Abstract base class for mutable containers of Pharm.Feature instances representing a pharmacophore model. More...

Inheritance diagram for CDPL.Pharm.Pharmacophore:

Public Member Functions
None	__init__ ()
	Initializes the `Pharmacophore` instance.

None	clear ()
	Removes all features and clears all properties of the pharmacophore.

Feature	addFeature ()
	Creates a new pharmacophore feature and adds it to the pharmacophore. More...

None	removeFeature (int idx)
	Removes the pharmacophore feature at the specified index. More...

None	copy (Pharmacophore pharm)
	Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the pharmacophore pharm. More...

None	copy (FeatureContainer cntnr)
	Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the feature container cntnr. More...

None	append (Pharmacophore pharm)
	Extends the current set of features by a copy of the features in the pharmacophore pharm. More...

None	append (FeatureContainer cntnr)
	Extends the current set of pharmacophore features by a copy of the features in the feature container cntnr. More...

None	remove (FeatureContainer cntnr)
	Removes the pharmacophore features referenced by the feature container cntnr from this instance. More...

Pharmacophore	assign (Pharmacophore pharm)
	Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the pharmacophore pharm. More...

Pharmacophore	assign (FeatureContainer cntnr)
	Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the feature container cntnr. More...

Pharmacophore	clone ()
	Creates a deep copy of the current pharmacophore state. More...

Feature	getFeature (int idx)
	Returns a reference to the feature at index idx. More...

bool	containsFeature (Feature feature)
	Tells whether the specified feature is part of the feature set. More...

int	getFeatureIndex (Feature feature)
	Returns the index of the specified feature. More...

int	getNumFeatures ()
	Returns the number of features. More...

None	orderFeatures (BoolFeature2Functor func)
	Orders the features according to criteria implemented by the provided feature comparison function. More...

Chem.Entity3D	getEntity (int idx)
	Returns a reference to the entity at index idx. More...

int	getNumEntities ()
	Returns the number of entities. More...

tuple	__getstate__ ()

Pharmacophore	__iadd__ (Pharmacophore pharm)
	Extends the current set of pharmacophore features by a copy of the features in the pharmacophore pharm. More...

Pharmacophore	__iadd__ (FeatureContainer cntnr)
	Extends the current set of pharmacophore features by a copy of the features in the feature container cntnr. More...

Pharmacophore	__isub__ (FeatureContainer cntnr)
	Removes the pharmacophore features referenced by the feature container cntnr from this `Pharmacophore` instance. More...

None	__delitem__ (int idx)

bool	__delitem__ (Base.LookupKey key)

Base.Any	__getitem__ (Base.LookupKey key)

Feature	__getitem__ (int idx)

bool	__contains__ (Base.LookupKey key)
	Returns the result of the membership test operation `key in self`. More...

bool	__contains__ (Feature feature)
	Returns the result of the membership test operation `feature in self`. More...

None	__setitem__ (Base.LookupKey key, Base.Any value)

int	__len__ ()

Public Member Functions inherited from CDPL.Chem.Entity3DContainer
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

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

int	getNumProperties ()
	Returns the number of property entries. More...

Any	getPropertyOrDefault (LookupKey key, Any def_value)

list	getPropertyKeys ()

list	getPropertyValues ()

list	getProperties ()
	Returns a reference to itself. More...

None	setProperty (LookupKey key, Any value)

bool	removeProperty (LookupKey key)
	Clears the value of the property specified by key. More...

Any	getProperty (LookupKey key, bool throw_=False)
	Returns the value of the property specified by key. More...

bool	isPropertySet (LookupKey key)
	Tells whether or not a value has been assigned to the property specified by key. More...

None	clearProperties ()
	Clears all property values.

None	addProperties (PropertyContainer cntnr)
	Adds the property value entries in the `PropertyContainer` instance cntnr. More...

None	copyProperties (PropertyContainer cntnr)
	Replaces the current set of properties by a copy of the entries in cntnr. More...

None	swap (PropertyContainer cntnr)
	Exchanges the properties of this container with the properties of the container cntnr. More...

Any	__getitem__ (LookupKey key)
	Returns the value of the property specified by key. More...

bool	__contains__ (LookupKey key)
	Returns the result of the membership test operation `key in self`. More...

