Classes
struct	TorsionValue
struct	Path14Configuration
	A structure used to store planar 14 paths - cis/trans. More...
struct	Bounds
struct	EmbedParameters
	Parameter object for controlling embedding. More...
struct	InternalCoordinates

Typedefs
using	PATH14_VECT = std::vector<Path14Configuration>
using	TorsionInfo
using	BondAngleInfo = boost::unordered_flat_map<std::size_t, double>
using	BondLengthInfo = std::vector<double>

Enumerations
enum class	TorsionType { CIS = 0 , TRANS , FLEXIBLE , CUSTOM , CISTRANS }
enum class	Type14 { IN_CHAIN , IN_RING , TWO_IN_SAME_RING , TWO_IN_DIFF_RING , SHARE_RING_BOND , MACROCYCLE_TWO_IN_SAME_RING , MACROCYCLE_ALL_IN_SAME_RING }
enum	EmbedFailureCauses { INITIAL_COORDS = 0 , FIRST_MINIMIZATION = 1 , CHECK_TETRAHEDRAL_CENTERS = 2 , CHECK_CHIRAL_CENTERS = 3 , MINIMIZE_FOURTH_DIMENSION = 4 , ETK_MINIMIZATION = 5 , FINAL_CHIRAL_BOUNDS = 6 , FINAL_CENTER_IN_VOLUME = 7 , LINEAR_DOUBLE_BOND = 8 , BAD_DOUBLE_BOND_STEREO = 9 , CHECK_CHIRAL_CENTERS2 = 10 , EXCEEDED_TIMEOUT = 11 , MINIMIZATION = 12 , KTERM_VIOLATION = 13 , CLASH = 14 , END_OF_ENUM = 15 }
enum class	InitialEmbeddingMode { DG_EMBEDDING = 0 , INTERNAL_COORDINATE_EMBEDDING = 1 , RANDOM_COORDINATE_EMBEDDING = 2 }
enum class	EmbedFF : std::uint8_t { UFF = 0 , MMFF = 1 }

