Namespaces
namespace	ETKDGForceConsts

Classes
struct	GaussianTorsionAngleContribsParams
class	GaussianTorsionAngleContribs
struct	PlanarityContribsParams
class	PlanarityContribs
	A term to capture all Inversion Contributionss. More...
struct	TorsionAngleContribsParams
class	TorsionAngleContribs
class	TorsionAngleContribM6
	the torsion term for multiplicity m = 1 - 6 More...
struct	ExpTorsionAngle
	A structure used to the experimental torsion patterns. More...
struct	GaussianExpTorsionAngle
struct	CrystalFFDetails

Concepts
concept	TorsionAngleType

Typedefs
using	CosineExp_T = std::pair<std::vector<int>, std::vector<double>>
using	GaussianExp_T
using	TorsionLookup = std::vector<std::vector<double>>
using	TorsionParamVariant = std::variant<CosineExp_T, GaussianExp_T>
using	TorsionAnglePtrVariant

Enumerations
enum class	TorsionParamKind { Cosine , Gaussian }

Functions
RDKIT_FORCEFIELDHELPERS_EXPORT double	getEnergy (const std::vector< double > &heights, const std::vector< double > &positions, const std::vector< double > &widths, const double phi)
RDKIT_FORCEFIELDHELPERS_EXPORT double	getdEdPhi (const std::vector< double > &heights, const std::vector< double > &positions, const std::vector< double > &widths, const double phi)
RDKIT_FORCEFIELDHELPERS_EXPORT double	calcTorsionEnergy (const std::vector< double > &forceConstants, const std::vector< int > &signs, const double cosPhi)
RDKIT_FORCEFIELDHELPERS_EXPORT double	calcTorsionEnergyM6 (const std::vector< double > &V, const std::vector< int > &signs, const double cosPhi)
	calculates and returns the torsional energy
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.
RDKIT_FORCEFIELDHELPERS_EXPORT void	getExperimentalTorsions (const RDKit::ROMol &mol, CrystalFFDetails &details, std::vector< std::tuple< unsigned int, std::vector< unsigned int >, TorsionAnglePtrVariant > > &torsionBonds, bool useExpTorsions=false, bool useSmallRingTorsions=false, bool useMacrocycleTorsions=false, bool useBasicKnowledge=false, unsigned int version=2, bool verbose=false)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_FORCEFIELDHELPERS_EXPORT void	populateRefTable (CrystalFFDetails &details)

Variables
constexpr std::size_t	lookup_grid_size = 180

Typedef Documentation

◆ CosineExp_T

using ForceFields::CrystalFF::CosineExp_T = std::pair<std::vector<int>, std::vector<double>>

Definition at line 83 of file TorsionPreferences.h.

◆ GaussianExp_T

using ForceFields::CrystalFF::GaussianExp_T

Initial value:

std::tuple<std::vector<double>, std::vector<double>,

std::vector<double>, double>

Definition at line 84 of file TorsionPreferences.h.

◆ TorsionAnglePtrVariant

using ForceFields::CrystalFF::TorsionAnglePtrVariant

Initial value:

std::variant<const ExpTorsionAngle *, const GaussianExpTorsionAngle *>

Points at the SMARTS-pattern entry (of whichever functional form was used) that produced a torsion match

Definition at line 105 of file TorsionPreferences.h.

◆ TorsionLookup

using ForceFields::CrystalFF::TorsionLookup = std::vector<std::vector<double>>

Definition at line 87 of file TorsionPreferences.h.

◆ TorsionParamVariant

using ForceFields::CrystalFF::TorsionParamVariant = std::variant<CosineExp_T, GaussianExp_T>

Holds either the cosine-series (ETKDGv1/v2) or the Gaussian-fit (ETKDGv4) parameters for a single torsion term

Definition at line 101 of file TorsionPreferences.h.

Enumeration Type Documentation

◆ TorsionParamKind

enum class ForceFields::CrystalFF::TorsionParamKind

strong

Which functional form the parameters stored in a CrystalFFDetails instance use

Enumerator
Cosine
Gaussian

Definition at line 94 of file TorsionPreferences.h.

Function Documentation

◆ calcTorsionEnergy()

RDKIT_FORCEFIELDHELPERS_EXPORT double ForceFields::CrystalFF::calcTorsionEnergy	(	const std::vector< double > &	forceConstants,
		const std::vector< int > &	signs,
		const double	cosPhi )

Calculate the torsion energy as described in 10.1021/acs.jcim.5b00654, this can be used with any i > 0.

