Chemical Data Processing Library C++ API - Version 1.1.1
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#include <MolecularGraph.hpp>
Public Types | |
typedef std::shared_ptr< MolecularGraph > | SharedPointer |
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 Atom & | getAtom (std::size_t idx) const =0 |
Returns a const reference to the Chem::Atom instance at index idx. More... | |
virtual Atom & | getAtom (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 Entity3D & | getEntity (std::size_t idx) const |
Returns a const reference to the Chem::Entity3D instance at index idx. More... | |
virtual Entity3D & | getEntity (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 AtomContainer & | getAtoms () const |
Returns a const reference to itself. More... | |
AtomContainer & | getAtoms () |
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 Entity3DContainer & | getEntities () const |
Returns a const reference to itself. More... | |
Entity3DContainer & | getEntities () |
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 Bond & | getBond (std::size_t idx) const =0 |
Returns a const reference to the Chem::Bond instance at index idx. More... | |
virtual Bond & | getBond (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 BondContainer & | getBonds () const |
Returns a const reference to itself. More... | |
BondContainer & | getBonds () |
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... | |
Protected Member Functions | |
MolecularGraph & | operator= (const MolecularGraph &molgraph) |
Assignment operator. More... | |
Protected Member Functions inherited from CDPL::Chem::AtomContainer | |
virtual | ~AtomContainer () |
Virtual destructor. More... | |
AtomContainer & | operator= (const AtomContainer &cntnr) |
Assignment operator. 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::Chem::BondContainer | |
virtual | ~BondContainer () |
Virtual destructor. More... | |
BondContainer & | operator= (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... | |
PropertyContainer & | operator= (const PropertyContainer &cntnr) |
Assignment operator. More... | |
typedef std::shared_ptr<MolecularGraph> CDPL::Chem::MolecularGraph::SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated MolecularGraph
instances.
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inlinevirtual |
Virtual destructor.
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pure virtual |
Creates a copy of the molecular graph.
Implemented in CDPL::ConfGen::CanonicalFragment, CDPL::Chem::Fragment, and CDPL::Chem::BasicMolecule.
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protected |
Assignment operator.
molgraph | The other MolecularGraph instance to copy. |