Functions
RDKIT_DISTGEOMHELPERS_EXPORT void	initBoundsMat (DistGeom::BoundsMatrix *mmat, double defaultMin=0.0, double defaultMax=1000.0)
	Set default upper and lower distance bounds in a distance matrix.
RDKIT_DISTGEOMHELPERS_EXPORT void	initBoundsMat (DistGeom::BoundsMatPtr mmat, double defaultMin=0.0, double defaultMax=1000.0)
RDKIT_DISTGEOMHELPERS_EXPORT void	setTopolBounds (const ROMol &mol, DistGeom::BoundsMatPtr mmat, const EmbedParameters &params, bool scaleVDW=false, bool set15bounds=true, bool set14bounds=true, bool set13bounds=true, PATH14_VECT paths14=nullptr, const EmbedFF embedForceField=EmbedFF::UFF, InternalCoordinates internalCoords=nullptr)
void	setTopolBounds (const ROMol &mol, DistGeom::BoundsMatPtr mmat, bool set15bounds=true, bool scaleVDW=false, bool useMacrocycle14config=false, bool forceTransAmides=true, bool set14bounds=true, bool set13bounds=true, const EmbedFF embedForceField=EmbedFF::UFF)
RDKIT_DISTGEOMHELPERS_EXPORT void	setTopolBounds (const ROMol &mol, DistGeom::BoundsMatPtr mmat, std::vector< std::pair< int, int > > &bonds, std::vector< std::vector< int > > &angles, const EmbedParameters &params, bool scaleVDW=false, bool set15bounds=true, bool set14bounds=true, bool set13bounds=true, PATH14_VECT paths14=nullptr, const EmbedFF embedForceField=EmbedFF::UFF, InternalCoordinates internalCoords=nullptr)
void	setTopolBounds (const ROMol &mol, DistGeom::BoundsMatPtr mmat, std::vector< std::pair< int, int > > &bonds, std::vector< std::vector< int > > &angles, bool set15bounds=true, bool scaleVDW=false, bool useMacrocycle14config=false, bool forceTransAmides=true, bool set14bounds=true, bool set13bounds=true, const EmbedFF embedForceField=EmbedFF::UFF)
RDKIT_DISTGEOMHELPERS_EXPORT void	collectBondsAndAngles (const ROMol &mol, std::vector< std::pair< int, int > > &bonds, std::vector< std::vector< int > > &angles)
	generate the vectors of bonds and angles used by (ET)KDG
DistGeom::TorsionRange	ringTorsion (const std::size_t rSize)
std::size_t	getUnifiedId (const unsigned int id1, const unsigned int id2, const unsigned int n)
std::size_t	getUnifiedId (const unsigned int id1, const unsigned int id2, const unsigned int id3, const unsigned int n)
template<unsigned int numBondIds>
auto	unifiedIdToBondIds (std::size_t id, const unsigned int n)
Bounds	merge (std::vector< Bounds > bounds)
RDKIT_DISTGEOMHELPERS_EXPORT void	updateEmbedParametersFromJSON (EmbedParameters &params, const std::string &json)
	update parameters from a JSON string
RDKIT_DISTGEOMHELPERS_EXPORT std::string	embedParametersToJSON (const EmbedParameters &params)
	export parameters to JSON string
RDKIT_DISTGEOMHELPERS_EXPORT void	EmbedMultipleConfs (ROMol &mol, INT_VECT &res, unsigned int numConfs, EmbedParameters &params)
	Embed multiple conformations for a molecule.
INT_VECT	EmbedMultipleConfs (ROMol &mol, unsigned int numConfs, EmbedParameters &params)
int	EmbedMolecule (ROMol &mol, EmbedParameters &params)
int	EmbedMolecule (ROMol &mol, unsigned int maxIterations=0, int seed=-1, bool clearConfs=true, bool useRandomCoords=false, double boxSizeMult=2.0, bool randNegEig=true, unsigned int numZeroFail=1, const std::map< int, RDGeom::Point3D > *coordMap=nullptr, double optimizerForceTol=1e-3, bool ignoreSmoothingFailures=false, bool enforceChirality=true, bool useExpTorsionAnglePrefs=false, bool useBasicKnowledge=false, bool verbose=false, double basinThresh=5.0, bool onlyHeavyAtomsForRMS=false, unsigned int ETversion=2, bool useSmallRingTorsions=false, bool useMacrocycleTorsions=true, bool useMacrocycle14config=true)
void	EmbedMultipleConfs (ROMol &mol, INT_VECT &res, unsigned int numConfs=10, int numThreads=1, unsigned int maxIterations=30, int seed=-1, bool clearConfs=true, bool useRandomCoords=false, double boxSizeMult=2.0, bool randNegEig=true, unsigned int numZeroFail=1, double pruneRmsThresh=-1.0, const std::map< int, RDGeom::Point3D > *coordMap=nullptr, double optimizerForceTol=1e-3, bool ignoreSmoothingFailures=false, bool enforceChirality=true, bool useExpTorsionAnglePrefs=false, bool useBasicKnowledge=false, bool verbose=false, double basinThresh=5.0, bool onlyHeavyAtomsForRMS=false, unsigned int ETversion=2, bool useSmallRingTorsions=false, bool useMacrocycleTorsions=true, bool useMacrocycle14config=true, unsigned int timeout=0)
INT_VECT	EmbedMultipleConfs (ROMol &mol, unsigned int numConfs=10, unsigned int maxIterations=30, int seed=-1, bool clearConfs=true, bool useRandomCoords=false, double boxSizeMult=2.0, bool randNegEig=true, unsigned int numZeroFail=1, double pruneRmsThresh=-1.0, const std::map< int, RDGeom::Point3D > *coordMap=nullptr, double optimizerForceTol=1e-3, bool ignoreSmoothingFailures=false, bool enforceChirality=true, bool useExpTorsionAnglePrefs=false, bool useBasicKnowledge=false, bool verbose=false, double basinThresh=5.0, bool onlyHeavyAtomsForRMS=false, unsigned int ETversion=2, bool useSmallRingTorsions=false, bool useMacrocycleTorsions=false, bool useMacrocycle14config=false, unsigned int timeout=0)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
std::ostream &	operator<< (std::ostream &os, const InitialEmbeddingMode &mode)
std::istream &	operator>> (std::istream &is, InitialEmbeddingMode &mode)
std::ostream &	operator<< (std::ostream &os, const EmbedFF &eff)
std::istream &	operator>> (std::istream &is, EmbedFF &eff)
RDKIT_DISTGEOMHELPERS_EXPORT void	setMoleculeDFS (const ROMol &mol, DistGeom::ZMatrix &zmat, const InternalCoordinates &internalCoords)
RDKIT_DISTGEOMHELPERS_EXPORT void	setMoleculeDFS (const ROMol &mol, DistGeom::ZMatrix &zmat, const InternalCoordinates &internalCoords, unsigned int firstAtomIdx, unsigned int secondAtomIdx)
RDKIT_DISTGEOMHELPERS_EXPORT void	correctChiralCenters (const ROMol &mol, DistGeom::ZMatrix &zmat)

