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

#include <Pharmacophore.hpp>

Inheritance diagram for CDPL::Pharm::Pharmacophore:

Public Types
typedef std::shared_ptr< Pharmacophore >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `Pharmacophore` instances. More...

typedef FeatureContainer::ConstFeatureIterator	ConstFeatureIterator
	A constant random access iterator used to iterate over the stored `const` Pharm::Feature instances. More...

typedef FeatureContainer::FeatureIterator	FeatureIterator
	A mutable random access iterator used to iterate over the stored Pharm::Feature instances. More...

Public Types inherited from CDPL::Pharm::FeatureContainer
typedef std::shared_ptr< FeatureContainer >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `FeatureContainer` instances. More...

typedef Util::IndexedElementIterator< const Feature, ConstFeatureAccessor >	ConstFeatureIterator
	A constant random access iterator used to iterate over the stored `const` Pharm::Feature instances. More...

typedef Util::IndexedElementIterator< Feature, FeatureAccessor >	FeatureIterator
	A mutable random access iterator used to iterate over the stored Pharm::Feature instances. More...

Public Types inherited from CDPL::Chem::Entity3DContainer
typedef Util::IndexedElementIterator< const Entity3D, ConstEntityAccessor >	ConstEntityIterator
	A constant random access iterator used to iterate over the stored `const` Chem::Entity3D instances. More...

typedef Util::IndexedElementIterator< Entity3D, EntityAccessor >	EntityIterator
	A mutable random access iterator used to iterate over the stored Chem::Entity3D instances. More...

Public Types inherited from CDPL::Base::PropertyContainer
typedef PropertyMap::value_type	PropertyEntry
	A Base::LookupKey / Base::Any pair that stores the property value for a given property key. More...

typedef PropertyMap::const_iterator	ConstPropertyIterator
	A constant iterator used to iterate over the property entries. More...

Public Member Functions
virtual	~Pharmacophore ()
	Virtual destructor. More...

virtual void	clear ()=0
	Removes all features and clears all properties of the pharmacophore. More...

virtual Feature &	addFeature ()=0
	Creates a new pharmacophore feature and adds it to the pharmacophore. More...

virtual void	removeFeature (std::size_t idx)=0
	Removes the pharmacophore feature at the specified index. More...

FeatureIterator	removeFeature (const FeatureIterator &it)
	Removes the pharmacophore feature specified by the iterator it. More...

virtual void	copy (const Pharmacophore &pharm)=0
	Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the pharmacophore pharm. More...

virtual void	copy (const FeatureContainer &cntnr)=0
	Replaces the current set of pharmacophore features and properties by a copy of the features and properties of the feature container cntnr. More...

virtual void	append (const Pharmacophore &pharm)=0
	Extends the current set of features by a copy of the features in the pharmacophore pharm. More...

virtual void	append (const FeatureContainer &cntnr)=0
	Extends the current set of pharmacophore features by a copy of the features in the feature container cntnr. More...

virtual void	remove (const FeatureContainer &cntnr)=0
	Removes the pharmacophore features referenced by the feature container cntnr from this instance. More...

virtual SharedPointer	clone () const =0
	Creates a deep copy of the current pharmacophore state. More...

Pharmacophore &	operator= (const 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 &	operator= (const 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 &	operator+= (const Pharmacophore &pharm)
	Extends the current set of pharmacophore features by a copy of the features in the pharmacophore pharm. More...

Pharmacophore &	operator+= (const FeatureContainer &cntnr)
	Extends the current set of pharmacophore features by a copy of the features in the feature container cntnr. More...

Pharmacophore &	operator-= (const FeatureContainer &cntnr)
	Removes the pharmacophore features referenced by the feature container cntnr from this `Pharmacophore` instance. More...

ConstFeatureIterator	getFeaturesBegin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Pharm::Feature instances. More...

FeatureIterator	getFeaturesBegin ()
	Returns a mutable iterator pointing to the beginning of the stored Pharm::Feature instances. More...

