Constructs geometric constraints (distance, planarity, volume) for distance-geometry-based 3D structure generation. More...

#include <DGConstraintGenerator.hpp>

Public Types
typedef std::pair< std::size_t, Chem::StereoDescriptor >	StereoCenterData
	Pair holding an atom or bond index plus the associated stereo descriptor. More...

typedef StereoCenterDataArray::const_iterator	ConstStereoCenterDataIterator
	A constant iterator over StereoCenterData entries. More...

Public Member Functions
	DGConstraintGenerator ()
	Constructs the `DGConstraintGenerator` instance. More...

DGConstraintGeneratorSettings &	getSettings ()
	Returns a reference to the constraint-generation settings. More...

const DGConstraintGeneratorSettings &	getSettings () const
	Returns a `const` reference to the constraint-generation settings. More...

void	addAtomStereoCenter (const Chem::Atom &atom, const Chem::StereoDescriptor &descr)
	Registers an atom stereo center to be constrained. More...

void	addBondStereoCenter (const Chem::Bond &bond, const Chem::StereoDescriptor &descr)
	Registers a bond stereo center to be constrained. More...

void	setup (const Chem::MolecularGraph &molgraph)
	Initializes the generator for the molecular graph molgraph using default geometry data. More...

void	setup (const Chem::MolecularGraph &molgraph, const ForceField::MMFF94InteractionData &ia_data)
	Initializes the generator for the molecular graph molgraph using bond lengths and angles obtained from ia_data. More...

const Util::BitSet &	getExcludedHydrogenMask () const
	Returns the bit mask of hydrogen atoms that have been excluded from constraint generation. More...

std::size_t	getNumAtomStereoCenters () const
	Returns the number of registered atom stereo centers. More...

std::size_t	getNumBondStereoCenters () const
	Returns the number of registered bond stereo centers. More...

const StereoCenterData &	getAtomStereoCenterData (std::size_t idx) const
	Returns the stereo-center data for the atom stereo center at index idx. More...

const StereoCenterData &	getBondStereoCenterData (std::size_t idx) const
	Returns the stereo-center data for the bond stereo center at index idx. More...

ConstStereoCenterDataIterator	getAtomStereoCenterDataBegin () const
	Returns a constant iterator pointing to the first atom stereo center. More...

ConstStereoCenterDataIterator	getAtomStereoCenterDataEnd () const
	Returns a constant iterator pointing one past the last atom stereo center. More...

ConstStereoCenterDataIterator	getBondStereoCenterDataBegin () const
	Returns a constant iterator pointing to the first bond stereo center. More...

ConstStereoCenterDataIterator	getBondStereoCenterDataEnd () const
	Returns a constant iterator pointing one past the last bond stereo center. More...

void	addFixedSubstructureConstraints (const Chem::AtomContainer &atoms, const Math::Vector3DArray &coords, Util::DG3DCoordinatesGenerator &coords_gen)
	Adds distance and volume constraints that fix the supplied substructure to the given coordinates. More...

void	addBondLengthConstraints (Util::DG3DCoordinatesGenerator &coords_gen)
	Adds bond-length distance constraints to coords_gen. More...

void	addBondAngleConstraints (Util::DG3DCoordinatesGenerator &coords_gen)
	Adds bond-angle (1,3) distance constraints to coords_gen. More...

void	add14DistanceConstraints (Util::DG3DCoordinatesGenerator &coords_gen)
	Adds 1,4-distance constraints (cis/trans bounds) to coords_gen. More...

void	addDefaultDistanceConstraints (Util::DG3DCoordinatesGenerator &coords_gen)
	Adds default (Van der Waals-derived) lower/upper distance constraints between all non-bonded atom pairs to coords_gen. More...

void	addAtomConfigurationConstraints (Util::DG3DCoordinatesGenerator &coords_gen)
	Adds volume constraints enforcing the registered atom stereo-center configurations to coords_gen. More...

void	addBondConfigurationConstraints (Util::DG3DCoordinatesGenerator &coords_gen)
	Adds distance and volume constraints enforcing the registered bond stereo-center configurations to coords_gen. More...

void	addAtomPlanarityConstraints (Util::DG3DCoordinatesGenerator &coords_gen)
	Adds planarity (zero-volume) constraints for sp2-hybridized / aromatic atoms to coords_gen. More...

void	addBondPlanarityConstraints (Util::DG3DCoordinatesGenerator &coords_gen)
	Adds planarity (zero-volume) constraints for double and aromatic bonds to coords_gen. More...

Detailed Description

Constructs geometric constraints (distance, planarity, volume) for distance-geometry-based 3D structure generation.

Given a molecular graph (and optionally an MMFF94 force field interaction parameter set) the generator derives ideal bond lengths, bond angles and 1,4-distances, identifies atom and bond stereo centers and emits the corresponding constraints into a Util::DG3DCoordinatesGenerator. The constraint set is used by ConfGen::DGStructureGenerator to produce a 3D embedding of the molecular graph.

Member Typedef Documentation

◆ StereoCenterData

typedef std::pair<std::size_t, Chem::StereoDescriptor> CDPL::ConfGen::DGConstraintGenerator::StereoCenterData

Pair holding an atom or bond index plus the associated stereo descriptor.

◆ ConstStereoCenterDataIterator

typedef StereoCenterDataArray::const_iterator CDPL::ConfGen::DGConstraintGenerator::ConstStereoCenterDataIterator

A constant iterator over StereoCenterData entries.

Constructor & Destructor Documentation

◆ DGConstraintGenerator()

CDPL::ConfGen::DGConstraintGenerator::DGConstraintGenerator ( )

Constructs the DGConstraintGenerator instance.

