CDPL.ConfGen.DGStructureGenerator Class Reference

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

Inheritance diagram for CDPL.ConfGen.DGStructureGenerator:

Public Member Functions
None	__init__ ()
	Constructs the DGStructureGenerator instance.
None	__init__ (DGStructureGenerator gen)
	Initializes a copy of the DGStructureGenerator instance gen. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
DGStructureGenerator	assign (DGStructureGenerator gen)
	Replaces the current state of self with a copy of the state of the DGStructureGenerator instance gen. More...
Util.BitSet	getExcludedHydrogenMask ()
	Returns the bit mask of hydrogens excluded from the coordinate-generation step. More...
None	setup (Chem.MolecularGraph molgraph)
	Sets up the generator for molgraph using geometry defaults derived from each atom's element number and hybridization state. More...
None	setup (Chem.MolecularGraph molgraph, ForceField.MMFF94InteractionData ia_data)
	Sets up the generator for molgraph using the supplied MMFF94 interaction data. More...
bool	generate (Math.Vector3DArray coords)
	Generates a 3D coordinate set that respects the configured distance constraints. More...
int	getNumAtomStereoCenters ()
	Returns the number of atom stereo centers in the set-up molecular graph. More...
int	getNumBondStereoCenters ()
	Returns the number of bond stereo centers in the set-up molecular graph. More...
bool	checkAtomConfigurations (Math.Vector3DArray coords)
	Validates the per-atom stereo-configurations of coords against the perceived stereo descriptors. More...
bool	checkBondConfigurations (Math.Vector3DArray coords)
	Validates the per-bond stereo-configurations of coords against the perceived stereo descriptors. More...
DGStructureGeneratorSettings	getSettings ()
	Returns the current generator settings. More...
DGConstraintGenerator	getConstraintGenerator ()
	Returns the embedded constraint generator used to produce the distance/volume constraints. More...

Properties
	objectID = property(getObjectID)
	numAtomStereoCenters = property(getNumAtomStereoCenters)
	numBondStereoCenters = property(getNumBondStereoCenters)
	settings = property(getSettings)
	constraintGenerator = property(getConstraintGenerator)
	exclHydrogenMask = property(getExcludedHydrogenMask)

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

__init__()

None CDPL.ConfGen.DGStructureGenerator.__init__

(

DGStructureGenerator

gen

)

Initializes a copy of the DGStructureGenerator instance gen.

Parameters

gen	The DGStructureGenerator instance to copy.

Member Function Documentation

getObjectID()

int CDPL.ConfGen.DGStructureGenerator.getObjectID

(

)

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

Different Python DGStructureGenerator 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 DGStructureGenerator 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()

DGStructureGenerator CDPL.ConfGen.DGStructureGenerator.assign

(

DGStructureGenerator

gen

)

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

Parameters

gen	The DGStructureGenerator instance to copy.

Returns

self

getExcludedHydrogenMask()

Util.BitSet CDPL.ConfGen.DGStructureGenerator.getExcludedHydrogenMask

(

)

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

Returns

A reference to the bit mask.

setup() [1/2]

None CDPL.ConfGen.DGStructureGenerator.setup

(

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() [2/2]

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

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.

getNumAtomStereoCenters()

int CDPL.ConfGen.DGStructureGenerator.getNumAtomStereoCenters

(

)

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

Returns

The atom stereo-center count.

getNumBondStereoCenters()

int CDPL.ConfGen.DGStructureGenerator.getNumBondStereoCenters

(

)

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

Returns

The bond stereo-center count.

checkAtomConfigurations()

bool CDPL.ConfGen.DGStructureGenerator.checkAtomConfigurations

(

Math.Vector3DArray

coords

)

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

)

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.

getSettings()

DGStructureGeneratorSettings CDPL.ConfGen.DGStructureGenerator.getSettings

(

)

Returns the current generator settings.

Returns

A reference to the settings.

getConstraintGenerator()

DGConstraintGenerator CDPL.ConfGen.DGStructureGenerator.getConstraintGenerator

(

)

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

Returns

A reference to the constraint generator.