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TorsionPreferences.h
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//
// Copyright (C) 2017-2023 Sereina Riniker 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_TORSIONPREFERENCES_H_
#define _RD_TORSIONPREFERENCES_H_
#include <vector>
#include <string>
#include <memory>
#include <boost/dynamic_bitset.hpp>
namespace RDKit {
class ROMol;
} // namespace RDKit
namespace ForceFields {
namespace CrystalFF {
//! A structure used to the experimental torsion patterns
struct RDKIT_FORCEFIELDHELPERS_EXPORT ExpTorsionAngle {
unsigned int torsionIdx;
std::string smarts;
std::vector<double> V;
std::vector<int> signs;
std::unique_ptr<const RDKit::ROMol> dp_pattern;
unsigned int idx[4];
};
struct CrystalFFDetails {
std::vector<std::vector<int>> expTorsionAtoms;
std::vector<std::pair<std::vector<int>, std::vector<double>>>
expTorsionAngles;
std::vector<std::vector<int>> improperAtoms;
std::vector<std::pair<int, int>> bonds;
std::vector<std::vector<int>> angles;
std::vector<int> atomNums;
double boundsMatForceScaling;
boost::dynamic_bitset<> constrainedAtoms;
};
//! Get the experimental torsional angles in a molecule
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 = 1, bool verbose = false);
//! \overload
RDKIT_FORCEFIELDHELPERS_EXPORT void getExperimentalTorsions(
const RDKit::ROMol &mol, CrystalFFDetails &details,
std::vector<std::tuple<unsigned int, std::vector<unsigned int>,
const ExpTorsionAngle *>> &torsionBonds,
bool useExpTorsions = false, bool useSmallRingTorsions = false,
bool useMacrocycleTorsions = false, bool useBasicKnowledge = false,
unsigned int version = 1, bool verbose = false);
} // namespace CrystalFF
} // namespace ForceFields
#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=1, 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