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

MolecularGraph. More...

#include <MolecularGraph.hpp>

+ Inheritance diagram for CDPL::Chem::MolecularGraph:

Public Types

typedef std::shared_ptr< MolecularGraphSharedPointer
 A reference-counted smart pointer [SHPTR] for dynamically allocated MolecularGraph instances. More...
 
- Public Types inherited from CDPL::Chem::AtomContainer
typedef Util::IndexedElementIterator< const Atom, ConstAtomAccessor > ConstAtomIterator
 A constant random access iterator used to iterate over the stored const Chem::Atom objects. More...
 
typedef Util::IndexedElementIterator< Atom, AtomAccessor > AtomIterator
 A mutable random access iterator used to iterate over the stored Chem::Atom 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::Chem::BondContainer
typedef Util::IndexedElementIterator< const Bond, ConstBondAccessor > ConstBondIterator
 A constant random access iterator used to iterate over the stored const Chem::Bond objects. More...
 
typedef Util::IndexedElementIterator< Bond, BondAccessor > BondIterator
 A mutable random access iterator used to iterate over the stored Chem::Bond 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 ~MolecularGraph ()
 Virtual destructor. More...
 
virtual SharedPointer clone () const =0
 Creates a copy of the molecular graph. More...
 
- Public Member Functions inherited from CDPL::Chem::AtomContainer
virtual std::size_t getNumAtoms () const =0
 Returns the number of stored Chem::Atom objects. More...
 
virtual const AtomgetAtom (std::size_t idx) const =0
 Returns a const reference to the Chem::Atom instance at index idx. More...
 
virtual AtomgetAtom (std::size_t idx)=0
 Returns a non-const reference to the atom at index idx. More...
 
ConstAtomIterator getAtomsBegin () const
 Returns a constant iterator pointing to the beginning of the stored const Chem::Atom objects. More...
 
ConstAtomIterator getAtomsEnd () const
 Returns a constant iterator pointing to the end of the stored const Chem::Atom objects. More...
 
AtomIterator getAtomsBegin ()
 Returns a mutable iterator pointing to the beginning of the stored Chem::Atom objects. More...
 
AtomIterator getAtomsEnd ()
 Returns a mutable iterator pointing to the end of the stored Chem::Atom objects. More...
 
ConstAtomIterator begin () const
 Returns a constant iterator pointing to the beginning of the stored const Chem::Atom objects. More...
 
ConstAtomIterator end () const
 Returns a constant iterator pointing to the end of the stored const Chem::Atom objects. More...
 
AtomIterator begin ()
 Returns a mutable iterator pointing to the beginning of the stored Chem::Atom objects. More...
 
AtomIterator end ()
 Returns a mutable iterator pointing to the end of the stored Chem::Atom objects. More...
 
virtual bool containsAtom (const Atom &atom) const =0
 Tells whether the specified Chem::Atom instance is stored in this container. More...
 
virtual std::size_t getAtomIndex (const Atom &atom) const =0
 Returns the index of the specified Chem::Atom instance in this container. More...
 
virtual std::size_t getNumEntities () const
 Returns the number of stored Chem::Entity3D objects. More...
 
virtual const Entity3DgetEntity (std::size_t idx) const
 Returns a const reference to the Chem::Entity3D instance at index idx. More...
 
virtual Entity3DgetEntity (std::size_t idx)
 Returns a non-const reference to the entity at index idx. More...
 
virtual void orderAtoms (const AtomCompareFunction &func)=0
 Orders the stored atoms according to criteria implemented by the provided atom comparison function. More...
 
const AtomContainergetAtoms () const
 Returns a const reference to itself. More...
 
AtomContainergetAtoms ()
 Returns a reference to itself. 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::Chem::BondContainer
virtual std::size_t getNumBonds () const =0
 Returns the number of stored Chem::Bond objects. More...
 
virtual const BondgetBond (std::size_t idx) const =0
 Returns a const reference to the Chem::Bond instance at index idx. More...
 
virtual BondgetBond (std::size_t idx)=0
 Returns a non-const reference to the bond at index idx. More...
 
ConstBondIterator getBondsBegin () const
 Returns a constant iterator pointing to the beginning of the stored const Chem::Bond objects. More...
 
ConstBondIterator getBondsEnd () const
 Returns a constant iterator pointing to the end of the stored const Chem::Bond objects. More...
 
BondIterator getBondsBegin ()
 Returns a mutable iterator pointing to the beginning of the stored Chem::Bond objects. More...
 
BondIterator getBondsEnd ()
 Returns a mutable iterator pointing to the end of the stored Chem::Bond objects. More...
 
ConstBondIterator begin () const
 Returns a constant iterator pointing to the beginning of the stored const Chem::Bond objects. More...
 
ConstBondIterator end () const
 Returns a constant iterator pointing to the end of the stored const Chem::Bond objects. More...
 
BondIterator begin ()
 Returns a mutable iterator pointing to the beginning of the stored Chem::Bond objects. More...
 
BondIterator end ()
 Returns a mutable iterator pointing to the end of the stored Chem::Bond objects. More...
 
virtual bool containsBond (const Bond &bond) const =0
 Tells whether the specified Chem::Bond instance is stored in this container. More...
 
virtual std::size_t getBondIndex (const Bond &bond) const =0
 Returns the index of the specified Chem::Bond instance in this container. More...
 
virtual void orderBonds (const BondCompareFunction &func)=0
 Orders the stored bonds according to criteria implemented by the provided bond comparison function. More...
 
const BondContainergetBonds () const
 Returns a const reference to itself. More...
 
BondContainergetBonds ()
 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...
 

Protected Member Functions

MolecularGraphoperator= (const MolecularGraph &molgraph)
 Assignment operator. More...
 
- Protected Member Functions inherited from CDPL::Chem::AtomContainer
virtual ~AtomContainer ()
 Virtual destructor. More...
 
AtomContaineroperator= (const AtomContainer &cntnr)
 Assignment operator. 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::Chem::BondContainer
virtual ~BondContainer ()
 Virtual destructor. More...
 
BondContaineroperator= (const BondContainer &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

MolecularGraph.

Member Typedef Documentation

◆ SharedPointer

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

Constructor & Destructor Documentation

◆ ~MolecularGraph()

virtual CDPL::Chem::MolecularGraph::~MolecularGraph ( )
inlinevirtual

Virtual destructor.

Member Function Documentation

◆ clone()

virtual SharedPointer CDPL::Chem::MolecularGraph::clone ( ) const
pure virtual

Creates a copy of the molecular graph.

Returns
A smart pointer to the copy of the molecular graph.

Implemented in CDPL::ConfGen::CanonicalFragment, CDPL::Chem::Fragment, and CDPL::Chem::BasicMolecule.

◆ operator=()

MolecularGraph& CDPL::Chem::MolecularGraph::operator= ( const MolecularGraph molgraph)
protected

Assignment operator.

Parameters
molgraphThe other MolecularGraph instance to copy.
Returns
A reference to itself.

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