ConstFeatureIterator	getFeaturesEnd () const
	Returns a constant iterator pointing to the end of the stored `const` Pharm::Feature instances. More...

FeatureIterator	getFeaturesEnd ()
	Returns a mutable iterator pointing to the end of the stored Pharm::Feature instances. More...

Public Member Functions inherited from CDPL::Pharm::FeatureContainer
virtual	~FeatureContainer ()
	Virtual destructor. More...

virtual std::size_t	getNumFeatures () const =0
	Returns the number of features. More...

virtual const Feature &	getFeature (std::size_t idx) const =0
	Returns a `const` reference to the feature at index idx. More...

virtual Feature &	getFeature (std::size_t idx)=0
	Returns a non-`const` reference to the feature at index idx. More...

virtual std::size_t	getFeatureIndex (const Feature &feature) const =0
	Returns the index of the specified feature. More...

virtual bool	containsFeature (const Feature &feature) const =0
	Tells whether the specified feature is part of the feature set. More...

ConstFeatureIterator	getFeaturesBegin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Pharm::Feature instances. More...

ConstFeatureIterator	getFeaturesEnd () const
	Returns a constant iterator pointing to the end of the stored `const` Pharm::Feature instances. More...

FeatureIterator	getFeaturesBegin ()
	Returns a mutable iterator pointing to the beginning of the stored Pharm::Feature instances. More...

FeatureIterator	getFeaturesEnd ()
	Returns a mutable iterator pointing to the end of the stored Pharm::Feature instances. More...

ConstFeatureIterator	begin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Pharm::Feature instances. More...

ConstFeatureIterator	end () const
	Returns a constant iterator pointing to the end of the stored `const` Pharm::Feature instances. More...

FeatureIterator	begin ()
	Returns a mutable iterator pointing to the beginning of the stored Pharm::Feature instances. More...

FeatureIterator	end ()
	Returns a mutable iterator pointing to the end of the stored Pharm::Feature instances. More...

virtual void	orderFeatures (const FeatureCompareFunction &func)=0
	Orders the features according to criteria implemented by the provided feature comparison function. More...

virtual std::size_t	getNumEntities () const
	Returns the number of entities. More...

virtual const Chem::Entity3D &	getEntity (std::size_t idx) const
	Returns a `const` reference to the entity at index idx. More...

virtual Chem::Entity3D &	getEntity (std::size_t idx)
	Returns a non-`const` reference to the entity at index idx. More...

Public Member Functions inherited from CDPL::Chem::Entity3DContainer
ConstEntityIterator	getEntitiesBegin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Chem::Entity3D instances. More...

ConstEntityIterator	getEntitiesEnd () const
	Returns a constant iterator pointing to the end of the stored `const` Chem::Entity3D instances. More...

EntityIterator	getEntitiesBegin ()
	Returns a mutable iterator pointing to the beginning of the stored Chem::Entity3D instances. More...

EntityIterator	getEntitiesEnd ()
	Returns a mutable iterator pointing to the end of the stored Chem::Entity3D instances. More...

ConstEntityIterator	begin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Chem::Entity3D instances. More...

ConstEntityIterator	end () const
	Returns a constant iterator pointing to the end of the stored `const` Chem::Entity3D instances. More...

EntityIterator	begin ()
	Returns a mutable iterator pointing to the beginning of the stored Chem::Entity3D instances. More...

EntityIterator	end ()
	Returns a mutable iterator pointing to the end of the stored Chem::Entity3D instances. More...

const Entity3DContainer &	getEntities () const
	Returns a `const` reference to itself. More...

Entity3DContainer &	getEntities ()
	Returns a reference to itself. More...

Public Member Functions inherited from CDPL::Base::PropertyContainer
std::size_t	getNumProperties () const
	Returns the number of property entries. More...

template<typename T >
void	setProperty (const LookupKey &key, T &&val)
	Sets the value of the property specified by key to val. More...

template<typename T >
const T &	getProperty (const LookupKey &key) const
	Returns the value of the property specified by key as a `const` reference to an object of type T. More...

template<typename T >
const T &	getPropertyOrDefault (const LookupKey &key, const T &def_val) const
	Returns the value of the property specified by key as a `const` reference to an object of type T, or the default value def_val if an entry does not exist. More...