Variables
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters	DG
	Parameters corresponding to plain Distance Geometry.
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters	KDG
	Parameters corresponding to Sereina Riniker's KDG approach.
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters	ETDG
	Parameters corresponding to Sereina Riniker's ETDG approach.
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters	ETDGv2
	Parameters corresponding to Sereina Riniker's ETDG approach - version 2.
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters	ETKDG
	Parameters corresponding to Sereina Riniker's ETKDG approach.
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters	ETKDGv2
	Parameters corresponding to Sereina Riniker's ETKDG approach - version 2.
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters	ETKDGv3
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters	srETKDGv3
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters	ETKDGv4

Typedef Documentation

◆ BondAngleInfo

using RDKit::DGeomHelpers::BondAngleInfo = boost::unordered_flat_map<std::size_t, double>

Definition at line 24 of file ZMatrixBuilder.h.

◆ BondLengthInfo

using RDKit::DGeomHelpers::BondLengthInfo = std::vector<double>

Definition at line 25 of file ZMatrixBuilder.h.

◆ PATH14_VECT

using RDKit::DGeomHelpers::PATH14_VECT = std::vector<Path14Configuration>

Definition at line 102 of file BoundsMatrixBuilderDetails.h.

◆ TorsionInfo

using RDKit::DGeomHelpers::TorsionInfo

Initial value:

boost::unordered_flat_map<std::size_t, DistGeom::TorsionCandidates>

Definition at line 22 of file ZMatrixBuilder.h.

Enumeration Type Documentation

◆ EmbedFailureCauses

enum RDKit::DGeomHelpers::EmbedFailureCauses

Enumerator
INITIAL_COORDS
FIRST_MINIMIZATION
CHECK_TETRAHEDRAL_CENTERS
CHECK_CHIRAL_CENTERS
MINIMIZE_FOURTH_DIMENSION
ETK_MINIMIZATION
FINAL_CHIRAL_BOUNDS
FINAL_CENTER_IN_VOLUME
LINEAR_DOUBLE_BOND
BAD_DOUBLE_BOND_STEREO
CHECK_CHIRAL_CENTERS2
EXCEEDED_TIMEOUT
MINIMIZATION
KTERM_VIOLATION
CLASH
END_OF_ENUM

Definition at line 37 of file Embedder.h.

◆ EmbedFF

enum class RDKit::DGeomHelpers::EmbedFF : std::uint8_t

strong

Enumerator
UFF
MMFF

Definition at line 62 of file Embedder.h.

◆ InitialEmbeddingMode

enum class RDKit::DGeomHelpers::InitialEmbeddingMode

strong

Enumerator
DG_EMBEDDING
INTERNAL_COORDINATE_EMBEDDING
RANDOM_COORDINATE_EMBEDDING

Definition at line 56 of file Embedder.h.

◆ TorsionType

enum class RDKit::DGeomHelpers::TorsionType

strong

Enumerator
CIS
TRANS
FLEXIBLE
CUSTOM
CISTRANS

Definition at line 29 of file BoundsMatrixBuilderDetails.h.

◆ Type14

enum class RDKit::DGeomHelpers::Type14

strong

Enumerator
IN_CHAIN
IN_RING
TWO_IN_SAME_RING
TWO_IN_DIFF_RING
SHARE_RING_BOND
MACROCYCLE_TWO_IN_SAME_RING
MACROCYCLE_ALL_IN_SAME_RING

Definition at line 37 of file BoundsMatrixBuilderDetails.h.

Function Documentation

◆ collectBondsAndAngles()

RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::collectBondsAndAngles	(	const ROMol &	mol,
		std::vector< std::pair< int, int > > &	bonds,
		std::vector< std::vector< int > > &	angles )

generate the vectors of bonds and angles used by (ET)KDG

References RDKIT_DISTGEOMHELPERS_EXPORT.

◆ correctChiralCenters()

RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::correctChiralCenters	(	const ROMol &	mol,
		DistGeom::ZMatrix &	zmat )

Corrects sign for offsets of improper torsions to account for chiral chemistry

Parameters

mol	Corresponding molecule
zmat	ZMatrix

References RDKIT_DISTGEOMHELPERS_EXPORT.

◆ EmbedMolecule() [1/2]

int RDKit::DGeomHelpers::EmbedMolecule	(	ROMol &	mol,
		EmbedParameters &	params )

inline

Compute an embedding (in 3D) for the specified molecule using Distance Geometry

Definition at line 214 of file Embedder.h.

References EmbedMultipleConfs().

