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Chemical Data Processing Library C++ API - Version 1.2.3
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#include <Atom.hpp>
Inheritance diagram for CDPL::Chem::Atom:Public Types | |
| typedef AtomContainer::AtomIterator | AtomIterator |
| A mutable random access iterator used to iterate over the connected atoms. More... | |
| typedef AtomContainer::ConstAtomIterator | ConstAtomIterator |
| A constant random access iterator used to iterate over the connected atoms. More... | |
| typedef BondContainer::BondIterator | BondIterator |
| A mutable random access iterator used to iterate over the incident bonds. More... | |
| typedef BondContainer::ConstBondIterator | ConstBondIterator |
| A constant random access iterator used to iterate over the incident bonds. 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 const Molecule & | getMolecule () const =0 |
Returns a const reference to the parent molecule. More... | |
| virtual Molecule & | getMolecule ()=0 |
Returns a non-const reference to the parent molecule. More... | |
| virtual const Bond & | getBondToAtom (const Atom &atom) const =0 |
Returns a const reference to the Chem::Bond object that connects this atom to the argument atom. More... | |
| virtual Bond & | getBondToAtom (const Atom &atom)=0 |
Returns a non-const reference to the Chem::Bond object that connects this atom to the argument atom. More... | |
| virtual const Bond * | findBondToAtom (const Atom &atom) const =0 |
Returns a pointer to the const Chem::Bond object that connects this atom to the argument atom. More... | |
| virtual Bond * | findBondToAtom (const Atom &atom)=0 |
Returns a pointer to the non-const Chem::Bond object that connects this atom to the argument atom. More... | |
| virtual std::size_t | getIndex () const =0 |
| Returns the index of the atom in its parent molecule. More... | |
| virtual std::size_t | getNumAtoms () const =0 |
| Returns the number of connected atoms. More... | |
| virtual std::size_t | getNumBonds () const =0 |
| Returns the number of incident bonds. More... | |
| virtual const Bond & | getBond (std::size_t idx) const =0 |
Returns a const reference to the incident bond at index idx. More... | |
| virtual Bond & | getBond (std::size_t idx)=0 |
Returns a non-const reference to the incident bond at index idx. More... | |
| virtual const Atom & | getAtom (std::size_t idx) const =0 |
Returns a const reference to the connected atom at index idx. More... | |
| virtual Atom & | getAtom (std::size_t idx)=0 |
Returns a non-const reference to the connected atom at index idx. More... | |
| virtual bool | containsAtom (const Atom &atom) const =0 |
| Tells whether this atom and the argument atom are connected by a bond. More... | |
| virtual bool | containsBond (const Bond &bond) const =0 |
| Tells whether the specified bond is incident to this atom. More... | |
| virtual std::size_t | getAtomIndex (const Atom &atom) const =0 |
| Returns the index of the specified connected atom. More... | |
| virtual std::size_t | getBondIndex (const Bond &bond) const =0 |
| Returns the index of the specified incident bond. More... | |
| Atom & | operator= (const Atom &atom) |
| Assignment operator that replaces the current set of properties with the properties of atom;. More... | |
| ConstAtomIterator | getAtomsBegin () const |
Returns a constant iterator pointing to the beginning 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... | |
| ConstAtomIterator | getAtomsEnd () const |
Returns a constant iterator pointing to the end of the stored const Chem::Atom objects. More... | |
| AtomIterator | getAtomsEnd () |
| Returns a mutable iterator pointing to the end of the stored Chem::Atom objects. More... | |
| ConstBondIterator | getBondsBegin () const |
Returns a constant iterator pointing to the beginning 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... | |
| ConstBondIterator | getBondsEnd () const |
Returns a constant iterator pointing to the end of the stored const Chem::Bond objects. More... | |
| BondIterator | getBondsEnd () |
| Returns a mutable iterator pointing to the end of the stored Chem::Bond objects. More... | |
Public Member Functions inherited from CDPL::Chem::AtomContainer | |
| 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 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 | |
| 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 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 | |
| virtual | ~Atom () |
| Virtual destructor. 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::Chem::Entity3D | |
| Entity3D () | |
| Default constructor. More... | |
| Entity3D (const Entity3D &entity) | |
Constructs a copy of the Entity3D instance entity. More... | |
| virtual | ~Entity3D () |
| Virtual destructor. More... | |
| Entity3D & | operator= (const Entity3D &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... | |
Atom.
A mutable random access iterator used to iterate over the connected atoms.
A constant random access iterator used to iterate over the connected atoms.
A mutable random access iterator used to iterate over the incident bonds.
A constant random access iterator used to iterate over the incident bonds.
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inlineprotectedvirtual |
Virtual destructor.
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pure virtual |
Returns a const reference to the parent molecule.
const reference to the parent molecule. Implemented in CDPL::Chem::BasicAtom.
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pure virtual |
Returns a non-const reference to the parent molecule.
const reference to the parent molecule. Implemented in CDPL::Chem::BasicAtom.
Returns a const reference to the Chem::Bond object that connects this atom to the argument atom.
| atom | The adjacent atom for which to return the connecting bond. |
const reference to the Chem::Bond object connecting this atom and the argument atom. | Base::ItemNotFound | if the argument atom is not connected to this atom. |
Implemented in CDPL::Chem::BasicAtom.
