#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 objects. More...

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

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

typedef Util::IndexedElementIterator< Entity3D, EntityAccessor >	EntityIterator
	A mutable random access iterator used to iterate over the stored Chem::Entity3D objects. 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 std::size_t	getNumFeatures () const =0
	Returns the number of pharmacophore features. More...

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

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

virtual bool	containsFeature (const Feature &feature) const =0
	Tells whether the specified feature instance is stored in this pharmacophore. 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 pharmacophore 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 `Pharmacophore` instance. More...

virtual SharedPointer	clone () const =0
	Creates a 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 objects. More...

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

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

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

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

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

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

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

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

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

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

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

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

virtual std::size_t	getNumEntities () const
	Returns the number of stored Chem::Entity3D objects. More...

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

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

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

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

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

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

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

EntityIterator	end ()
	Returns a mutable iterator pointing to the end of the stored Chem::Entity3D objects. 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 a stored value 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)
	Clears the value of the property specified by key. More...

void	clearProperties ()
	Clears all property values. More...

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

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

void	swap (PropertyContainer &cntnr)
	Exchanges the properties of this container with the properties of the container 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 pharmacophore features and properties by a copy of the features and 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

Pharmacophore.

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 objects.

◆ FeatureIterator

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

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

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.

◆ getNumFeatures()

virtual std::size_t CDPL::Pharm::Pharmacophore::getNumFeatures ( ) const

pure virtual

Returns the number of pharmacophore features.

Returns: The number of features.

Implements CDPL::Pharm::FeatureContainer.

Implemented in CDPL::Pharm::BasicPharmacophore.

◆ getFeature() [1/2]

virtual const Feature& CDPL::Pharm::Pharmacophore::getFeature ( std::size_t idx ) const

pure virtual

Returns a const reference to the pharmacophore feature at index idx.

Parameters

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

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

Exceptions

Base::IndexError if the number of pharmacophore features is zero or idx is not in the range [0, getNumFeatures() - 1].

Implements CDPL::Pharm::FeatureContainer.

Implemented in CDPL::Pharm::BasicPharmacophore.

◆ getFeature() [2/2]

virtual Feature& CDPL::Pharm::Pharmacophore::getFeature ( std::size_t idx )

pure virtual

Returns a non-const reference to the pharmacophore feature at index idx.

Parameters

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

Returns: A non-const reference to the feature at the specified index.

Exceptions

Base::IndexError if the number of featuress is zero or idx is not in the range [0, getNumFeatures() - 1].

Implements CDPL::Pharm::FeatureContainer.

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 the number of features is zero or idx is not in the range [0, getNumFeatures() - 1].

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 the number of features is zero or it is not in the range [getFeaturesBegin(), getFeaturesEnd() - 1].

◆ getFeatureIndex()

virtual std::size_t CDPL::Pharm::Pharmacophore::getFeatureIndex ( const Feature & feature ) const

pure virtual

Returns the index of the specified feature in this pharmacophore.

Parameters

feature The feature instance for which to return the index.

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

Exceptions

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

Implements CDPL::Pharm::FeatureContainer.

Implemented in CDPL::Pharm::BasicPharmacophore.

◆ containsFeature()

virtual bool CDPL::Pharm::Pharmacophore::containsFeature ( const Feature & feature ) const

pure virtual

Tells whether the specified feature instance is stored in this pharmacophore.

Parameters

feature The feature to look for.

Returns: true if feature is stored in the pharmacophore, and false otherwise.

Implements CDPL::Pharm::FeatureContainer.

Implemented in CDPL::Pharm::BasicPharmacophore.

◆ 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 Pharm::FeatureContainer instance 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 pharmacophore 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 Pharm::FeatureContainer instance 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 Pharmacophore instance.

Parameters

cntnr The Pharm::FeatureContainer instance providing the features to remove.

Note: Does not affect any properties if this != &cntr.

Implemented in CDPL::Pharm::BasicPharmacophore.

◆ clone()

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

pure virtual

Creates a 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 Pharm::FeatureContainer instance 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 Pharm::FeatureContainer instance 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 Pharm::FeatureContainer instance 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 objects.

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

◆ getFeaturesBegin() [2/2]

FeatureIterator CDPL::Pharm::FeatureContainer::getFeaturesBegin

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

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

◆ getFeaturesEnd() [1/2]

ConstFeatureIterator CDPL::Pharm::FeatureContainer::getFeaturesEnd

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

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

◆ getFeaturesEnd() [2/2]

FeatureIterator CDPL::Pharm::FeatureContainer::getFeaturesEnd

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

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

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()

◆ getNumFeatures()

◆ getFeature() [1/2]

◆ getFeature() [2/2]

◆ addFeature()

◆ removeFeature() [1/2]

◆ removeFeature() [2/2]

◆ getFeatureIndex()

◆ containsFeature()

◆ 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]