Referenced by EmbedMolecule().

◆ EmbedMolecule() [2/2]

int RDKit::DGeomHelpers::EmbedMolecule	(	ROMol &	mol,
		unsigned int	maxIterations = 0,
		int	seed = -1,
		bool	clearConfs = true,
		bool	useRandomCoords = false,
		double	boxSizeMult = 2.0,
		bool	randNegEig = true,
		unsigned int	numZeroFail = 1,
		const std::map< int, RDGeom::Point3D > *	coordMap = nullptr,
		double	optimizerForceTol = 1e-3,
		bool	ignoreSmoothingFailures = false,
		bool	enforceChirality = true,
		bool	useExpTorsionAnglePrefs = false,
		bool	useBasicKnowledge = false,
		bool	verbose = false,
		double	basinThresh = 5.0,
		bool	onlyHeavyAtomsForRMS = false,
		unsigned int	ETversion = 2,
		bool	useSmallRingTorsions = false,
		bool	useMacrocycleTorsions = true,
		bool	useMacrocycle14config = true )

inline

Compute an embedding (in 3D) for the specified molecule using Distance Geometry

The following operations are performed (in order) here:

Build a distance bounds matrix based on the topology, including 1-5 distances but not VDW scaling
Triangle smooth this bounds matrix
If step 2 fails - repeat step 1, this time without 1-5 bounds and with vdW scaling, and repeat step 2
Pick a distance matrix at random using the bounds matrix
Compute initial coordinates from the distance matrix
Repeat steps 3 and 4 until maxIterations is reached or embedding is successful

Adjust initial coordinates by minimizing a Distance Violation error function NOTE**: if the molecule has multiple fragments, they will be embedded separately, this means that they will likely occupy the same region of space.

Parameters

mol	Molecule of interest
maxIterations	Max. number of times the embedding will be tried if coordinates are not obtained successfully. The default value is 10x the number of atoms.
seed	provides a seed for the random number generator (so that the same coordinates can be obtained for a molecule on multiple runs). If negative, the RNG will not be seeded.
clearConfs	Clear all existing conformations on the molecule
useRandomCoords	Start the embedding from random coordinates instead of using eigenvalues of the distance matrix.
boxSizeMult	Determines the size of the box that is used for random coordinates. If this is a positive number, the side length will equal the largest element of the distance matrix times `boxSizeMult`. If this is a negative number, the side length will equal `-boxSizeMult` (i.e. independent of the elements of the distance matrix).
randNegEig	Picks coordinates at random when a embedding process produces negative eigenvalues
numZeroFail	Fail embedding if we find this many or more zero eigenvalues (within a tolerance)
coordMap	a map of int to Point3D, between atom IDs and their locations their locations. If this container is provided, the coordinates are used to set distance constraints on the embedding. The resulting conformer(s) should have distances between the specified atoms that reproduce those between the points in `coordMap`. Because the embedding produces a molecule in an arbitrary reference frame, an alignment step is required to actually reproduce the provided coordinates.
optimizerForceTol	set the tolerance on forces in the distgeom optimizer (this shouldn't normally be altered in client code).
ignoreSmoothingFailures	try to embed the molecule even if triangle bounds smoothing fails
enforceChirality	enforce the correct chirality if chiral centers are present
useExpTorsionAnglePrefs	impose experimental torsion-angle preferences
useBasicKnowledge	impose "basic knowledge" terms such as flat aromatic rings, ketones, etc.
verbose	print output of experimental torsion-angle preferences
basinThresh	set the basin threshold for the DGeom force field, (this shouldn't normally be altered in client code).
onlyHeavyAtomsForRMS	only use the heavy atoms when doing RMS filtering
ETversion	version of torsion preferences to use
useSmallRingTorsions	optional torsions to improve small ring conformer sampling
useMacrocycleTorsions	optional torsions to improve macrocycle conformer sampling
useMacrocycle14config	If 1-4 distances bound heuristics for macrocycles is used

Returns: ID of the conformer added to the molecule, -1 if the emdedding failed

Definition at line 297 of file Embedder.h.

References EmbedMolecule().

◆ EmbedMultipleConfs() [1/4]

RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::EmbedMultipleConfs	(	ROMol &	mol,
		INT_VECT &	res,
		unsigned int	numConfs,
		EmbedParameters &	params )

Embed multiple conformations for a molecule.

References RDKIT_DISTGEOMHELPERS_EXPORT.

Referenced by EmbedMolecule(), EmbedMultipleConfs(), EmbedMultipleConfs(), and EmbedMultipleConfs().