Returns a non-const reference to the Chem::Bond object that connects this atom to the argument atom.
| atom | The adjacent atom for which to return the connecting bond. |
const reference to the Chem::Bond object connecting this atom and the argument atom. | Base::ItemNotFound | if the argument atom is not connected to this atom. |
Implemented in CDPL::Chem::BasicAtom.
Returns a pointer to the const Chem::Bond object that connects this atom to the argument atom.
| atom | The adjacent atom for which to return a pointer to the connecting bond. |
const Chem::Bond object that connects this atom to the argument atom, or null if the argument atom is not connected. Implemented in CDPL::Chem::BasicAtom.
Returns a pointer to the non-const Chem::Bond object that connects this atom to the argument atom.
| atom | The adjacent atom for which to return a pointer to the connecting bond. |
const Chem::Bond object that connects this atom to the argument atom, or null if the argument atom is not connected. Implemented in CDPL::Chem::BasicAtom.
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pure virtual |
Returns the index of the atom in its parent molecule.
Implemented in CDPL::Chem::BasicAtom.
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pure virtual |
Returns the number of connected atoms.
Equivalent to getNumBonds().
Implements CDPL::Chem::AtomContainer.
Implemented in CDPL::Chem::BasicAtom.
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pure virtual |
Returns the number of incident bonds.
Equivalent to getNumAtoms().
Implements CDPL::Chem::BondContainer.
Implemented in CDPL::Chem::BasicAtom.
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pure virtual |
Returns a const reference to the incident bond at index idx.
| idx | The index of the incident bond to return. |
const reference to the incident bond at index idx. | Base::IndexError | if idx is not in the range [0, getNumBonds() - 1]. |
Implements CDPL::Chem::BondContainer.
Implemented in CDPL::Chem::BasicAtom.
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pure virtual |
Returns a non-const reference to the incident bond at index idx.
| idx | The index of the incident bond to return. |
const reference to the incident bond at index idx. | Base::IndexError | if idx is not in the range [0, getNumBonds() - 1]. |
Implements CDPL::Chem::BondContainer.
Implemented in CDPL::Chem::BasicAtom.
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pure virtual |
Returns a const reference to the connected atom at index idx.
| idx | The index of the atom to return. |
const reference to the connected atom at index idx. | Base::IndexError | if idx is not in the range [0, getNumAtoms() - 1]. |
Implements CDPL::Chem::AtomContainer.
Implemented in CDPL::Chem::BasicAtom.
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pure virtual |
Returns a non-const reference to the connected atom at index idx.
| idx | The index of the atom to return. |
const reference to the connected atom at index idx. | Base::IndexError | if idx is not in the range [0, getNumAtoms() - 1]. |
Implements CDPL::Chem::AtomContainer.
Implemented in CDPL::Chem::BasicAtom.
Tells whether this atom and the argument atom are connected by a bond.
| atom | The atom to test for adjacency. |
true if the argument atom is connected to this atom, and false otherwise. Implements CDPL::Chem::AtomContainer.
Implemented in CDPL::Chem::BasicAtom.
Tells whether the specified bond is incident to this atom.
| bond | The bond to test for incidence. |
true if the argument bond is incident to this atom, and false otherwise. Implements CDPL::Chem::BondContainer.
Implemented in CDPL::Chem::BasicAtom.
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pure virtual |
Returns the index of the specified connected atom.
| atom | The connected atom for which to return the index. |
| Base::ItemNotFound | if the specified atom is not connected to this atom. |
Implements CDPL::Chem::AtomContainer.
Implemented in CDPL::Chem::BasicAtom.
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pure virtual |
Returns the index of the specified incident bond.
| bond | The bond for which to return the index. |
| Base::ItemNotFound | if the specified bond is not incident to this atom. |
Implements CDPL::Chem::BondContainer.
Implemented in CDPL::Chem::BasicAtom.
Assignment operator that replaces the current set of properties with the properties of atom;.
| atom | The atom whose properties get copied. |
| ConstAtomIterator CDPL::Chem::AtomContainer::getAtomsBegin |
Returns a constant iterator pointing to the beginning of the stored const Chem::Atom objects.
const Chem::Atom objects. | AtomIterator CDPL::Chem::AtomContainer::getAtomsBegin |
Returns a mutable iterator pointing to the beginning of the stored Chem::Atom objects.
| ConstAtomIterator CDPL::Chem::AtomContainer::getAtomsEnd |
Returns a constant iterator pointing to the end of the stored const Chem::Atom objects.
const Chem::Atom objects. | AtomIterator CDPL::Chem::AtomContainer::getAtomsEnd |
Returns a mutable iterator pointing to the end of the stored Chem::Atom objects.
| ConstBondIterator CDPL::Chem::BondContainer::getBondsBegin |
Returns a constant iterator pointing to the beginning of the stored const Chem::Bond objects.
const Chem::Bond objects. | BondIterator CDPL::Chem::BondContainer::getBondsBegin |
Returns a mutable iterator pointing to the beginning of the stored Chem::Bond objects.
| ConstBondIterator CDPL::Chem::BondContainer::getBondsEnd |
Returns a constant iterator pointing to the end of the stored const Chem::Bond objects.
const Chem::Bond objects. | BondIterator CDPL::Chem::BondContainer::getBondsEnd |
Returns a mutable iterator pointing to the end of the stored Chem::Bond objects.