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

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

ConstPropertyIterator	getPropertiesBegin () const
	Returns a constant iterator pointing to the beginning of the property entries. More...

ConstPropertyIterator	getPropertiesEnd () const
	Returns a constant iterator pointing to the end of the property entries. More...

ConstPropertyIterator	begin () const
	Returns a constant iterator pointing to the beginning of the property entries. More...

ConstPropertyIterator	end () const
	Returns a constant iterator pointing to the end of the property entries. More...

bool	removeProperty (const LookupKey &key)
	Removes the entry for the property specified by key. More...

void	clearProperties ()
	Erases all container entries. More...

void	addProperties (const PropertyContainer &cntnr)
	Adds the property entries of the `PropertyContainer` instance cntnr. More...

void	copyProperties (const PropertyContainer &cntnr)
	Replaces the current property entries by a copy of the entries in cntnr. More...

void	swap (PropertyContainer &cntnr)
	Exchanges the property entries of this container with the ones of cntnr. More...

const PropertyContainer &	getProperties () const
	Returns a `const` reference to itself. More...

Additional Inherited Members
Protected Member Functions inherited from CDPL::Pharm::FeatureContainer
FeatureContainer &	operator= (const FeatureContainer &cntnr)
	Replaces the current set of properties by a copy of the properties of the container cntnr. More...

Protected Member Functions inherited from CDPL::Chem::Entity3DContainer
virtual	~Entity3DContainer ()
	Virtual destructor. More...

Entity3DContainer &	operator= (const Entity3DContainer &cntnr)
	Assignment operator. More...

Protected Member Functions inherited from CDPL::Base::PropertyContainer
	PropertyContainer ()
	Constructs an empty `PropertyContainer` instance. More...

	PropertyContainer (const PropertyContainer &cntnr)
	Constructs a copy of the `PropertyContainer` instance cntnr. More...

virtual	~PropertyContainer ()
	Virtual destructor. More...

PropertyContainer &	operator= (const PropertyContainer &cntnr)
	Assignment operator. More...

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 Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<Pharmacophore> CDPL::Pharm::Pharmacophore::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated Pharmacophore instances.

◆ ConstFeatureIterator

typedef FeatureContainer::ConstFeatureIterator CDPL::Pharm::Pharmacophore::ConstFeatureIterator

A constant random access iterator used to iterate over the stored const Pharm::Feature instances.

◆ FeatureIterator

typedef FeatureContainer::FeatureIterator CDPL::Pharm::Pharmacophore::FeatureIterator

A mutable random access iterator used to iterate over the stored Pharm::Feature instances.

Constructor & Destructor Documentation

◆ ~Pharmacophore()

virtual CDPL::Pharm::Pharmacophore::~Pharmacophore ( )

inlinevirtual

Virtual destructor.

Member Function Documentation

◆ clear()

virtual void CDPL::Pharm::Pharmacophore::clear ( )

pure virtual

Removes all features and clears all properties of the pharmacophore.

Implemented in CDPL::Pharm::BasicPharmacophore.

◆ addFeature()

virtual Feature& CDPL::Pharm::Pharmacophore::addFeature ( )

pure virtual

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

Returns: A reference to the newly created features.

Implemented in CDPL::Pharm::BasicPharmacophore.

◆ removeFeature() [1/2]

virtual void CDPL::Pharm::Pharmacophore::removeFeature ( std::size_t idx )

pure virtual

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()).

Implemented in CDPL::Pharm::BasicPharmacophore.

◆ removeFeature() [2/2]

FeatureIterator CDPL::Pharm::Pharmacophore::removeFeature ( const FeatureIterator & it )

Removes the pharmacophore feature specified by the iterator it.

Parameters

it	An iterator that specifies the feature to remove.

Returns: A mutable iterator pointing to the next feature in the list.

Exceptions

Base::RangeError if it is not in the range [getFeaturesBegin(), getFeaturesEnd()).

