Classes
class	BoundsMatrix
	Class to store the distance bound. More...

class	ChiralSet
	Class used to store a quartet of points and chiral volume bounds on them. More...

class	ChiralViolationContrib

class	DistViolationContrib

class	FourthDimContrib

Typedefs
typedef boost::shared_ptr< BoundsMatrix >	BoundsMatPtr

typedef boost::shared_ptr< ChiralSet >	ChiralSetPtr

typedef std::vector< ChiralSetPtr >	VECT_CHIRALSET

Functions
double	pickRandomDistMat (const BoundsMatrix &mmat, RDNumeric::SymmMatrix< double > &distmat, int seed=-1)

double	pickRandomDistMat (const BoundsMatrix &mmat, RDNumeric::SymmMatrix< double > &distmat, RDKit::double_source_type &rng)

bool	computeInitialCoords (const RDNumeric::SymmMatrix< double > &distmat, RDGeom::PointPtrVect &positions, bool randNegEig=false, unsigned int numZeroFail=2, int seed=-1)
	Compute an initial embedded in 3D based on a distance matrix. More...

bool	computeInitialCoords (const RDNumeric::SymmMatrix< double > &distmat, RDGeom::PointPtrVect &positions, RDKit::double_source_type &rng, bool randNegEig=false, unsigned int numZeroFail=2)

bool	computeRandomCoords (RDGeom::PointPtrVect &positions, double boxSize, int seed=-1)
	places atoms randomly in a box More...

bool	computeRandomCoords (RDGeom::PointPtrVect &positions, double boxSize, RDKit::double_source_type &rng)

ForceFields::ForceField *	constructForceField (const BoundsMatrix &mmat, RDGeom::PointPtrVect &positions, const VECT_CHIRALSET &csets, double weightChiral=1.0, double weightFourthDim=0.1, std::map< std::pair< int, int >, double > *extraWeights=0, double basinSizeTol=5.0)
	Setup the error function for violation of distance bounds as a forcefield. More...

ForceFields::ForceField *	construct3DForceField (const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions, const std::vector< std::pair< int, int > > &bonds, const std::vector< std::vector< int > > &angles, const std::vector< std::vector< int > > &expTorsionAtoms, const std::vector< std::pair< std::vector< int >, std::vector< double > > > &expTorsionAngles, const std::vector< std::vector< int > > &improperAtoms, const std::vector< int > &atomNums)
	Force field with experimental torsion angle preferences and 1-2/1-3 distance. More...

ForceFields::ForceField *	constructPlain3DForceField (const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions, const std::vector< std::pair< int, int > > &bonds, const std::vector< std::vector< int > > &angles, const std::vector< std::vector< int > > &expTorsionAtoms, const std::vector< std::pair< std::vector< int >, std::vector< double > > > &expTorsionAngles, const std::vector< int > &atomNums)
	Force field with experimental torsion angle preferences and 1-2/1-3 distance. More...

bool	triangleSmoothBounds (BoundsMatrix *boundsMat, double tol=0.)

bool	triangleSmoothBounds (BoundsMatPtr boundsMat, double tol=0.)

Typedef Documentation

◆ BoundsMatPtr

typedef boost::shared_ptr<BoundsMatrix> DistGeom::BoundsMatPtr

Definition at line 116 of file BoundsMatrix.h.

◆ ChiralSetPtr

typedef boost::shared_ptr<ChiralSet> DistGeom::ChiralSetPtr

Definition at line 53 of file ChiralSet.h.

◆ VECT_CHIRALSET

typedef std::vector<ChiralSetPtr> DistGeom::VECT_CHIRALSET

Definition at line 54 of file ChiralSet.h.

Function Documentation

◆ computeInitialCoords() [1/2]

bool DistGeom::computeInitialCoords	(	const RDNumeric::SymmMatrix< double > &	distmat,
		RDGeom::PointPtrVect &	positions,
		bool	randNegEig = `false`,
		unsigned int	numZeroFail = `2`,
		int	seed = `-1`
	)

Compute an initial embedded in 3D based on a distance matrix.

This function follows the embed algorithm mentioned in "Distance Geometry and Molecular Conformation" by G.M.Crippen and T.F.Havel (pages 312-313)

Parameters

distmat	Distance matrix
positions	A vector of pointers to Points to write out the resulting coordinates
randNegEig	If set to true and if any of the eigen values are negative, we will pick the corresponding components of the coordinates at random
numZeroFail	Fail embedding is more this many (or more) eigen values are zero
seed	the random number seed to use

Returns: true if the embedding was successful

◆ computeInitialCoords() [2/2]

bool DistGeom::computeInitialCoords	(	const RDNumeric::SymmMatrix< double > &	distmat,
		RDGeom::PointPtrVect &	positions,
		RDKit::double_source_type &	rng,
		bool	randNegEig = `false`,
		unsigned int	numZeroFail = `2`
	)

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

◆ computeRandomCoords() [1/2]

bool DistGeom::computeRandomCoords	(	RDGeom::PointPtrVect &	positions,
		double	boxSize,
		int	seed = `-1`
	)

places atoms randomly in a box

Parameters

positions	A vector of pointers to Points to write out the resulting coordinates
boxSize	the side-length of the cubic box
seed	the random number seed to use

Returns: true if the coordinate generation was successful

◆ computeRandomCoords() [2/2]

bool DistGeom::computeRandomCoords	(	RDGeom::PointPtrVect &	positions,
		double	boxSize,
		RDKit::double_source_type &	rng
	)

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

◆ construct3DForceField()

ForceFields::ForceField* DistGeom::construct3DForceField	(	const BoundsMatrix &	mmat,
		RDGeom::Point3DPtrVect &	positions,
		const std::vector< std::pair< int, int > > &	bonds,
		const std::vector< std::vector< int > > &	angles,
		const std::vector< std::vector< int > > &	expTorsionAtoms,
		const std::vector< std::pair< std::vector< int >, std::vector< double > > > &	expTorsionAngles,
		const std::vector< std::vector< int > > &	improperAtoms,
		const std::vector< int > &	atomNums
	)

Force field with experimental torsion angle preferences and 1-2/1-3 distance.

