffOopParams);
39
40 double getEnergy(double *pos) const override;
41 void getGrad(double *pos, double *grad) const override;
42 OopBendContrib *copy() const override { return new OopBendContrib(*this); }
43
44 void getSingleGrad(double* pos, double* grad, unsigned int termIdx) const;
45
46 private:
47 std::vector<int> d_at1Idxs, d_at2Idxs, d_at3Idxs, d_at4Idxs;
48 std::vector<double> d_koop;
49};
50
51namespace Utils {
52//! calculates and returns the Wilson angle (in degrees)
53 RDKIT_FORCEFIELD_EXPORT double calcOopChi(const RDGeom::Point3D &iPoint,
54 const RDGeom::Point3D &jPoint,
55 const RDGeom::Point3D &kPoint,
56 const RDGeom::Point3D &lPoint);
57//! returns the out-of-plane force constant koop
58 RDKIT_FORCEFIELD_EXPORT double calcOopBendForceConstant(
59 const MMFFOop *mmffOopParams);
60//! calculates and returns the out-of-plane MMFF energy
61 RDKIT_FORCEFIELD_EXPORT double calcOopBendEnergy(const double chi,
62 const double koop);
63} // namespace Utils
64} // namespace MMFF
65} // namespace ForceFields
66#endif
Contrib.h
ForceFields::ForceFieldContrib::ForceField
friend class ForceField
Definition Contrib.h:20
ForceFields::ForceFieldContrib::ForceFieldContrib
ForceFieldContrib()
Definition Contrib.h:22
ForceFields::MMFF::MMFFOop
class to store MMFF parameters for out-of-plane bending
Definition MMFF/Params.h:118
ForceFields::MMFF::OopBendContrib::addTerm
void addTerm(unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, const MMFFOop *mmffOopParams)
ForceFields::MMFF::OopBendContrib::getSingleGrad
void getSingleGrad(double *pos, double *grad, unsigned int termIdx) const
ForceFields::MMFF::OopBendContrib::getGrad
void getGrad(double *pos, double *grad) const override
calculates our contribution to the gradients of a position
ForceFields::MMFF::OopBendContrib::OopBendContrib
OopBendContrib(ForceField *owner)
Constructor.
ForceFields::MMFF::OopBendContrib::OopBendContrib
OopBendContrib()
Definition OopBend.h:23
ForceFields::MMFF::OopBendContrib::getEnergy
double getEnergy(double *pos) const override
returns our contribution to the energy of a position
ForceFields::MMFF::OopBendContrib::copy
OopBendContrib * copy() const override
return a copy
Definition OopBend.h:42
RDGeom::Point3D
Definition point.h:53
export.h
RDKIT_FORCEFIELD_EXPORT
#define RDKIT_FORCEFIELD_EXPORT
Definition export.h:201
ForceFields::MMFF::Utils
Definition MMFF/AngleBend.h:52
ForceFields::MMFF::Utils::calcOopChi
RDKIT_FORCEFIELD_EXPORT double calcOopChi(const RDGeom::Point3D &iPoint, const RDGeom::Point3D &jPoint, const RDGeom::Point3D &kPoint, const RDGeom::Point3D &lPoint)
calculates and returns the Wilson angle (in degrees)
ForceFields::MMFF::Utils::calcOopBendEnergy
RDKIT_FORCEFIELD_EXPORT double calcOopBendEnergy(const double chi, const double koop)
calculates and returns the out-of-plane MMFF energy
ForceFields::MMFF::Utils::calcOopBendForceConstant
RDKIT_FORCEFIELD_EXPORT double calcOopBendForceConstant(const MMFFOop *mmffOopParams)
returns the out-of-plane force constant koop
ForceFields::MMFF
Definition MMFF/AngleBend.h:17
ForceFields
Definition TorsionAngleContribs.h:21
point.h