Loading...
Searching...
No Matches
TorsionPreferences.h
Go to the documentation of this file.
//
// Copyright (C) 2017-2026 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];
};
namespace ETKDGForceConsts {
struct Params {
double distance{1.0};
double fourthDim{1.0};
double chiral{1.0};
double kTermAngle{1.0};
double kTermImproper{10.0};
double kTermTorsion{100.0};
double etTermScaling{1.0};
};
namespace SEQ {
constexpr Params Cosine;
}
namespace AIO {
constexpr Params Cosine = {.distance = 2.15,
.fourthDim = 2.15,
.kTermAngle = 0.1,
.kTermImproper = .001,
.kTermTorsion = 2.15,
.etTermScaling = 0.1};
} // namespace AIO
} // namespace FC
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;
double *distMat;
ETKDGForceConsts::Params forceConsts;
};
//! 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 = 2, 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 = 2, bool verbose = false);
} // namespace CrystalFF
} // namespace ForceFields
#endif
RDKit::ROMol
Definition ROMol.h:319
export.h
RDKIT_FORCEFIELDHELPERS_EXPORT
#define RDKIT_FORCEFIELDHELPERS_EXPORT
Definition export.h:209
ForceFields::CrystalFF::ETKDGForceConsts::AIO
Definition TorsionPreferences.h:49
ForceFields::CrystalFF::ETKDGForceConsts::AIO::Cosine
constexpr Params Cosine
Definition TorsionPreferences.h:50
ForceFields::CrystalFF::ETKDGForceConsts::SEQ
Definition TorsionPreferences.h:46
ForceFields::CrystalFF::ETKDGForceConsts::SEQ::Cosine
constexpr Params Cosine
Definition TorsionPreferences.h:47
ForceFields::CrystalFF::ETKDGForceConsts
Definition TorsionPreferences.h:35
ForceFields::CrystalFF
Definition PlanarityContribs.h:19
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 PlanarityContribs.h:18
RDKit
Std stuff.
Definition Abbreviations.h:19
ForceFields::CrystalFF::CrystalFFDetails
Definition TorsionPreferences.h:58
ForceFields::CrystalFF::CrystalFFDetails::atomNums
std::vector< int > atomNums
Definition TorsionPreferences.h:65
ForceFields::CrystalFF::CrystalFFDetails::constrainedAtoms
boost::dynamic_bitset constrainedAtoms
Definition TorsionPreferences.h:67
ForceFields::CrystalFF::CrystalFFDetails::forceConsts
ETKDGForceConsts::Params forceConsts
Definition TorsionPreferences.h:69
ForceFields::CrystalFF::CrystalFFDetails::distMat
double * distMat
Definition TorsionPreferences.h:68
ForceFields::CrystalFF::CrystalFFDetails::boundsMatForceScaling
double boundsMatForceScaling
Definition TorsionPreferences.h:66
ForceFields::CrystalFF::CrystalFFDetails::improperAtoms
std::vector< std::vector< int > > improperAtoms
Definition TorsionPreferences.h:62
ForceFields::CrystalFF::CrystalFFDetails::bonds
std::vector< std::pair< int, int > > bonds
Definition TorsionPreferences.h:63
ForceFields::CrystalFF::CrystalFFDetails::expTorsionAngles
std::vector< std::pair< std::vector< int >, std::vector< double > > > expTorsionAngles
Definition TorsionPreferences.h:61
ForceFields::CrystalFF::CrystalFFDetails::expTorsionAtoms
std::vector< std::vector< int > > expTorsionAtoms
Definition TorsionPreferences.h:59
ForceFields::CrystalFF::CrystalFFDetails::angles
std::vector< std::vector< int > > angles
Definition TorsionPreferences.h:64
ForceFields::CrystalFF::ETKDGForceConsts::Params
Definition TorsionPreferences.h:36
ForceFields::CrystalFF::ETKDGForceConsts::Params::kTermTorsion
double kTermTorsion
Definition TorsionPreferences.h:42
ForceFields::CrystalFF::ETKDGForceConsts::Params::kTermAngle
double kTermAngle
Definition TorsionPreferences.h:40
ForceFields::CrystalFF::ETKDGForceConsts::Params::kTermImproper
double kTermImproper
Definition TorsionPreferences.h:41
ForceFields::CrystalFF::ETKDGForceConsts::Params::chiral
double chiral
Definition TorsionPreferences.h:39
ForceFields::CrystalFF::ETKDGForceConsts::Params::distance
double distance
Definition TorsionPreferences.h:37
ForceFields::CrystalFF::ETKDGForceConsts::Params::fourthDim
double fourthDim
Definition TorsionPreferences.h:38
ForceFields::CrystalFF::ETKDGForceConsts::Params::etTermScaling
double etTermScaling
Definition TorsionPreferences.h:43
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