Chemical Data Processing Library C++ API - Version 1.1.1
Public Types | Public Member Functions | List of all members
CDPL::Pharm::Pharmacophore Class Referenceabstract

Pharmacophore. More...

#include <Pharmacophore.hpp>

+ Inheritance diagram for CDPL::Pharm::Pharmacophore:

Public Types

typedef std::shared_ptr< PharmacophoreSharedPointer
 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< FeatureContainerSharedPointer
 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 FeaturegetFeature (std::size_t idx) const =0
 Returns a const reference to the pharmacophore feature at index idx. More...
 
virtual FeaturegetFeature (std::size_t idx)=0
 Returns a non-const reference to the pharmacophore feature at index idx. More...
 
virtual FeatureaddFeature ()=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...
 
Pharmacophoreoperator= (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...
 
Pharmacophoreoperator= (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...
 
Pharmacophoreoperator+= (const Pharmacophore &pharm)
 Extends the current set of pharmacophore features by a copy of the features in the pharmacophore pharm. More...
 
Pharmacophoreoperator+= (const FeatureContainer &cntnr)
 Extends the current set of pharmacophore features by a copy of the features in the feature container cntnr. More...
 
Pharmacophoreoperator-= (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::Entity3DgetEntity (std::size_t idx) const
 Returns a const reference to the Chem::Entity3D instance at index idx. More...
 
virtual Chem::Entity3DgetEntity (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 Entity3DContainergetEntities () const
 Returns a const reference to itself. More...
 
Entity3DContainergetEntities ()
 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 AnygetProperty (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 PropertyContainergetProperties () const
 Returns a const reference to itself. More...
 

Additional Inherited Members

- Protected Member Functions inherited from CDPL::Pharm::FeatureContainer
FeatureContaineroperator= (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...
 
Entity3DContaineroperator= (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...
 
PropertyContaineroperator= (const PropertyContainer &cntnr)
 Assignment operator. More...
 

Detailed Description

Pharmacophore.

Member Typedef Documentation

◆ SharedPointer

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

◆ ConstFeatureIterator

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

◆ 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
idxThe zero-based index of the feature to return.
Returns
A const reference to the feature at the specified index.
Exceptions
Base::IndexErrorif 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
idxThe zero-based index of the feature to return.
Returns
A non-const reference to the feature at the specified index.
Exceptions
Base::IndexErrorif 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
idxThe index of the feature to remove.
Exceptions
Base::IndexErrorif 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
itAn iterator that specifies the feature to remove.
Returns
A mutable iterator pointing to the next feature in the list.
Exceptions
Base::RangeErrorif 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
featureThe feature instance for which to return the index.
Returns
The zero-based index of the specified feature instance.
Exceptions
Base::ItemNotFoundif 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
featureThe 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
pharmThe 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
cntnrThe 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
pharmThe 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
cntnrThe 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
cntnrThe 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
pharmThe 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
cntnrThe 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
pharmThe 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
cntnrThe 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
cntnrThe 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: