RDKit::DGeomHelpers Namespace Reference

Functions
void	initBoundsMat (DistGeom::BoundsMatrix *mmat, double defaultMin=0.0, double defaultMax=1000.0)
	Set default upper and lower distance bounds in a distance matrix.
void	initBoundsMat (DistGeom::BoundsMatPtr mmat, double defaultMin=0.0, double defaultMax=1000.0)
void	setTopolBounds (const ROMol &mol, DistGeom::BoundsMatPtr mmat, bool set15bounds=true, bool scaleVDW=false)
	Set upper and lower distance bounds between atoms in a molecule based on topology.
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=0, double optimizerForceTol=1e-3, double basinThresh=5.0)
	Compute an embedding (in 3D) for the specified molecule using Distance Geometry.
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=0, double optimizerForceTol=1e-3, double basinThresh=5.0)

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Function Documentation

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 = 0,
		double	optimizerForceTol = 1e-3,
		double	basinThresh = 5.0
	)

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).
	basinThresh	set the basin threshold for the DGeom force field, (this shouldn't normally be altered in client code).

Returns:

ID of the conformations added to the molecule, -1 if the emdedding failed

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 = 0,
		double	optimizerForceTol = 1e-3,
		double	basinThresh = 5.0
	)

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
	numConfs	Number of conformations to be generated
	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. Prunining is greedy; i.e. the first embedded conformation is retained and from then on only those that are atleast 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).
	basinThresh	set the basin threshold for the DGeom force field, (this shouldn't normally be altered in client code).

Returns:

an INT_VECT of conformer ids

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

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

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

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.

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.