◆ EmbedMultipleConfs() [2/4]

void RDKit::DGeomHelpers::EmbedMultipleConfs	(	ROMol &	mol,
		INT_VECT &	res,
		unsigned int	numConfs = 10,
		int	numThreads = 1,
		unsigned int	maxIterations = 30,
		int	seed = -1,
		bool	clearConfs = true,
		bool	useRandomCoords = false,
		double	boxSizeMult = 2.0,
		bool	randNegEig = true,
		unsigned int	numZeroFail = 1,
		double	pruneRmsThresh = -1.0,
		const std::map< int, RDGeom::Point3D > *	coordMap = nullptr,
		double	optimizerForceTol = 1e-3,
		bool	ignoreSmoothingFailures = false,
		bool	enforceChirality = true,
		bool	useExpTorsionAnglePrefs = false,
		bool	useBasicKnowledge = false,
		bool	verbose = false,
		double	basinThresh = 5.0,
		bool	onlyHeavyAtomsForRMS = false,
		unsigned int	ETversion = 2,
		bool	useSmallRingTorsions = false,
		bool	useMacrocycleTorsions = true,
		bool	useMacrocycle14config = true,
		unsigned int	timeout = 0 )

inline

This is kind of equivalent to calling EmbedMolecule multiple times - just that the bounds matrix is computed only once from the topology NOTE**: if the molecule has multiple fragments, they will be embedded separately, this means that they will likely occupy the same region of space.

Parameters

mol	Molecule of interest
res	Used to return the resulting conformer ids
numConfs	Number of conformations to be generated
numThreads	Sets the number of threads to use (more than one thread will only be used if the RDKit was built with multithread support). If set to zero, the max supported by the system will be used.
maxIterations	Max. number of times the embedding will be tried if coordinates are not obtained successfully. The default value is 10x the number of atoms.
seed	provides a seed for the random number generator (so that the same coordinates can be obtained for a molecule on multiple runs). If negative, the RNG will not be seeded.
clearConfs	Clear all existing conformations on the molecule
useRandomCoords	Start the embedding from random coordinates instead of using eigenvalues of the distance matrix.
boxSizeMult	Determines the size of the box that is used for random coordinates. If this is a positive number, the side length will equal the largest element of the distance matrix times `boxSizeMult`. If this is a negative number, the side length will equal `-boxSizeMult` (i.e. independent of the elements of the distance matrix).
randNegEig	Picks coordinates at random when a embedding process produces negative eigenvalues
numZeroFail	Fail embedding if we find this many or more zero eigenvalues (within a tolerance)
pruneRmsThresh	Retain only the conformations out of 'numConfs' after embedding that are at least this far apart from each other. RMSD is computed on the heavy atoms. Pruning is greedy; i.e. the first embedded conformation is retained and from then on only those that are at least pruneRmsThresh away from already retained conformations are kept. The pruning is done after embedding and bounds violation minimization. No pruning by default.
coordMap	a map of int to Point3D, between atom IDs and their locations their locations. If this container is provided, the coordinates are used to set distance constraints on the embedding. The resulting conformer(s) should have distances between the specified atoms that reproduce those between the points in `coordMap`. Because the embedding produces a molecule in an arbitrary reference frame, an alignment step is required to actually reproduce the provided coordinates.
optimizerForceTol	set the tolerance on forces in the DGeom optimizer (this shouldn't normally be altered in client code).
ignoreSmoothingFailures	try to embed the molecule even if triangle bounds smoothing fails
enforceChirality	enforce the correct chirality if chiral centers are present
useExpTorsionAnglePrefs	impose experimental torsion-angle preferences
useBasicKnowledge	impose "basic knowledge" terms such as flat aromatic rings, ketones, etc.
verbose	print output of experimental torsion-angle preferences
basinThresh	set the basin threshold for the DGeom force field, (this shouldn't normally be altered in client code).
onlyHeavyAtomsForRMS	only use the heavy atoms when doing RMS filtering
ETversion	version of torsion preferences to use
useSmallRingTorsions	optional torsions to improve small ring conformer sampling
useMacrocycleTorsions	optional torsions to improve macrocycle conformer sampling
useMacrocycle14config	If 1-4 distances bound heuristics for macrocycles is used

Definition at line 409 of file Embedder.h.

References EmbedMultipleConfs().

◆ EmbedMultipleConfs() [3/4]

INT_VECT RDKit::DGeomHelpers::EmbedMultipleConfs	(	ROMol &	mol,
		unsigned int	numConfs,
		EmbedParameters &	params )

inline

Definition at line 205 of file Embedder.h.

References EmbedMultipleConfs().

