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

Inheritance diagram for CDPL.ConfGen.DGConstraintGenerator:

Classes
class	StereoCenterData
	Pair holding an atom or bond index plus the associated stereo descriptor. More...

Public Member Functions
None	__init__ ()
	Constructs the `DGConstraintGenerator` instance.

None	__init__ (DGConstraintGenerator gen)
	Initializes a copy of the `DGConstraintGenerator` instance gen. More...

int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

DGConstraintGenerator	assign (DGConstraintGenerator gen)
	Replaces the current state of self with a copy of the state of the `DGConstraintGenerator` instance gen. More...

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

None	setup (Chem.MolecularGraph molgraph)
	Initializes the generator for the molecular graph molgraph using default geometry data. More...

None	setup (Chem.MolecularGraph molgraph, ForceField.MMFF94InteractionData ia_data)
	Initializes the generator for the molecular graph molgraph using bond lengths and angles obtained from ia_data. More...

int	getNumAtomStereoCenters ()
	Returns the number of registered atom stereo centers. More...

StereoCenterData	getAtomStereoCenterData (int idx)
	Returns the stereo-center data for the atom stereo center at index idx. More...

StereoCenterData	getBondStereoCenterData (int idx)
	Returns the stereo-center data for the bond stereo center at index idx. More...

int	getNumBondStereoCenters ()
	Returns the number of registered bond stereo centers. More...

None	addBondLengthConstraints (Util.DG3DCoordinatesGenerator coords_gen)
	Adds bond-length distance constraints to coords_gen. More...

None	addBondAngleConstraints (Util.DG3DCoordinatesGenerator coords_gen)
	Adds bond-angle (1,3) distance constraints to coords_gen. More...

None	add14DistanceConstraints (Util.DG3DCoordinatesGenerator coords_gen)
	Adds 1,4-distance constraints (cis/trans bounds) to coords_gen. More...

None	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...

None	addAtomPlanarityConstraints (Util.DG3DCoordinatesGenerator coords_gen)
	Adds planarity (zero-volume) constraints for sp2-hybridized / aromatic atoms to coords_gen. More...

None	addBondPlanarityConstraints (Util.DG3DCoordinatesGenerator coords_gen)
	Adds planarity (zero-volume) constraints for double and aromatic bonds to coords_gen. More...

None	addAtomConfigurationConstraints (Util.DG3DCoordinatesGenerator coords_gen)
	Adds volume constraints enforcing the registered atom stereo-center configurations to coords_gen. More...

None	addBondConfigurationConstraints (Util.DG3DCoordinatesGenerator coords_gen)
	Adds distance and volume constraints enforcing the registered bond stereo-center configurations to coords_gen. More...

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

Properties
	objectID = property(getObjectID)

	settings = property(getSettings)

	numAtomStereoCenters = property(getNumAtomStereoCenters)

	numBondStereoCenters = property(getNumBondStereoCenters)

	exclHydrogenMask = property(getExcludedHydrogenMask)

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.

Constructor & Destructor Documentation

◆ init()

None CDPL.ConfGen.DGConstraintGenerator.__init__ ( DGConstraintGenerator gen )

Initializes a copy of the DGConstraintGenerator instance gen.

Parameters

gen	The `DGConstraintGenerator` instance to copy.

Member Function Documentation

◆ getObjectID()

int CDPL.ConfGen.DGConstraintGenerator.getObjectID ( )

Returns the numeric identifier (ID) of the wrapped C++ class instance.

Different Python DGConstraintGenerator instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two DGConstraintGenerator instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().

Returns: The numeric ID of the internally referenced C++ class instance.

◆ assign()

DGConstraintGenerator CDPL.ConfGen.DGConstraintGenerator.assign ( DGConstraintGenerator gen )

Replaces the current state of self with a copy of the state of the DGConstraintGenerator instance gen.

Parameters

gen	The `DGConstraintGenerator` instance to copy.

Returns: self

◆ getExcludedHydrogenMask()

Util.BitSet CDPL.ConfGen.DGConstraintGenerator.getExcludedHydrogenMask ( )

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

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

◆ setup() [1/2]

None CDPL.ConfGen.DGConstraintGenerator.setup ( 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]

None CDPL.ConfGen.DGConstraintGenerator.setup	(	Chem.MolecularGraph	molgraph,
		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.

◆ getNumAtomStereoCenters()

int CDPL.ConfGen.DGConstraintGenerator.getNumAtomStereoCenters ( )

Returns the number of registered atom stereo centers.

Returns: The number of atom stereo centers.

◆ getAtomStereoCenterData()

StereoCenterData CDPL.ConfGen.DGConstraintGenerator.getAtomStereoCenterData ( int idx )

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

Parameters

idx	The zero-based stereo-center index.

Returns: A 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()

StereoCenterData CDPL.ConfGen.DGConstraintGenerator.getBondStereoCenterData ( int idx )

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

Parameters

idx	The zero-based stereo-center index.

Returns: A 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].

◆ getNumBondStereoCenters()

int CDPL.ConfGen.DGConstraintGenerator.getNumBondStereoCenters ( )

Returns the number of registered bond stereo centers.

Returns: The number of bond stereo centers.

◆ addBondLengthConstraints()

None CDPL.ConfGen.DGConstraintGenerator.addBondLengthConstraints ( Util.DG3DCoordinatesGenerator coords_gen )

Adds bond-length distance constraints to coords_gen.

Parameters