Parameters

mmat	Distance bounds matrix
positions	A vector of pointers to 3D Points to write out the resulting coordinates
bonds	A list of 1-2 partners (bonds)
angles	A list of 1-3 partners (angles)
expTorsionAtoms	A list of groups of 4 atom indices for experimental torsions
expTorsionAngles	A list of corresponding torsion angle-potential parameters
improperAtoms	A list of groups of 4 atom indices for inversion terms
atomNums	A list of atomic numbers for all atoms in the molecule

Returns: a pointer to a ForceField suitable for imposing experimental torsion angle preferences NOTE: the caller is responsible for deleting this force field.

◆ constructForceField()

ForceFields::ForceField* DistGeom::constructForceField	(	const BoundsMatrix &	mmat,
		RDGeom::PointPtrVect &	positions,
		const VECT_CHIRALSET &	csets,
		double	weightChiral = `1.0`,
		double	weightFourthDim = `0.1`,
		std::map< std::pair< int, int >, double > *	extraWeights = `0`,
		double	basinSizeTol = `5.0`
	)

Setup the error function for violation of distance bounds as a forcefield.

This is based on function E3 on page 311 of "Distance Geometry in Molecular Modeling" Jeffrey M.Blaney and J.Scott Dixon, Review in Computational Chemistry, Volume V

Parameters

mmat	Distance bounds matrix
positions	A vector of pointers to Points to write out the resulting coordinates
csets	The vector of chiral points (type: ChiralSet)
weightChiral	weight to be used to enforce chirality
weightFourthDim	another chiral weight
extraWeights	an optional set of weights for distance bounds violations
basinSizeTol	Optional: any distance bound with a basin (distance between max and min bounds) larger than this value will not be included in the force field used to cleanup the structure.

Returns: a pointer to a ForceField suitable for cleaning up the violations. NOTE: the caller is responsible for deleting this force field.

◆ constructPlain3DForceField()

ForceFields::ForceField* DistGeom::constructPlain3DForceField	(	const BoundsMatrix &	mmat,
		RDGeom::Point3DPtrVect &	positions,
		const std::vector< std::pair< int, int > > &	bonds,
		const std::vector< std::vector< int > > &	angles,
		const std::vector< std::vector< int > > &	expTorsionAtoms,
		const std::vector< std::pair< std::vector< int >, std::vector< double > > > &	expTorsionAngles,
		const std::vector< int > &	atomNums
	)

Force field with experimental torsion angle preferences and 1-2/1-3 distance.

Parameters

mmat	Distance bounds matrix
positions	A vector of pointers to 3D Points to write out the resulting coordinates
bonds	A list of 1-2 partners (bonds)
angles	A list of 1-3 partners (angles)
expTorsionAtoms	A list of groups of 4 atom indices for experimental torsions
expTorsionAngles	A list of corresponding torsion angle-potential parameters
atomNums	A list of atomic numbers for all atoms in the molecule

Returns: a pointer to a ForceField suitable for imposing experimental torsion angle preferences NOTE: the caller is responsible for deleting this force field.

◆ pickRandomDistMat() [1/2]

double DistGeom::pickRandomDistMat	(	const BoundsMatrix &	mmat,
		RDNumeric::SymmMatrix< double > &	distmat,
		int	seed = `-1`
	)

Pick a distance matrix at random such that the distance satisfy the bounds in the BoundsMatrix

Parameters

mmat	Bounds matrix
distmat	Storage for randomly chosen distances
seed	the random number seed to use

Returns: the largest element of the distance matrix

◆ pickRandomDistMat() [2/2]

double DistGeom::pickRandomDistMat	(	const BoundsMatrix &	mmat,
		RDNumeric::SymmMatrix< double > &	distmat,
		RDKit::double_source_type &	rng
	)

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

◆ triangleSmoothBounds() [1/2]

bool DistGeom::triangleSmoothBounds	(	BoundsMatrix *	boundsMat,
		double	tol = `0.`
	)

Smooth the upper and lower bound in a metric matrix so that triangle inequality is not violated

This an implementation of the O(N^3) algorithm given on pages 252-253 of "Distance Geometry and Molecular Conformation" by G.M.Crippen and T.F.Havel Research Studies Press, 1988. There are other (slightly) more implementations (see pages 301-302 in the above book), but that is for later

Parameters

boundsMat	A pointer to the distance bounds matrix
tol	a tolerance (percent) for errors in the smoothing process

◆ triangleSmoothBounds() [2/2]

bool DistGeom::triangleSmoothBounds	(	BoundsMatPtr	boundsMat,
		double	tol = `0.`
	)

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

Classes

Typedefs

Functions

Typedef Documentation

◆ BoundsMatPtr

◆ ChiralSetPtr

◆ VECT_CHIRALSET

Function Documentation

◆ computeInitialCoords() [1/2]

◆ computeInitialCoords() [2/2]

◆ computeRandomCoords() [1/2]

◆ computeRandomCoords() [2/2]

◆ construct3DForceField()

◆ constructForceField()

◆ constructPlain3DForceField()

◆ pickRandomDistMat() [1/2]

◆ pickRandomDistMat() [2/2]

◆ triangleSmoothBounds() [1/2]

◆ triangleSmoothBounds() [2/2]