◆ EmbedMultipleConfs() [4/4]

INT_VECT RDKit::DGeomHelpers::EmbedMultipleConfs	(	ROMol &	mol,
		unsigned int	numConfs = 10,
		unsigned int	maxIterations = 30,
		int	seed = -1,
		bool	clearConfs = true,
		bool	useRandomCoords = false,
		double	boxSizeMult = 2.0,
		bool	randNegEig = true,
		unsigned int	numZeroFail = 1,
		double	pruneRmsThresh = -1.0,
		const std::map< int, RDGeom::Point3D > *	coordMap = nullptr,
		double	optimizerForceTol = 1e-3,
		bool	ignoreSmoothingFailures = false,
		bool	enforceChirality = true,
		bool	useExpTorsionAnglePrefs = false,
		bool	useBasicKnowledge = false,
		bool	verbose = false,
		double	basinThresh = 5.0,
		bool	onlyHeavyAtomsForRMS = false,
		unsigned int	ETversion = 2,
		bool	useSmallRingTorsions = false,
		bool	useMacrocycleTorsions = false,
		bool	useMacrocycle14config = false,
		unsigned int	timeout = 0 )

inline

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

Definition at line 449 of file Embedder.h.

References EmbedMultipleConfs().

◆ embedParametersToJSON()

RDKIT_DISTGEOMHELPERS_EXPORT std::string RDKit::DGeomHelpers::embedParametersToJSON ( const EmbedParameters & params )

export parameters to JSON string

References RDKIT_DISTGEOMHELPERS_EXPORT.

◆ getUnifiedId() [1/2]

std::size_t RDKit::DGeomHelpers::getUnifiedId	(	const unsigned int	id1,
		const unsigned int	id2,
		const unsigned int	id3,
		const unsigned int	n )

inline

Definition at line 112 of file BoundsMatrixBuilderDetails.h.

◆ getUnifiedId() [2/2]

std::size_t RDKit::DGeomHelpers::getUnifiedId	(	const unsigned int	id1,
		const unsigned int	id2,
		const unsigned int	n )

inline

Definition at line 104 of file BoundsMatrixBuilderDetails.h.

◆ initBoundsMat() [1/2]

RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::initBoundsMat	(	DistGeom::BoundsMatPtr	mmat,
		double	defaultMin = 0.0,
		double	defaultMax = 1000.0 )

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

References RDKIT_DISTGEOMHELPERS_EXPORT.

◆ initBoundsMat() [2/2]

RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::initBoundsMat	(	DistGeom::BoundsMatrix *	mmat,
		double	defaultMin = 0.0,
		double	defaultMax = 1000.0 )

Set default upper and lower distance bounds in a distance matrix.

Parameters

mmat	pointer to the bounds matrix to be altered
defaultMin	default value for the lower distance bounds
defaultMax	default value for the upper distance bounds

References RDKIT_DISTGEOMHELPERS_EXPORT.

◆ merge()

Bounds RDKit::DGeomHelpers::merge ( std::vector< Bounds > bounds )

inline

Definition at line 148 of file BoundsMatrixBuilderDetails.h.

References RDKit::DGeomHelpers::Bounds::lower, and PRECONDITION.

◆ operator<<() [1/2]

std::ostream & RDKit::DGeomHelpers::operator<<	(	std::ostream &	os,
		const EmbedFF &	eff )

inline

Definition at line 523 of file Embedder.h.

References MMFF, and UFF.

◆ operator<<() [2/2]

std::ostream & RDKit::DGeomHelpers::operator<<	(	std::ostream &	os,
		const InitialEmbeddingMode &	mode )

inline

Definition at line 491 of file Embedder.h.

References DG_EMBEDDING, INTERNAL_COORDINATE_EMBEDDING, and RANDOM_COORDINATE_EMBEDDING.

◆ operator>>() [1/2]

std::istream & RDKit::DGeomHelpers::operator>>	(	std::istream &	is,
		EmbedFF &	eff )

inline

Definition at line 537 of file Embedder.h.

References BOOST_LOG, MMFF, rdWarningLog, and UFF.

◆ operator>>() [2/2]

std::istream & RDKit::DGeomHelpers::operator>>	(	std::istream &	is,
		InitialEmbeddingMode &	mode )

inline

Definition at line 507 of file Embedder.h.

References DG_EMBEDDING, INTERNAL_COORDINATE_EMBEDDING, and RANDOM_COORDINATE_EMBEDDING.

◆ ringTorsion()

DistGeom::TorsionRange RDKit::DGeomHelpers::ringTorsion ( const std::size_t rSize )

inline

Definition at line 54 of file BoundsMatrixBuilderDetails.h.

