RDKit: TorsionPreferences.h Source File

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TorsionPreferences.h
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1//
2// Copyright (C) 2017-2023 Sereina Riniker and other RDKit contributors
3//
4// @@ All Rights Reserved @@
5// This file is part of the RDKit.
6// The contents are covered by the terms of the BSD license
7// which is included in the file license.txt, found at the root
8// of the RDKit source tree.
9//
10#include <RDGeneral/export.h>
11#ifndef _RD_TORSIONPREFERENCES_H_
12#define _RD_TORSIONPREFERENCES_H_
13#include <vector>
14#include <string>
15#include <memory>
16#include <boost/dynamic_bitset.hpp>
17
18namespace RDKit {
19class ROMol;
20} // namespace RDKit
21
22namespace ForceFields {
23namespace CrystalFF {
24
25//! A structure used to the experimental torsion patterns
26 struct RDKIT_FORCEFIELDHELPERS_EXPORT ExpTorsionAngle {
27 unsigned int torsionIdx;
28 std::string smarts;
29 std::vector<double> V;
30 std::vector<int> signs;
31 std::unique_ptr<const RDKit::ROMol> dp_pattern;
32 unsigned int idx[4];
33};
34
35 struct CrystalFFDetails {
36 std::vector<std::vector<int>> expTorsionAtoms;
37 std::vector<std::pair<std::vector<int>, std::vector<double>>>
38 expTorsionAngles;
39 std::vector<std::vector<int>> improperAtoms;
40 std::vector<std::pair<int, int>> bonds;
41 std::vector<std::vector<int>> angles;
42 std::vector<int> atomNums;
43 double boundsMatForceScaling;
44 boost::dynamic_bitset<> constrainedAtoms;
45};
46
47//! Get the experimental torsional angles in a molecule
48 RDKIT_FORCEFIELDHELPERS_EXPORT void getExperimentalTorsions(
49 const RDKit::ROMol &mol, CrystalFFDetails &details,
50 bool useExpTorsions = false, bool useSmallRingTorsions = false,
51 bool useMacrocycleTorsions = false, bool useBasicKnowledge = false,
52 unsigned int version = 2, bool verbose = false);
53
54//! \overload
55 RDKIT_FORCEFIELDHELPERS_EXPORT void getExperimentalTorsions(
56 const RDKit::ROMol &mol, CrystalFFDetails &details,
57 std::vector<std::tuple<unsigned int, std::vector<unsigned int>,
58 const ExpTorsionAngle *>> &torsionBonds,
59 bool useExpTorsions = false, bool useSmallRingTorsions = false,
60 bool useMacrocycleTorsions = false, bool useBasicKnowledge = false,
61 unsigned int version = 2, bool verbose = false);
62
63} // namespace CrystalFF
64} // namespace ForceFields
65
66#endif
RDKit::ROMol
Definition ROMol.h:199
export.h
RDKIT_FORCEFIELDHELPERS_EXPORT
#define RDKIT_FORCEFIELDHELPERS_EXPORT
Definition export.h:209
ForceFields::CrystalFF
Definition TorsionAngleContribs.h:27
ForceFields::CrystalFF::getExperimentalTorsions
RDKIT_FORCEFIELDHELPERS_EXPORT void getExperimentalTorsions(const RDKit::ROMol &mol, CrystalFFDetails &details, bool useExpTorsions=false, bool useSmallRingTorsions=false, bool useMacrocycleTorsions=false, bool useBasicKnowledge=false, unsigned int version=2, bool verbose=false)
Get the experimental torsional angles in a molecule.
ForceFields
Definition TorsionAngleContribs.h:21
RDKit
Std stuff.
Definition Abbreviations.h:19
ForceFields::CrystalFF::CrystalFFDetails
Definition TorsionPreferences.h:35
ForceFields::CrystalFF::CrystalFFDetails::atomNums
std::vector< int > atomNums
Definition TorsionPreferences.h:42
ForceFields::CrystalFF::CrystalFFDetails::constrainedAtoms
boost::dynamic_bitset constrainedAtoms
Definition TorsionPreferences.h:44
ForceFields::CrystalFF::CrystalFFDetails::boundsMatForceScaling
double boundsMatForceScaling
Definition TorsionPreferences.h:43
ForceFields::CrystalFF::CrystalFFDetails::improperAtoms
std::vector< std::vector< int > > improperAtoms
Definition TorsionPreferences.h:39
ForceFields::CrystalFF::CrystalFFDetails::bonds
std::vector< std::pair< int, int > > bonds
Definition TorsionPreferences.h:40
ForceFields::CrystalFF::CrystalFFDetails::expTorsionAngles
std::vector< std::pair< std::vector< int >, std::vector< double > > > expTorsionAngles
Definition TorsionPreferences.h:38
ForceFields::CrystalFF::CrystalFFDetails::expTorsionAtoms
std::vector< std::vector< int > > expTorsionAtoms
Definition TorsionPreferences.h:36
ForceFields::CrystalFF::CrystalFFDetails::angles
std::vector< std::vector< int > > angles
Definition TorsionPreferences.h:41
ForceFields::CrystalFF::ExpTorsionAngle
A structure used to the experimental torsion patterns.
Definition TorsionPreferences.h:26
ForceFields::CrystalFF::ExpTorsionAngle::smarts
std::string smarts
Definition TorsionPreferences.h:28
ForceFields::CrystalFF::ExpTorsionAngle::torsionIdx
unsigned int torsionIdx
Definition TorsionPreferences.h:27
ForceFields::CrystalFF::ExpTorsionAngle::dp_pattern
std::unique_ptr< const RDKit::ROMol > dp_pattern
Definition TorsionPreferences.h:31
ForceFields::CrystalFF::ExpTorsionAngle::signs
std::vector< int > signs
Definition TorsionPreferences.h:30
ForceFields::CrystalFF::ExpTorsionAngle::idx
unsigned int idx[4]
Definition TorsionPreferences.h:32
ForceFields::CrystalFF::ExpTorsionAngle::V
std::vector< double > V
Definition TorsionPreferences.h:29