RDKit::DGeomHelpers Namespace Reference

Classes
struct	EmbedParameters
	Parameter object for controlling embedding. More...

Enumerations
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 , END_OF_ENUM = 11 }

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, bool set15bounds=true, bool scaleVDW=false, bool useMacrocycle14config=false, bool forceTransAmides=true)
RDKIT_DISTGEOMHELPERS_EXPORT 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)
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
RDKIT_DISTGEOMHELPERS_EXPORT void	updateEmbedParametersFromJSON (EmbedParameters &params, const std::string &json)
	update parameters from a 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)
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)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Variables
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	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

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
END_OF_ENUM

Definition at line 25 of file Embedder.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

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 216 of file Embedder.h.

References EmbedMultipleConfs(), and RDKit::rdvalue_is().

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:

1. Build a distance bounds matrix based on the topology, including 1-5 distances but not VDW scaling
2. Triangle smooth this bounds matrix
3. If step 2 fails - repeat step 1, this time without 1-5 bounds and with vdW scaling, and repeat step 2
4. Pick a distance matrix at random using the bounds matrix
5. Compute initial coordinates from the distance matrix
6. Repeat steps 3 and 4 until maxIterations is reached or embedding is successful
7. 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 299 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.

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 )

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 build 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 397 of file Embedder.h.

References EmbedMultipleConfs(), and RDKit::rdvalue_is().

EmbedMultipleConfs() [3/4]

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

inline

Definition at line 207 of file Embedder.h.

References EmbedMultipleConfs(), and RDKit::rdvalue_is().

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 )

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 420 of file Embedder.h.

References EmbedMultipleConfs(), and RDKit::rdvalue_is().

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.

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

setTopolBounds() [1/2]

RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::setTopolBounds	(	const ROMol &	mol,
		DistGeom::BoundsMatPtr	mmat,
		bool	set15bounds = true,
		bool	scaleVDW = false,
		bool	useMacrocycle14config = false,
		bool	forceTransAmides = true )

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	If true scale the sum of the vdW radii while setting lower bounds so that a smaller value (0.7*(vdw1 + vdw2) ) is used for paths that are less five bonds apart.
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.

setTopolBounds() [2/2]

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,
		bool	set15bounds = true,
		bool	scaleVDW = false,
		bool	useMacrocycle14config = false,
		bool	forceTransAmides = true )

updateEmbedParametersFromJSON()

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

update parameters from a JSON string

Variable Documentation

ETDG

RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters RDKit::DGeomHelpers::ETDG

extern

Parameters corresponding to Sereina Riniker's ETDG approach.

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

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