CDPL::ConfGen::DGStructureGenerator Class Reference

Distance-geometry-based generation of raw 3D structures for molecular graphs. More...

#include <DGStructureGenerator.hpp>

Public Member Functions
	DGStructureGenerator ()
	Constructs the DGStructureGenerator instance. More...
DGStructureGeneratorSettings &	getSettings ()
	Returns the current generator settings (mutable). More...
const DGStructureGeneratorSettings &	getSettings () const
	Returns the current generator settings. More...
const Util::BitSet &	getExcludedHydrogenMask () const
	Returns the bit mask of hydrogens excluded from the coordinate-generation step. More...
void	setup (const Chem::MolecularGraph &molgraph)
	Sets up the generator for molgraph using geometry defaults derived from each atom's element number and hybridization state. More...
void	setup (const Chem::MolecularGraph &molgraph, const ForceField::MMFF94InteractionData &ia_data)
	Sets up the generator for molgraph using the supplied MMFF94 interaction data. More...
void	setup (const Chem::MolecularGraph &molgraph, const Chem::FragmentList &fixed_substr_frags, const Math::Vector3DArray &fixed_substr_coords)
	Sets up the generator for molgraph while keeping the substructure fragments in fixed_substr_frags at the supplied 3D coordinates. More...
void	setup (const Chem::MolecularGraph &molgraph, const ForceField::MMFF94InteractionData &ia_data, const Chem::FragmentList &fixed_substr_frags, const Math::Vector3DArray &fixed_substr_coords)
	Sets up the generator for molgraph using the supplied MMFF94 interaction data and fixed-substructure data. More...
bool	generate (Math::Vector3DArray &coords)
	Generates a 3D coordinate set that respects the configured distance constraints. More...
bool	checkAtomConfigurations (Math::Vector3DArray &coords) const
	Validates the per-atom stereo-configurations of coords against the perceived stereo descriptors. More...
bool	checkBondConfigurations (Math::Vector3DArray &coords) const
	Validates the per-bond stereo-configurations of coords against the perceived stereo descriptors. More...
std::size_t	getNumAtomStereoCenters () const
	Returns the number of atom stereo centers in the set-up molecular graph. More...
std::size_t	getNumBondStereoCenters () const
	Returns the number of bond stereo centers in the set-up molecular graph. More...
const DGConstraintGenerator &	getConstraintGenerator () const
	Returns the embedded constraint generator used to produce the distance/volume constraints. More...

Detailed Description

Distance-geometry-based generation of raw 3D structures for molecular graphs.

Constraints are produced by an embedded ConfGen::DGConstraintGenerator and used to embed the coordinates via a two-phase Util::DG3DCoordinatesGenerator pipeline. After generation, atom and bond stereo configurations can be validated against the perceived stereo descriptors.

Constructor & Destructor Documentation

DGStructureGenerator()

CDPL::ConfGen::DGStructureGenerator::DGStructureGenerator

(

)

Constructs the DGStructureGenerator instance.

Member Function Documentation

getSettings() [1/2]

DGStructureGeneratorSettings& CDPL::ConfGen::DGStructureGenerator::getSettings

(

)

Returns the current generator settings (mutable).

Returns

A reference to the settings.

getSettings() [2/2]

const DGStructureGeneratorSettings& CDPL::ConfGen::DGStructureGenerator::getSettings

(

)

const

Returns the current generator settings.

Returns

A const reference to the settings.

getExcludedHydrogenMask()

const Util::BitSet& CDPL::ConfGen::DGStructureGenerator::getExcludedHydrogenMask

(

)

const

Returns the bit mask of hydrogens excluded from the coordinate-generation step.

Returns

A const reference to the bit mask.

setup() [1/4]

void CDPL::ConfGen::DGStructureGenerator::setup

(

const Chem::MolecularGraph &

molgraph

)

Sets up the generator for molgraph using geometry defaults derived from each atom's element number and hybridization state.

No MMFF94 parameterization is carried out; reference bond lengths and angles are taken from element-/hybridization-based lookup tables.

Parameters

molgraph

The input molecular graph.

setup() [2/4]

void CDPL::ConfGen::DGStructureGenerator::setup	(	const Chem::MolecularGraph &	molgraph,
		const ForceField::MMFF94InteractionData &	ia_data
	)

Sets up the generator for molgraph using the supplied MMFF94 interaction data.

Parameters

molgraph	The input molecular graph.
ia_data	The pre-computed MMFF94 interaction data.

setup() [3/4]

void CDPL::ConfGen::DGStructureGenerator::setup	(	const Chem::MolecularGraph &	molgraph,
		const Chem::FragmentList &	fixed_substr_frags,
		const Math::Vector3DArray &	fixed_substr_coords
	)

Sets up the generator for molgraph while keeping the substructure fragments in fixed_substr_frags at the supplied 3D coordinates.

Parameters

molgraph	The input molecular graph.
fixed_substr_frags	The substructure fragments that must retain their 3D coordinates.
fixed_substr_coords	The 3D coordinates assigned to the fixed substructures.

Since

1.1

setup() [4/4]

void CDPL::ConfGen::DGStructureGenerator::setup	(	const Chem::MolecularGraph &	molgraph,
		const ForceField::MMFF94InteractionData &	ia_data,
		const Chem::FragmentList &	fixed_substr_frags,
		const Math::Vector3DArray &	fixed_substr_coords
	)

Sets up the generator for molgraph using the supplied MMFF94 interaction data and fixed-substructure data.

Parameters

molgraph	The input molecular graph.
ia_data	The pre-computed MMFF94 interaction data.
fixed_substr_frags	The substructure fragments that must retain their 3D coordinates.
fixed_substr_coords	The 3D coordinates assigned to the fixed substructures.

Since

1.1

generate()

bool CDPL::ConfGen::DGStructureGenerator::generate

(

Math::Vector3DArray &

coords

)

Generates a 3D coordinate set that respects the configured distance constraints.

Parameters

coords

The output 3D coordinate array.

Returns

true if the embedding succeeded, and false otherwise.

checkAtomConfigurations()

bool CDPL::ConfGen::DGStructureGenerator::checkAtomConfigurations

(

Math::Vector3DArray &

coords

)

const

Validates the per-atom stereo-configurations of coords against the perceived stereo descriptors.

Parameters

coords

The 3D coordinates to test.

Returns

true if all per-atom stereo-configurations are valid, and false otherwise.

checkBondConfigurations()

bool CDPL::ConfGen::DGStructureGenerator::checkBondConfigurations

(

Math::Vector3DArray &

coords

)

const

Validates the per-bond stereo-configurations of coords against the perceived stereo descriptors.

Parameters

coords

The 3D coordinates to test.

Returns

true if all per-bond stereo-configurations are valid, and false otherwise.

getNumAtomStereoCenters()

std::size_t CDPL::ConfGen::DGStructureGenerator::getNumAtomStereoCenters

(

)

const

Returns the number of atom stereo centers in the set-up molecular graph.

Returns

The atom stereo-center count.

getNumBondStereoCenters()

std::size_t CDPL::ConfGen::DGStructureGenerator::getNumBondStereoCenters

(

)

const

Returns the number of bond stereo centers in the set-up molecular graph.

Returns

The bond stereo-center count.

getConstraintGenerator()

const DGConstraintGenerator& CDPL::ConfGen::DGStructureGenerator::getConstraintGenerator

(

)

const

Returns the embedded constraint generator used to produce the distance/volume constraints.

Returns

A const reference to the constraint generator.

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The documentation for this class was generated from the following file:

• DGStructureGenerator.hpp