CDPL.Pharm.HydrophobicAtomFeatureGenerator Class Reference

HydrophobicAtomFeatureGenerator. More...

Inheritance diagram for CDPL.Pharm.HydrophobicAtomFeatureGenerator:

Public Member Functions
None	__init__ ()
	Constructs the HydrophobicAtomFeatureGenerator 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__ (HydrophobicAtomFeatureGenerator gen)
	Constructs a copy of the HydrophobicAtomFeatureGenerator instance gen. More...
HydrophobicAtomFeatureGenerator	assign (HydrophobicAtomFeatureGenerator gen)
	Copies the HydrophobicAtomFeatureGenerator 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	setHydrophobicityThreshold (float thresh)
	Specifies the minimum hydrophobicity of an atom 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	getHydrophobicityThreshold ()
	Returns the minimum hydrophobicity of an atom 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 = 0.5

Properties
	featureType = property(getFeatureType, setFeatureType)
	featureGeometry = property(getFeatureGeometry, setFeatureGeometry)
	featureTolerance = property(getFeatureTolerance, setFeatureTolerance)
	hydThreshold = property(getHydrophobicityThreshold, setHydrophobicityThreshold)
Properties inherited from CDPL.Pharm.FeatureGenerator
	objectID = property(getObjectID)
	atomCoordsFunction = property(getAtom3DCoordinatesFunction, setAtom3DCoordinatesFunction)

Detailed Description

HydrophobicAtomFeatureGenerator.

See also

[CATA]

Constructor & Destructor Documentation

__init__() [1/2]

None CDPL.Pharm.HydrophobicAtomFeatureGenerator.__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.HydrophobicAtomFeatureGenerator.__init__

(

HydrophobicAtomFeatureGenerator

gen

)

Constructs a copy of the HydrophobicAtomFeatureGenerator instance gen.

Parameters

gen	The HydrophobicAtomFeatureGenerator to copy.

Member Function Documentation

assign()

HydrophobicAtomFeatureGenerator CDPL.Pharm.HydrophobicAtomFeatureGenerator.assign

(

HydrophobicAtomFeatureGenerator

gen

)

Copies the HydrophobicAtomFeatureGenerator instance gen.

Parameters

gen	The HydrophobicAtomFeatureGenerator to copy.

Returns

self

setFeatureType()

None CDPL.Pharm.HydrophobicAtomFeatureGenerator.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 HydrophobicAtomFeatureGenerator.DEF_FEATURE_TYPE.

See also

FeatureProperty.TYPE

setFeatureGeometry()

None CDPL.Pharm.HydrophobicAtomFeatureGenerator.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 HydrophobicAtomFeatureGenerator.DEF_FEATURE_GEOM.

See also

FeatureProperty.GEOMETRY

setFeatureTolerance()

None CDPL.Pharm.HydrophobicAtomFeatureGenerator.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 HydrophobicAtomFeatureGenerator.DEF_FEATURE_TOL.

See also

FeatureProperty.TOLERANCE

setHydrophobicityThreshold()

None CDPL.Pharm.HydrophobicAtomFeatureGenerator.setHydrophobicityThreshold

(

float

thresh

)

Specifies the minimum hydrophobicity of an atom that is required for the generation of a new feature.

Parameters

thresh

The minimum atom hydrophobicity.

Note

The default value is specified by the constant HydrophobicAtomFeatureGenerator.DEF_HYD_THRESHOLD.

getFeatureType()

int CDPL.Pharm.HydrophobicAtomFeatureGenerator.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.HydrophobicAtomFeatureGenerator.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.HydrophobicAtomFeatureGenerator.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

getHydrophobicityThreshold()

float CDPL.Pharm.HydrophobicAtomFeatureGenerator.getHydrophobicityThreshold

(

)

Returns the minimum hydrophobicity of an atom that is required for the generation of a new feature.

Returns

The specified minimum atom hydrophobicity.