None	__setitem__ (LookupKey key, Any value)

bool	__delitem__ (LookupKey key)

Additional Inherited Members
Properties inherited from CDPL.Pharm.FeatureContainer
	numFeatures = property(getNumFeatures)

Properties inherited from CDPL.Chem.Entity3DContainer
	objectID = property(getObjectID)

	numEntities = property(getNumEntities)

Properties inherited from CDPL.Base.PropertyContainer
	objectID = property(getObjectID)

	propertyKeys = property(getPropertyKeys)

	propertyValues = property(getPropertyValues)

	properties = property(getProperties)

	numProperties = property(getNumProperties)

Detailed Description

Abstract base class for mutable containers of Pharm.Feature instances representing a pharmacophore model.

Pharmacophore extends the read-only Pharm.FeatureContainer interface with feature creation/removal, content replacement (copy, append, remove) and a cloning facility for polymorphic deep copies.

Member Function Documentation

◆ addFeature()

Feature CDPL.Pharm.Pharmacophore.addFeature ( )

Creates a new pharmacophore feature and adds it to the pharmacophore.

Returns: A reference to the newly created features.

◆ removeFeature()

None CDPL.Pharm.Pharmacophore.removeFeature ( int idx )

Removes the pharmacophore feature at the specified index.

Parameters

idx	The index of the feature to remove.

Exceptions

Base.IndexError if idx is not in the range [0, getNumFeatures()).

◆ copy() [1/2]

None CDPL.Pharm.Pharmacophore.copy ( Pharmacophore pharm )

Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the pharmacophore pharm.

Parameters

pharm The pharmacophore to copy.

Reimplemented in CDPL.Pharm.BasicPharmacophore.

◆ copy() [2/2]

None CDPL.Pharm.Pharmacophore.copy ( FeatureContainer cntnr )

Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the feature container cntnr.

Parameters

cntnr The feature container providing the features and properties to copy.

Reimplemented in CDPL.Pharm.BasicPharmacophore.

◆ append() [1/2]

None CDPL.Pharm.Pharmacophore.append ( Pharmacophore pharm )

Extends the current set of features by a copy of the features in the pharmacophore pharm.

Parameters

pharm The pharmacophore providing the features to append.

Note: Does not affect any properties.

Reimplemented in CDPL.Pharm.BasicPharmacophore.

◆ append() [2/2]

None CDPL.Pharm.Pharmacophore.append ( FeatureContainer cntnr )

Extends the current set of pharmacophore features by a copy of the features in the feature container cntnr.

Parameters

cntnr The feature container providing the features to append.

Note: Does not affect any properties.

Reimplemented in CDPL.Pharm.BasicPharmacophore.

◆ remove()

None CDPL.Pharm.Pharmacophore.remove ( FeatureContainer cntnr )

Removes the pharmacophore features referenced by the feature container cntnr from this instance.

Parameters

cntnr The feature container providing the features to remove.

Note: Equivalent to clear() if this == &cntr.

◆ assign() [1/2]

Pharmacophore CDPL.Pharm.Pharmacophore.assign ( Pharmacophore pharm )

Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the pharmacophore pharm.

Internally calls copy() to perform the actual work.

Parameters

pharm The pharmacophore to copy.

Returns: self

Reimplemented in CDPL.Pharm.BasicPharmacophore.

◆ assign() [2/2]

Pharmacophore CDPL.Pharm.Pharmacophore.assign ( FeatureContainer cntnr )

Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the feature container cntnr.

Internally calls copy() to perform the actual work.

Parameters

cntnr The feature container providing the features and properties to copy.

Returns: self

Reimplemented in CDPL.Pharm.BasicPharmacophore.

◆ clone()

Pharmacophore CDPL.Pharm.Pharmacophore.clone ( )

Creates a deep copy of the current pharmacophore state.

Returns: A smart reference to the copy of the pharmacophore.

◆ getFeature()

Feature CDPL.Pharm.Pharmacophore.getFeature ( int idx )

Returns a reference to the feature at index idx.

Parameters

idx	The zero-based index of the feature to return.

Returns: A reference to the feature at the specified index.

Exceptions

Base.IndexError if idx is not in the range [0, getNumFeatures()).

Reimplemented from CDPL.Pharm.FeatureContainer.

◆ containsFeature()

bool CDPL.Pharm.Pharmacophore.containsFeature ( Feature feature )

Tells whether the specified feature is part of the feature set.

Parameters

feature The feature to look for.

