Inheritance diagram for CDPL.Pharm.HydrophobicFeatureGenerator:

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

None	__init__ (Chem.MolecularGraph molgraph, Pharmacophore pharm)
	Perceives hydrophobic group features of the molecular graph a\ molgraph and adds them to the pharmacophore pharm. More...

None	__init__ (HydrophobicFeatureGenerator gen)
	Constructs a copy of the `HydrophobicFeatureGenerator` instance gen. More...

HydrophobicFeatureGenerator	assign (HydrophobicFeatureGenerator gen)
	Copies the `HydrophobicFeatureGenerator` instance gen. More...

None	setFeatureType (int type)
	Specifies the value of the feature type property that has to be set on newly generated features. More...

None	setFeatureGeometry (int geom)
	Specifies the value of the feature geometry property that has to be set on newly generated features. More...

None	setFeatureTolerance (float tol)
	Specifies the value of the feature tolerance property that has to be set on newly generated features. More...

None	setRingHydrophobicityThreshold (float thresh)
	Specifies the minimum summed hydrophobicity of the atoms in small rings that is required for the generation of a new feature. More...

None	setChainHydrophobicityThreshold (float thresh)
	Specifies the minimum summed hydrophobicity of the atoms in chain fragments that is required for the generation of a new feature. More...

None	setGroupHydrophobicityThreshold (float thresh)
	Specifies the minimum summed hydrophobicity of the atoms in group fragments that is required for the generation of a new feature. More...

int	getFeatureType ()
	Returns the value of the feature type property that gets set on newly generated features. More...

int	getFeatureGeometry ()
	Returns the value of the feature geometry property that gets set on newly generated features. More...

float	getFeatureTolerance ()
	Returns the value of the feature tolerance property that gets set on newly generated features. More...

float	getRingHydrophobicityThreshold ()
	Returns the minimum summed hydrophobicity of the atoms in small rings that is required for the generation of a new feature. More...

float	getChainHydrophobicityThreshold ()
	Returns the minimum summed hydrophobicity of the atoms in chain fragments that is required for the generation of a new feature. More...

float	getGroupHydrophobicityThreshold ()
	Returns the minimum summed hydrophobicity of the atoms in group fragments that is required for the generation of a new feature. More...

Public Member Functions inherited from CDPL.Pharm.PatternBasedFeatureGenerator
None	__init__ (PatternBasedFeatureGenerator gen)
	Constructs a copy of the `PatternBasedFeatureGenerator` instance gen. More...

None	addIncludePattern (Chem.MolecularGraph pattern, int type, float tol, int geom, float length=1.0)
	Appends a new feature include pattern to the current set of patterns. More...

None	addExcludePattern (Chem.MolecularGraph pattern)
	Appends a new feature include pattern to the current set of patterns. More...

None	clearIncludePatterns ()
	Clears the current set of include patterns.

None	clearExcludePatterns ()
	Clears the current set of exclude patterns.

PatternBasedFeatureGenerator	assign (PatternBasedFeatureGenerator gen)
	Replaces the current set include/exclude patterns by the patterns in the `PatternBasedFeatureGenerator` instance gen. More...

None	generate (Chem.MolecularGraph molgraph, Pharmacophore pharm)
	Perceives pharmacophore features according to the specified include/exclude patterns and adds them to the pharmacophore pharm. More...

None	__call__ (Chem.MolecularGraph molgraph, Pharmacophore pharm)

Public Member Functions inherited from CDPL.Pharm.FeatureGenerator
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

None	setAtom3DCoordinatesFunction (Chem.Atom3DCoordinatesFunction func)
	Specifies a function for the retrieval of atom 3D-coordinates. More...

Chem.Atom3DCoordinatesFunction	getAtom3DCoordinatesFunction ()
	Returns the function that was registered for the retrieval of atom 3D-coordinates. More...

FeatureGenerator	clone ()

Static Public Attributes
float	DEF_FEATURE_TOL = 1.5

int	DEF_FEATURE_TYPE = 1

int	DEF_FEATURE_GEOM = 1

float	DEF_HYD_THRESHOLD_RING = 2.0

float	DEF_HYD_THRESHOLD_CHAIN = 0.8

float	DEF_HYD_THRESHOLD_GROUP = 0.8

Properties
	featureType = property(getFeatureType, setFeatureType)

	featureGeometry = property(getFeatureGeometry, setFeatureGeometry)

	featureTolerance = property(getFeatureTolerance, setFeatureTolerance)

	ringHydThreshold = property(getRingHydrophobicityThreshold, setRingHydrophobicityThreshold)

	chainHydThreshold = property(getChainHydrophobicityThreshold, setChainHydrophobicityThreshold)

	groupHydThreshold = property(getGroupHydrophobicityThreshold, setGroupHydrophobicityThreshold)

Properties inherited from CDPL.Pharm.FeatureGenerator
	objectID = property(getObjectID)

	atomCoordsFunction = property(getAtom3DCoordinatesFunction, setAtom3DCoordinatesFunction)

Detailed Description

HydrophobicFeatureGenerator.

See also: [CATA]

Constructor & Destructor Documentation

◆ init() [1/2]

None CDPL.Pharm.HydrophobicFeatureGenerator.__init__	(	Chem.MolecularGraph	molgraph,
		Pharmacophore	pharm
	)

Perceives hydrophobic group features of the molecular graph a\ molgraph and adds them to the pharmacophore pharm.

Parameters

molgraph	The molecular graph for which to perceive the features.
pharm	The output pharmacophore where to add the generated features.

