Generates Shape.GaussianShape instances from molecular graphs. More...

Inheritance diagram for CDPL.Shape.GaussianShapeGenerator:

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

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

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

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

None	setPharmacophoreGenerator (Pharm.PharmacophoreGenerator gen)
	Specifies the pharmacophore generator used when emitting pharmacophore shapes. More...

Pharm.PharmacophoreGenerator	getPharmacophoreGenerator ()
	Returns the currently configured pharmacophore generator. More...

Pharm.DefaultPharmacophoreGenerator	getDefaultPharmacophoreGenerator ()
	Returns the built-in default pharmacophore generator (mutable). More...

None	setAtomRadius (float radius)
	Sets the sphere radius used for all atoms (negative value: use atom-specific Van der Waals radii). More...

float	getAtomRadius ()
	Returns the currently configured atom sphere radius. More...

None	setAtomHardness (float hardness)
	Sets the Gaussian hardness used for all atom spheres. More...

float	getAtomHardness ()
	Returns the currently configured atom Gaussian hardness. More...

None	setFeatureRadius (float radius)
	Sets the sphere radius used for all features (negative value: use feature-specific tolerances). More...

float	getFeatureRadius ()
	Returns the currently configured feature sphere radius. More...

None	setFeatureHardness (float hardness)
	Sets the Gaussian hardness used for all feature spheres. More...

float	getFeatureHardness ()
	Returns the currently configured feature Gaussian hardness. More...

None	generatePharmacophoreShape (bool generate)
	Specifies whether a pharmacophore (feature-based) shape shall be generated. More...

bool	generatePharmacophoreShape ()
	Tells whether a pharmacophore (feature-based) shape is generated. More...

None	generateMoleculeShape (bool generate)
	Specifies whether a molecular (atom-based) shape shall be generated. More...

bool	generateMoleculeShape ()
	Tells whether a molecular (atom-based) shape is generated. More...

None	multiConformerMode (bool multi_conf)
	Specifies whether to emit one shape per conformer (instead of using the first conformer only). More...

bool	multiConformerMode ()
	Tells whether the generator runs in multi-conformer mode. More...

None	includeHydrogens (bool include)
	Specifies whether hydrogens are included when generating the molecular shape. More...

bool	includeHydrogens ()
	Tells whether hydrogens are included when generating the molecular shape. More...

GaussianShapeSet	generate (Chem.MolecularGraph molgraph)
	Generates the set of Gaussian shapes for molgraph. More...

GaussianShapeSet	getShapes ()
	Returns the shapes produced by the most recent call to generate(). More...

Properties
	objectID = property(getObjectID)

	pharmacophoreGenerator = property(getPharmacophoreGenerator, setPharmacophoreGenerator)

	defPharmacophoreGenerator = property(getDefaultPharmacophoreGenerator)

	shapes = property(getShapes)

	genPharmacophoreShape = property(generatePharmacophoreShape, generatePharmacophoreShape)

	genMoleculeShape = property(generateMoleculeShape, generateMoleculeShape)

	multiConfMode = property(multiConformerMode, multiConformerMode)

	incHydrogens = property(includeHydrogens, includeHydrogens)

	atomRadius = property(getAtomRadius, setAtomRadius)

	atomHardness = property(getAtomHardness, setAtomHardness)

	featureRadius = property(getFeatureRadius, setFeatureRadius)

	featureHardness = property(getFeatureHardness, setFeatureHardness)

Detailed Description

Generates Shape.GaussianShape instances from molecular graphs.

The generator can emit shape representations of the molecule itself (one sphere per atom), of a pharmacophore derived from the molecule (one sphere per feature), or both. In multi-conformer mode, one Gaussian shape is generated per conformer.

Constructor & Destructor Documentation

◆ init()

None CDPL.Shape.GaussianShapeGenerator.__init__ ( GaussianShapeGenerator gen )

Initializes a copy of the GaussianShapeGenerator instance gen.

Parameters

gen	The `GaussianShapeGenerator` instance to copy.

Member Function Documentation

◆ getObjectID()

int CDPL.Shape.GaussianShapeGenerator.getObjectID ( )

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

Different Python GaussianShapeGenerator 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 GaussianShapeGenerator 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()

GaussianShapeGenerator CDPL.Shape.GaussianShapeGenerator.assign ( GaussianShapeGenerator gen )

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

Parameters

gen	The `GaussianShapeGenerator` instance to copy.

Returns: self

◆ setPharmacophoreGenerator()

None CDPL.Shape.GaussianShapeGenerator.setPharmacophoreGenerator ( Pharm.PharmacophoreGenerator gen )

Specifies the pharmacophore generator used when emitting pharmacophore shapes.

Parameters

gen	The pharmacophore generator.

◆ getPharmacophoreGenerator()

Pharm.PharmacophoreGenerator CDPL.Shape.GaussianShapeGenerator.getPharmacophoreGenerator ( )

Returns the currently configured pharmacophore generator.

Returns: A reference to the pharmacophore generator.

◆ getDefaultPharmacophoreGenerator()

Pharm.DefaultPharmacophoreGenerator CDPL.Shape.GaussianShapeGenerator.getDefaultPharmacophoreGenerator ( )

Returns the built-in default pharmacophore generator (mutable).

Returns: A reference to the default pharmacophore generator.