Member Function Documentation

◆ getSettings() [1/2]

DGConstraintGeneratorSettings& CDPL::ConfGen::DGConstraintGenerator::getSettings ( )

Returns a reference to the constraint-generation settings.

Returns: A reference to the settings.

◆ getSettings() [2/2]

const DGConstraintGeneratorSettings& CDPL::ConfGen::DGConstraintGenerator::getSettings ( ) const

Returns a const reference to the constraint-generation settings.

Returns: A const reference to the settings.

◆ addAtomStereoCenter()

void CDPL::ConfGen::DGConstraintGenerator::addAtomStereoCenter	(	const Chem::Atom &	atom,
		const Chem::StereoDescriptor &	descr
	)

Registers an atom stereo center to be constrained.

Parameters

atom	The stereogenic atom.
descr	The stereo descriptor specifying the desired configuration.

◆ addBondStereoCenter()

void CDPL::ConfGen::DGConstraintGenerator::addBondStereoCenter	(	const Chem::Bond &	bond,
		const Chem::StereoDescriptor &	descr
	)

Registers a bond stereo center to be constrained.

Parameters

bond	The stereogenic bond.
descr	The stereo descriptor specifying the desired configuration.

◆ setup() [1/2]

void CDPL::ConfGen::DGConstraintGenerator::setup ( const Chem::MolecularGraph & molgraph )

Initializes the generator for the molecular graph molgraph using default geometry data.

Parameters

molgraph The molecular graph to process.

◆ setup() [2/2]

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

Initializes the generator for the molecular graph molgraph using bond lengths and angles obtained from ia_data.

Parameters

molgraph	The molecular graph to process.
ia_data	MMFF94 interaction data providing the reference bond lengths and angles.

◆ getExcludedHydrogenMask()

const Util::BitSet& CDPL::ConfGen::DGConstraintGenerator::getExcludedHydrogenMask ( ) const

Returns the bit mask of hydrogen atoms that have been excluded from constraint generation.

Returns: A const reference to the excluded-hydrogen bit mask.

◆ getNumAtomStereoCenters()

std::size_t CDPL::ConfGen::DGConstraintGenerator::getNumAtomStereoCenters ( ) const

Returns the number of registered atom stereo centers.

Returns: The number of atom stereo centers.

◆ getNumBondStereoCenters()

std::size_t CDPL::ConfGen::DGConstraintGenerator::getNumBondStereoCenters ( ) const

Returns the number of registered bond stereo centers.

Returns: The number of bond stereo centers.

◆ getAtomStereoCenterData()

const StereoCenterData& CDPL::ConfGen::DGConstraintGenerator::getAtomStereoCenterData ( std::size_t idx ) const

Returns the stereo-center data for the atom stereo center at index idx.

Parameters

idx	The zero-based stereo-center index.

Returns: A const reference to the stereo-center data.

Exceptions

Base::IndexError if the number of atom stereo centers is zero or idx is not in the range [0, getNumAtomStereoCenters() - 1].

◆ getBondStereoCenterData()

const StereoCenterData& CDPL::ConfGen::DGConstraintGenerator::getBondStereoCenterData ( std::size_t idx ) const

Returns the stereo-center data for the bond stereo center at index idx.

Parameters

idx	The zero-based stereo-center index.

Returns: A const reference to the stereo-center data.

Exceptions

Base::IndexError if the number of bond stereo centers is zero or idx is not in the range [0, getNumBondStereoCenters() - 1].

◆ getAtomStereoCenterDataBegin()

ConstStereoCenterDataIterator CDPL::ConfGen::DGConstraintGenerator::getAtomStereoCenterDataBegin ( ) const

Returns a constant iterator pointing to the first atom stereo center.

Returns: A constant iterator pointing to the first atom stereo center.

◆ getAtomStereoCenterDataEnd()

ConstStereoCenterDataIterator CDPL::ConfGen::DGConstraintGenerator::getAtomStereoCenterDataEnd ( ) const

Returns a constant iterator pointing one past the last atom stereo center.

Returns: A constant iterator pointing one past the last atom stereo center.

◆ getBondStereoCenterDataBegin()

ConstStereoCenterDataIterator CDPL::ConfGen::DGConstraintGenerator::getBondStereoCenterDataBegin ( ) const

Returns a constant iterator pointing to the first bond stereo center.

Returns: A constant iterator pointing to the first bond stereo center.

◆ getBondStereoCenterDataEnd()

ConstStereoCenterDataIterator CDPL::ConfGen::DGConstraintGenerator::getBondStereoCenterDataEnd ( ) const

Returns a constant iterator pointing one past the last bond stereo center.

Returns: A constant iterator pointing one past the last bond stereo center.

◆ addFixedSubstructureConstraints()

void CDPL::ConfGen::DGConstraintGenerator::addFixedSubstructureConstraints	(	const Chem::AtomContainer &	atoms,
		const Math::Vector3DArray &	coords,
		Util::DG3DCoordinatesGenerator &	coords_gen
	)

Adds distance and volume constraints that fix the supplied substructure to the given coordinates.

Parameters

atoms	The atoms whose positions shall be fixed.
coords	The 3D coordinates to fix the atoms to.
coords_gen	The coordinates generator to add the constraints to.

Since: 1.1

◆ addBondLengthConstraints()

void CDPL::ConfGen::DGConstraintGenerator::addBondLengthConstraints ( Util::DG3DCoordinatesGenerator & coords_gen )

Adds bond-length distance constraints to coords_gen.

Parameters