◆ init() [2/2]

None CDPL.Pharm.HydrophobicFeatureGenerator.__init__ ( HydrophobicFeatureGenerator gen )

Constructs a copy of the HydrophobicFeatureGenerator instance gen.

Parameters

gen	The `HydrophobicFeatureGenerator` to copy.

Member Function Documentation

◆ assign()

HydrophobicFeatureGenerator CDPL.Pharm.HydrophobicFeatureGenerator.assign ( HydrophobicFeatureGenerator gen )

Copies the HydrophobicFeatureGenerator instance gen.

Parameters

gen	The `HydrophobicFeatureGenerator` to copy.

Returns: self

◆ setFeatureType()

None CDPL.Pharm.HydrophobicFeatureGenerator.setFeatureType ( int type )

Specifies the value of the feature type property that has to be set on newly generated features.

Parameters

type	The value of the feature type property.

Note: The default type is specified by the constant HydrophobicFeatureGenerator.DEF_FEATURE_TYPE.

See also: FeatureProperty.TYPE

◆ setFeatureGeometry()

None CDPL.Pharm.HydrophobicFeatureGenerator.setFeatureGeometry ( int geom )

Specifies the value of the feature geometry property that has to be set on newly generated features.

Parameters

geom	The value of the feature geometry property.

Note: The default type is specified by the constant HydrophobicFeatureGenerator.DEF_FEATURE_GEOM.

See also: FeatureProperty.GEOMETRY

◆ setFeatureTolerance()

None CDPL.Pharm.HydrophobicFeatureGenerator.setFeatureTolerance ( float tol )

Specifies the value of the feature tolerance property that has to be set on newly generated features.

Parameters

tol	The value of the feature tolerance property.

Note: The default value is specified by the constant HydrophobicFeatureGenerator.DEF_FEATURE_TOL.

See also: FeatureProperty.TOLERANCE

◆ setRingHydrophobicityThreshold()

None CDPL.Pharm.HydrophobicFeatureGenerator.setRingHydrophobicityThreshold ( float thresh )

Specifies the minimum summed hydrophobicity of the atoms in small rings that is required for the generation of a new feature.

Parameters

thresh The minimum total atom hydrophobicity.

Note: The default value is specified by the constant HydrophobicFeatureGenerator.DEF_HYD_THRESHOLD_RING.

◆ setChainHydrophobicityThreshold()

None CDPL.Pharm.HydrophobicFeatureGenerator.setChainHydrophobicityThreshold ( float thresh )

Specifies the minimum summed hydrophobicity of the atoms in chain fragments that is required for the generation of a new feature.

Parameters

thresh The minimum total atom hydrophobicity.

Note: The default value is specified by the constant HydrophobicFeatureGenerator.DEF_HYD_THRESHOLD_CHAIN.

◆ setGroupHydrophobicityThreshold()

None CDPL.Pharm.HydrophobicFeatureGenerator.setGroupHydrophobicityThreshold ( float thresh )

Specifies the minimum summed hydrophobicity of the atoms in group fragments that is required for the generation of a new feature.

Parameters

thresh The minimum total atom hydrophobicity.

Note: The default value is specified by the constant HydrophobicFeatureGenerator.DEF_HYD_THRESHOLD_GROUP.

◆ getFeatureType()

int CDPL.Pharm.HydrophobicFeatureGenerator.getFeatureType ( )

Returns the value of the feature type property that gets set on newly generated features.

Returns: The used value of the feature type property.

See also: FeatureProperty.TYPE

◆ getFeatureGeometry()

int CDPL.Pharm.HydrophobicFeatureGenerator.getFeatureGeometry ( )

Returns the value of the feature geometry property that gets set on newly generated features.

Returns: The used value of the feature geometry property.

See also: FeatureProperty.GEOMETRY

◆ getFeatureTolerance()

float CDPL.Pharm.HydrophobicFeatureGenerator.getFeatureTolerance ( )

Returns the value of the feature tolerance property that gets set on newly generated features.

Returns: The value of the feature tolerance property.

See also: FeatureProperty.TOLERANCE

◆ getRingHydrophobicityThreshold()

float CDPL.Pharm.HydrophobicFeatureGenerator.getRingHydrophobicityThreshold ( )

Returns the minimum summed hydrophobicity of the atoms in small rings that is required for the generation of a new feature.

Returns: The specified minimum total atom hydrophobicity.

◆ getChainHydrophobicityThreshold()

float CDPL.Pharm.HydrophobicFeatureGenerator.getChainHydrophobicityThreshold ( )

Returns the minimum summed hydrophobicity of the atoms in chain fragments that is required for the generation of a new feature.

Returns: The specified minimum total atom hydrophobicity.

◆ getGroupHydrophobicityThreshold()

float CDPL.Pharm.HydrophobicFeatureGenerator.getGroupHydrophobicityThreshold ( )

Returns the minimum summed hydrophobicity of the atoms in group fragments that is required for the generation of a new feature.

Returns: The specified minimum total atom hydrophobicity.

Public Member Functions

Static Public Attributes

Properties

Detailed Description

Constructor & Destructor Documentation

◆ __init__() [1/2]

◆ __init__() [2/2]

Member Function Documentation

◆ assign()

◆ setFeatureType()

◆ setFeatureGeometry()

◆ setFeatureTolerance()

◆ setRingHydrophobicityThreshold()

◆ setChainHydrophobicityThreshold()

◆ setGroupHydrophobicityThreshold()

◆ getFeatureType()

◆ getFeatureGeometry()

◆ getFeatureTolerance()

◆ getRingHydrophobicityThreshold()

◆ getChainHydrophobicityThreshold()

◆ getGroupHydrophobicityThreshold()

◆ init() [1/2]

◆ init() [2/2]