References M_PI.

Referenced by RDKit::DGeomHelpers::Path14Configuration::toTorsionRange().

◆ setMoleculeDFS() [1/2]

RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::setMoleculeDFS	(	const ROMol &	mol,
		DistGeom::ZMatrix &	zmat,
		const InternalCoordinates &	internalCoords )

Generates a Z-Matrix via a DFS walk through the molecule, as starting point, a non-ring bond (if existing) with minimal degree is selected

Parameters

mol	Molecule for which the matrix should be constructes
zmat	Pointer to an initialized (!) but empty Z-Matrix that should be filled
internalCoords	Internal coordinates to be used for the ZMatrix (NOTE: the molecule that was given here must be the same used to construct the internal coordinates, since they are accessed by their bond ids)

References RDKIT_DISTGEOMHELPERS_EXPORT.

◆ setMoleculeDFS() [2/2]

RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::setMoleculeDFS	(	const ROMol &	mol,
		DistGeom::ZMatrix &	zmat,
		const InternalCoordinates &	internalCoords,
		unsigned int	firstAtomIdx,
		unsigned int	secondAtomIdx )

Generates a Z-Matrix via a DFS walk through the molecule, as starting point, the given two atoms are used

Parameters

mol	Molecule for which the matrix should be constructes
zmat	Pointer to an initialized (!) but empty Z-Matrix that should be filled
internalCoords	Internal coordinates to be used for the ZMatrix (NOTE: the molecule that was given here must be the same used to construct the internal coordinates, since they are accessed by their bond ids)
firstAtomIdx	First row in zmatrix
secondAtomIdx	Second row in zmatrix

References RDKIT_DISTGEOMHELPERS_EXPORT.

◆ setTopolBounds() [1/4]

void RDKit::DGeomHelpers::setTopolBounds	(	const ROMol &	mol,
		DistGeom::BoundsMatPtr	mmat,
		bool	set15bounds = true,
		bool	scaleVDW = false,
		bool	useMacrocycle14config = false,
		bool	forceTransAmides = true,
		bool	set14bounds = true,
		bool	set13bounds = true,
		const EmbedFF	embedForceField = EmbedFF::UFF )

inline

Set upper and lower distance bounds between atoms in a molecule based on topology

This consists of setting 1-2, 1-3 and 1-4 distance based on bond lengths, bond angles and torsion angle ranges. Optionally 1-5 bounds can also be set, in particular, for path that contain rigid 1-4 paths. The final step involves setting lower bound to the sum of the vdW radii for the remaining atom pairs.

Parameters

mol	The molecule of interest
mmat	Bounds matrix to the bounds are written
set15bounds	If true try to set 1-5 bounds also based on topology
scaleVDW	Ignored.
useMacrocycle14config	If 1-4 distances bound heuristics for macrocycles is used Note For some strained systems the bounds matrix resulting from setting 1-5 bounds may fail triangle smoothing. In these cases it is recommended to back out and recompute the bounds matrix with no 1-5 bounds and with vdW scaling.
forceTransAmides	If true, amide bonds are enforced to be trans
set14bounds	If true, set 1-4 distance bounds based on topology
set13bounds	If true, set 1-3 distance bounds based on topology

Definition at line 66 of file BoundsMatrixBuilder.h.

References setTopolBounds(), and UFF.

◆ setTopolBounds() [2/4]

RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::setTopolBounds	(	const ROMol &	mol,
		DistGeom::BoundsMatPtr	mmat,
		const EmbedParameters &	params,
		bool	scaleVDW = false,
		bool	set15bounds = true,
		bool	set14bounds = true,
		bool	set13bounds = true,
		PATH14_VECT *	paths14 = nullptr,
		const EmbedFF	embedForceField = EmbedFF::UFF,
		InternalCoordinates *	internalCoords = nullptr )

References RDKIT_DISTGEOMHELPERS_EXPORT, and UFF.

Referenced by setTopolBounds(), and setTopolBounds().

◆ setTopolBounds() [3/4]

void RDKit::DGeomHelpers::setTopolBounds	(	const ROMol &	mol,
		DistGeom::BoundsMatPtr	mmat,
		std::vector< std::pair< int, int > > &	bonds,
		std::vector< std::vector< int > > &	angles,
		bool	set15bounds = true,
		bool	scaleVDW = false,
		bool	useMacrocycle14config = false,
		bool	forceTransAmides = true,
		bool	set14bounds = true,
		bool	set13bounds = true,
		const EmbedFF	embedForceField = EmbedFF::UFF )

inline

Definition at line 89 of file BoundsMatrixBuilder.h.