Returns: True if feature is part of the set, and False otherwise.

Reimplemented from CDPL.Pharm.FeatureContainer.

◆ getFeatureIndex()

int CDPL.Pharm.Pharmacophore.getFeatureIndex ( Feature feature )

Returns the index of the specified feature.

Parameters

feature The feature for which to return the index.

Returns: The zero-based index of the specified feature.

Exceptions

Base.ItemNotFound if the specified feature could not be found.

Reimplemented from CDPL.Pharm.FeatureContainer.

◆ getNumFeatures()

int CDPL.Pharm.Pharmacophore.getNumFeatures ( )

Returns the number of features.

Returns: The number of features.

Reimplemented from CDPL.Pharm.FeatureContainer.

◆ orderFeatures()

None CDPL.Pharm.Pharmacophore.orderFeatures ( BoolFeature2Functor func )

Orders the features according to criteria implemented by the provided feature comparison function.

Parameters

func	The feature comparison function implementing the applied ordering criteria.

Reimplemented from CDPL.Pharm.FeatureContainer.

◆ getEntity()

Chem.Entity3D CDPL.Pharm.Pharmacophore.getEntity ( int idx )

Returns a reference to the entity at index idx.

Forwards to getFeature() and exists to satisfy the Chem.Entity3DContainer interface.

Parameters

idx	The zero-based entity index.

Returns: A reference to the entity at the specified index.

Exceptions

Base.IndexError if idx is not in the range [0, getNumFeatures()).

Reimplemented from CDPL.Pharm.FeatureContainer.

◆ getNumEntities()

int CDPL.Pharm.Pharmacophore.getNumEntities ( )

Returns the number of entities.

Forwards to getNumFeatures() and exists to satisfy the Chem.Entity3DContainer interface.

Returns: The number of contained features.

Reimplemented from CDPL.Pharm.FeatureContainer.

◆ iadd() [1/2]

Pharmacophore CDPL.Pharm.Pharmacophore.__iadd__ ( Pharmacophore pharm )

Extends the current set of pharmacophore features by a copy of the features in the pharmacophore pharm.

Internally calls append() to perform the actual work.

Parameters

pharm The pharmacophore providing the features to append.

Returns: self

Reimplemented in CDPL.Pharm.BasicPharmacophore.

◆ iadd() [2/2]

Pharmacophore CDPL.Pharm.Pharmacophore.__iadd__ ( FeatureContainer cntnr )

Extends the current set of pharmacophore features by a copy of the features in the feature container cntnr.

Internally calls append() to perform the actual work.

Parameters

cntnr The feature container providing the features to append.

Returns: self

Reimplemented in CDPL.Pharm.BasicPharmacophore.

◆ isub()

Pharmacophore CDPL.Pharm.Pharmacophore.__isub__ ( FeatureContainer cntnr )

Removes the pharmacophore features referenced by the feature container cntnr from this Pharmacophore instance.

Internally calls remove() to perform the actual work.

Parameters

cntnr The feature container providing the features to remove.

Returns: self

◆ contains() [1/2]

bool CDPL.Pharm.Pharmacophore.__contains__ ( Base.LookupKey key )

Returns the result of the membership test operation key in self.

Parameters

key	The value to test for membership.

Returns: The result of the membership test operation.

Reimplemented from CDPL.Pharm.FeatureContainer.

◆ contains() [2/2]

bool CDPL.Pharm.Pharmacophore.__contains__ ( Feature feature )

Returns the result of the membership test operation feature in self.

Parameters

feature The value to test for membership.

Returns: The result of the membership test operation.

Reimplemented from CDPL.Pharm.FeatureContainer.

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ addFeature()

◆ removeFeature()

◆ copy() [1/2]

◆ copy() [2/2]

◆ append() [1/2]

◆ append() [2/2]

◆ remove()

◆ assign() [1/2]

◆ assign() [2/2]

◆ clone()

◆ getFeature()

◆ containsFeature()

◆ getFeatureIndex()

◆ getNumFeatures()

◆ orderFeatures()

◆ getEntity()

◆ getNumEntities()

◆ __iadd__() [1/2]

◆ __iadd__() [2/2]

◆ __isub__()

◆ __contains__() [1/2]

◆ __contains__() [2/2]

◆ iadd() [1/2]

◆ iadd() [2/2]

◆ isub()

◆ contains() [1/2]

◆ contains() [2/2]