◆ copy() [1/2]

virtual void CDPL::Pharm::Pharmacophore::copy ( const Pharmacophore & pharm )

pure virtual

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.

Implemented in CDPL::Pharm::BasicPharmacophore.

◆ copy() [2/2]

virtual void CDPL::Pharm::Pharmacophore::copy ( const FeatureContainer & cntnr )

pure virtual

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.

Implemented in CDPL::Pharm::BasicPharmacophore.

◆ append() [1/2]

virtual void CDPL::Pharm::Pharmacophore::append ( const Pharmacophore & pharm )

pure virtual

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.

Implemented in CDPL::Pharm::BasicPharmacophore.

◆ append() [2/2]

virtual void CDPL::Pharm::Pharmacophore::append ( const FeatureContainer & cntnr )

pure virtual

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.

Implemented in CDPL::Pharm::BasicPharmacophore.

◆ remove()

virtual void CDPL::Pharm::Pharmacophore::remove ( const FeatureContainer & cntnr )

pure virtual

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.

Implemented in CDPL::Pharm::BasicPharmacophore.

◆ clone()

virtual SharedPointer CDPL::Pharm::Pharmacophore::clone ( ) const

pure virtual

Creates a deep copy of the current pharmacophore state.

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

Implemented in CDPL::Pharm::BasicPharmacophore.

◆ operator=() [1/2]

Pharmacophore& CDPL::Pharm::Pharmacophore::operator= ( const 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: A reference to itself.

◆ operator=() [2/2]

Pharmacophore& CDPL::Pharm::Pharmacophore::operator= ( const 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: A reference to itself.

◆ operator+=() [1/2]

Pharmacophore& CDPL::Pharm::Pharmacophore::operator+= ( const 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: A reference to itself.

◆ operator+=() [2/2]

Pharmacophore& CDPL::Pharm::Pharmacophore::operator+= ( const 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: A reference to itself.

◆ operator-=()

Pharmacophore& CDPL::Pharm::Pharmacophore::operator-= ( const 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: A reference to itself.

◆ getFeaturesBegin() [1/2]

ConstFeatureIterator CDPL::Pharm::FeatureContainer::getFeaturesBegin

Returns a constant iterator pointing to the beginning of the stored const Pharm::Feature instances.

Returns: A constant iterator pointing to the beginning of the stored const Pharm::Feature instances.

◆ getFeaturesBegin() [2/2]

FeatureIterator CDPL::Pharm::FeatureContainer::getFeaturesBegin

Returns a mutable iterator pointing to the beginning of the stored Pharm::Feature instances.

Returns: A mutable iterator pointing to the beginning of the stored Pharm::Feature instances.

◆ getFeaturesEnd() [1/2]

ConstFeatureIterator CDPL::Pharm::FeatureContainer::getFeaturesEnd

Returns a constant iterator pointing to the end of the stored const Pharm::Feature instances.

Returns: A constant iterator pointing to the end of the stored const Pharm::Feature instances.

◆ getFeaturesEnd() [2/2]

FeatureIterator CDPL::Pharm::FeatureContainer::getFeaturesEnd

Returns a mutable iterator pointing to the end of the stored Pharm::Feature instances.

Returns: A mutable iterator pointing to the end of the stored Pharm::Feature instances.

The documentation for this class was generated from the following file:

Pharmacophore.hpp

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ConstFeatureIterator

◆ FeatureIterator

Constructor & Destructor Documentation

◆ ~Pharmacophore()

Member Function Documentation

◆ clear()

◆ addFeature()

◆ removeFeature() [1/2]

◆ removeFeature() [2/2]

◆ copy() [1/2]

◆ copy() [2/2]

◆ append() [1/2]

◆ append() [2/2]

◆ remove()

◆ clone()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator+=() [1/2]

◆ operator+=() [2/2]

◆ operator-=()

◆ getFeaturesBegin() [1/2]

◆ getFeaturesBegin() [2/2]

◆ getFeaturesEnd() [1/2]

◆ getFeaturesEnd() [2/2]