◆ setAtomRadius()

None CDPL.Shape.GaussianShapeGenerator.setAtomRadius ( float radius )

Sets the sphere radius used for all atoms (negative value: use atom-specific Van der Waals radii).

Parameters

radius The new atom sphere radius.

◆ getAtomRadius()

float CDPL.Shape.GaussianShapeGenerator.getAtomRadius ( )

Returns the currently configured atom sphere radius.

Returns: The atom sphere radius.

◆ setAtomHardness()

None CDPL.Shape.GaussianShapeGenerator.setAtomHardness ( float hardness )

Sets the Gaussian hardness used for all atom spheres.

Parameters

hardness The new atom Gaussian hardness.

◆ getAtomHardness()

float CDPL.Shape.GaussianShapeGenerator.getAtomHardness ( )

Returns the currently configured atom Gaussian hardness.

Returns: The atom Gaussian hardness.

◆ setFeatureRadius()

None CDPL.Shape.GaussianShapeGenerator.setFeatureRadius ( float radius )

Sets the sphere radius used for all features (negative value: use feature-specific tolerances).

Parameters

radius The new feature sphere radius.

◆ getFeatureRadius()

float CDPL.Shape.GaussianShapeGenerator.getFeatureRadius ( )

Returns the currently configured feature sphere radius.

Returns: The feature sphere radius.

◆ setFeatureHardness()

None CDPL.Shape.GaussianShapeGenerator.setFeatureHardness ( float hardness )

Sets the Gaussian hardness used for all feature spheres.

Parameters

hardness The new feature Gaussian hardness.

◆ getFeatureHardness()

float CDPL.Shape.GaussianShapeGenerator.getFeatureHardness ( )

Returns the currently configured feature Gaussian hardness.

Returns: The feature Gaussian hardness.

◆ generatePharmacophoreShape() [1/2]

None CDPL.Shape.GaussianShapeGenerator.generatePharmacophoreShape ( bool generate )

Specifies whether a pharmacophore (feature-based) shape shall be generated.

Parameters

generate True to enable the generation of the pharmacophore shape, and False to disable it.

◆ generatePharmacophoreShape() [2/2]

bool CDPL.Shape.GaussianShapeGenerator.generatePharmacophoreShape ( )

Tells whether a pharmacophore (feature-based) shape is generated.

Returns: True if the pharmacophore shape is generated, and False otherwise.

◆ generateMoleculeShape() [1/2]

None CDPL.Shape.GaussianShapeGenerator.generateMoleculeShape ( bool generate )

Specifies whether a molecular (atom-based) shape shall be generated.

Parameters

generate True to enable the generation of the molecular shape, and False to disable it.

◆ generateMoleculeShape() [2/2]

bool CDPL.Shape.GaussianShapeGenerator.generateMoleculeShape ( )

Tells whether a molecular (atom-based) shape is generated.

Returns: True if the molecular shape is generated, and False otherwise.

◆ multiConformerMode() [1/2]

None CDPL.Shape.GaussianShapeGenerator.multiConformerMode ( bool multi_conf )

Specifies whether to emit one shape per conformer (instead of using the first conformer only).

Parameters

multi_conf True to enable multi-conformer mode, and False to use the first conformer only.

◆ multiConformerMode() [2/2]

bool CDPL.Shape.GaussianShapeGenerator.multiConformerMode ( )

Tells whether the generator runs in multi-conformer mode.

Returns: True if multi-conformer mode is enabled, and False otherwise.

◆ includeHydrogens() [1/2]

None CDPL.Shape.GaussianShapeGenerator.includeHydrogens ( bool include )

Specifies whether hydrogens are included when generating the molecular shape.

Parameters

include True to include hydrogens, and False to ignore them.

◆ includeHydrogens() [2/2]

bool CDPL.Shape.GaussianShapeGenerator.includeHydrogens ( )

Tells whether hydrogens are included when generating the molecular shape.

Returns: True if hydrogens are included, and False otherwise.

◆ generate()

GaussianShapeSet CDPL.Shape.GaussianShapeGenerator.generate ( Chem.MolecularGraph molgraph )

Generates the set of Gaussian shapes for molgraph.

Parameters

molgraph The molecular graph.

Returns: A reference to the generated Shape.GaussianShapeSet.

◆ getShapes()

GaussianShapeSet CDPL.Shape.GaussianShapeGenerator.getShapes ( )

Returns the shapes produced by the most recent call to generate().

Returns: A reference to the produced Shape.GaussianShapeSet.

Public Member Functions

Properties

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ getObjectID()

◆ assign()

◆ setPharmacophoreGenerator()

◆ getPharmacophoreGenerator()

◆ getDefaultPharmacophoreGenerator()

◆ setAtomRadius()

◆ getAtomRadius()

◆ setAtomHardness()

◆ getAtomHardness()

◆ setFeatureRadius()

◆ getFeatureRadius()

◆ setFeatureHardness()

◆ getFeatureHardness()

◆ generatePharmacophoreShape() [1/2]

◆ generatePharmacophoreShape() [2/2]

◆ generateMoleculeShape() [1/2]

◆ generateMoleculeShape() [2/2]

◆ multiConformerMode() [1/2]

◆ multiConformerMode() [2/2]

◆ includeHydrogens() [1/2]

◆ includeHydrogens() [2/2]

◆ generate()

◆ getShapes()

◆ init()