References setTopolBounds(), and UFF.

◆ setTopolBounds() [4/4]

RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::setTopolBounds	(	const ROMol &	mol,
		DistGeom::BoundsMatPtr	mmat,
		std::vector< std::pair< int, int > > &	bonds,
		std::vector< std::vector< int > > &	angles,
		const EmbedParameters &	params,
		bool	scaleVDW = false,
		bool	set15bounds = true,
		bool	set14bounds = true,
		bool	set13bounds = true,
		PATH14_VECT *	paths14 = nullptr,
		const EmbedFF	embedForceField = EmbedFF::UFF,
		InternalCoordinates *	internalCoords = nullptr )

References RDKIT_DISTGEOMHELPERS_EXPORT, and UFF.

◆ unifiedIdToBondIds()

template<unsigned int numBondIds>

auto RDKit::DGeomHelpers::unifiedIdToBondIds	(	std::size_t	id,
		const unsigned int	n )

Definition at line 121 of file BoundsMatrixBuilderDetails.h.

◆ updateEmbedParametersFromJSON()

RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::updateEmbedParametersFromJSON	(	EmbedParameters &	params,
		const std::string &	json )

update parameters from a JSON string

References RDKIT_DISTGEOMHELPERS_EXPORT.

Variable Documentation

◆ DG

RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters RDKit::DGeomHelpers::DG

extern

Parameters corresponding to plain Distance Geometry.

◆ ETDG

RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters RDKit::DGeomHelpers::ETDG

extern

Parameters corresponding to Sereina Riniker's ETDG approach.

◆ ETDGv2

RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters RDKit::DGeomHelpers::ETDGv2

extern

Parameters corresponding to Sereina Riniker's ETDG approach - version 2.

◆ ETKDG

RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters RDKit::DGeomHelpers::ETKDG

extern

Parameters corresponding to Sereina Riniker's ETKDG approach.

◆ ETKDGv2

RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters RDKit::DGeomHelpers::ETKDGv2

extern

Parameters corresponding to Sereina Riniker's ETKDG approach - version 2.

◆ ETKDGv3

RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters RDKit::DGeomHelpers::ETKDGv3

extern

Parameters corresponding improved ETKDG by Wang, Witek, Landrum and Riniker (10.1021/acs.jcim.0c00025) - the macrocycle part

◆ ETKDGv4

RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters RDKit::DGeomHelpers::ETKDGv4

extern

◆ KDG

RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters RDKit::DGeomHelpers::KDG

extern

Parameters corresponding to Sereina Riniker's KDG approach.

◆ srETKDGv3

RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters RDKit::DGeomHelpers::srETKDGv3

extern

Parameters corresponding improved ETKDG by Wang, Witek, Landrum and Riniker (10.1021/acs.jcim.0c00025) - the small ring part

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ BondAngleInfo

◆ BondLengthInfo

◆ PATH14_VECT

◆ TorsionInfo

Enumeration Type Documentation

◆ EmbedFailureCauses

◆ EmbedFF

◆ InitialEmbeddingMode

◆ TorsionType

◆ Type14

Function Documentation

◆ collectBondsAndAngles()

◆ correctChiralCenters()

◆ EmbedMolecule() [1/2]

◆ EmbedMolecule() [2/2]

◆ EmbedMultipleConfs() [1/4]

◆ EmbedMultipleConfs() [2/4]

◆ EmbedMultipleConfs() [3/4]

◆ EmbedMultipleConfs() [4/4]

◆ embedParametersToJSON()

◆ getUnifiedId() [1/2]

◆ getUnifiedId() [2/2]

◆ initBoundsMat() [1/2]

◆ initBoundsMat() [2/2]

◆ merge()

◆ operator<<() [1/2]

◆ operator<<() [2/2]

◆ operator>>() [1/2]

◆ operator>>() [2/2]

◆ ringTorsion()

◆ setMoleculeDFS() [1/2]

◆ setMoleculeDFS() [2/2]

◆ setTopolBounds() [1/4]

◆ setTopolBounds() [2/4]

◆ setTopolBounds() [3/4]

◆ setTopolBounds() [4/4]

◆ unifiedIdToBondIds()

◆ updateEmbedParametersFromJSON()

Variable Documentation

◆ DG

◆ ETDG

◆ ETDGv2

◆ ETKDG

◆ ETKDGv2

◆ ETKDGv3

◆ ETKDGv4

◆ KDG

◆ srETKDGv3