Parameters

forceConstants	Force constants for the different cosine fits
signs	Phases of the cosine fits
cosPhi	cosine of the torsion angle phi

References RDKIT_FORCEFIELDHELPERS_EXPORT.

◆ calcTorsionEnergyM6()

RDKIT_FORCEFIELDHELPERS_EXPORT double ForceFields::CrystalFF::calcTorsionEnergyM6	(	const std::vector< double > &	V,
		const std::vector< int > &	signs,
		const double	cosPhi )

calculates and returns the torsional energy

References RDKIT_FORCEFIELDHELPERS_EXPORT.

◆ getdEdPhi()

RDKIT_FORCEFIELDHELPERS_EXPORT double ForceFields::CrystalFF::getdEdPhi	(	const std::vector< double > &	heights,
		const std::vector< double > &	positions,
		const std::vector< double > &	widths,
		const double	phi )

Calculate the torsion gradient as described in 10.1021/acs.jcim.5b00654, this can be used with any any number of heights, positions and widths. The caller is responsible that the size of the three parameter objects are the same and non zero. widths need to be strictly positive.

Parameters

heights	heights of the gaussians
positions	positions of the gaussians
widths	widths of the gaussians
phi	the torsion angle in radians

References RDKIT_FORCEFIELDHELPERS_EXPORT.

◆ getEnergy()

RDKIT_FORCEFIELDHELPERS_EXPORT double ForceFields::CrystalFF::getEnergy	(	const std::vector< double > &	heights,
		const std::vector< double > &	positions,
		const std::vector< double > &	widths,
		const double	phi )

Calculate the torsion energy as described in 10.1021/acs.jcim.5b00654, this can be used with any any number of heights, positions and widths. The caller is responsible that the size of the three parameter objects are the same and non zero. widths need to be strictly positive.

Parameters

heights	heights of the gaussians
positions	positions of the gaussians
widths	widths of the gaussians
phi	the torsion angle in radians

References RDKIT_FORCEFIELDHELPERS_EXPORT.

◆ getExperimentalTorsions() [1/2]

RDKIT_FORCEFIELDHELPERS_EXPORT void ForceFields::CrystalFF::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.

References RDKIT_FORCEFIELDHELPERS_EXPORT.

◆ getExperimentalTorsions() [2/2]

RDKIT_FORCEFIELDHELPERS_EXPORT void ForceFields::CrystalFF::getExperimentalTorsions	(	const RDKit::ROMol &	mol,
		CrystalFFDetails &	details,
		std::vector< std::tuple< unsigned int, std::vector< unsigned int >, TorsionAnglePtrVariant > > &	torsionBonds,
		bool	useExpTorsions = false,
		bool	useSmallRingTorsions = false,
		bool	useMacrocycleTorsions = false,
		bool	useBasicKnowledge = false,
		unsigned int	version = 2,
		bool	verbose = false )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

References RDKIT_FORCEFIELDHELPERS_EXPORT.

◆ populateRefTable()

RDKIT_FORCEFIELDHELPERS_EXPORT void ForceFields::CrystalFF::populateRefTable ( CrystalFFDetails & details )

Populate the lookuptable for the minimizations The size of the lookup table is defined in GaussianTorsionAngleContribs.h!

References RDKIT_FORCEFIELDHELPERS_EXPORT.

Variable Documentation

◆ lookup_grid_size

std::size_t ForceFields::CrystalFF::lookup_grid_size = 180

constexpr

Size of the energies and gradients lookup table This is used in torsionPreferences.cpp.

Definition at line 32 of file GaussianTorsionAngleContribs.h.

Namespaces

Classes

Concepts

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ CosineExp_T

◆ GaussianExp_T

◆ TorsionAnglePtrVariant

◆ TorsionLookup

◆ TorsionParamVariant

Enumeration Type Documentation

◆ TorsionParamKind

Function Documentation

◆ calcTorsionEnergy()

◆ calcTorsionEnergyM6()

◆ getdEdPhi()

◆ getEnergy()

◆ getExperimentalTorsions() [1/2]

◆ getExperimentalTorsions() [2/2]

◆ populateRefTable()

Variable Documentation

◆ lookup_grid_size