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Chemical Data Processing Library C++ API - Version 1.4.0
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Concrete Chem::Atom implementation used as the atom type of Chem::BasicMolecule. More...
#include <BasicAtom.hpp>
Inheritance diagram for CDPL::Chem::BasicAtom:Public Types | |
| typedef boost::transform_iterator< AtomAccessor< BasicAtom >, NeighborList::iterator > | AtomIterator |
| Mutable random-access iterator over the connected (neighbor) atoms. More... | |
| typedef boost::transform_iterator< AtomAccessor< const BasicAtom >, NeighborList::const_iterator > | ConstAtomIterator |
| Constant random-access iterator over the connected (neighbor) atoms. More... | |
| typedef boost::transform_iterator< BondAccessor< BasicBond >, NeighborList::iterator > | BondIterator |
| Mutable random-access iterator over the incident bonds. More... | |
| typedef boost::transform_iterator< BondAccessor< const BasicBond >, NeighborList::const_iterator > | ConstBondIterator |
| Constant random-access iterator over the incident bonds. More... | |
Public Types inherited from CDPL::Chem::Atom | |
| 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 | |
| const Molecule & | getMolecule () const |
Returns a const reference to the molecule owning this atom. More... | |
| Molecule & | getMolecule () |
| Returns a mutable reference to the molecule owning this atom. More... | |
| std::size_t | getNumAtoms () const |
| Returns the number of connected (neighbor) atoms. More... | |
| std::size_t | getNumBonds () const |
| Returns the number of incident bonds (equal to getNumAtoms()). More... | |
| const Bond & | getBond (std::size_t idx) const |
Returns a const reference to the incident bond at index idx. More... | |
| Bond & | getBond (std::size_t idx) |
| Returns a mutable reference to the incident bond at index idx. More... | |
| const Bond & | getBondToAtom (const Atom &atom) const |
| Returns the incident bond that connects this atom with atom. More... | |
| Bond & | getBondToAtom (const Atom &atom) |
| Returns the incident bond that connects this atom with atom. More... | |
| const Bond * | findBondToAtom (const Atom &atom) const |
| Looks up the incident bond that connects this atom with atom without throwing. More... | |
| Bond * | findBondToAtom (const Atom &atom) |
| Looks up the incident bond that connects this atom with atom without throwing. More... | |
| const Atom & | getAtom (std::size_t idx) const |
Returns a const reference to the connected (neighbor) atom at index idx. More... | |
| Atom & | getAtom (std::size_t idx) |
| Returns a mutable reference to the connected (neighbor) atom at index idx. More... | |
| ConstAtomIterator | getAtomsBegin () const |
| Returns a constant iterator pointing to the beginning of the connected atoms. More... | |
| AtomIterator | getAtomsBegin () |
| Returns a mutable iterator pointing to the beginning of the connected atoms. More... | |
| ConstAtomIterator | getAtomsEnd () const |
| Returns a constant iterator pointing to the end of the connected atoms. More... | |
| AtomIterator | getAtomsEnd () |
| Returns a mutable iterator pointing to the end of the connected atoms. More... | |
| ConstBondIterator | getBondsBegin () const |
| Returns a constant iterator pointing to the beginning of the incident bonds. More... | |
| BondIterator | getBondsBegin () |
| Returns a mutable iterator pointing to the beginning of the incident bonds. More... | |
| ConstBondIterator | getBondsEnd () const |
| Returns a constant iterator pointing to the end of the incident bonds. More... | |
| BondIterator | getBondsEnd () |
| Returns a mutable iterator pointing to the end of the incident bonds. More... | |
| bool | containsAtom (const Atom &atom) const |
| Tells whether atom is a neighbor of this atom. More... | |
| bool | containsBond (const Bond &bond) const |
| Tells whether bond is an incident bond of this atom. More... | |
| std::size_t | getAtomIndex (const Atom &atom) const |
| Returns the index of the neighbor atom atom in the connected-atoms list. More... | |
| std::size_t | getBondIndex (const Bond &bond) const |
| Returns the index of the incident bond bond. More... | |
| std::size_t | getIndex () const |
| Returns the index of this atom in its owning molecule's atom list. More... | |
| void | orderAtoms (const AtomCompareFunction &func) |
| Reorders the connected (neighbor) atom list using the binary comparator func. More... | |
| void | orderBonds (const BondCompareFunction &func) |
| Reorders the incident bond list using the binary comparator func. More... | |
| BasicAtom & | operator= (const BasicAtom &atom) |
| Assignment operator that replaces the current set of properties with the properties of atom;. More... | |
| Atom & | operator= (const Atom &atom) |
| Assignment operator that replaces the current set of properties with the properties of atom;. More... | |
Public Member Functions inherited from CDPL::Chem::Atom | |
| 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 (equivalent to getNumAtoms()). More... | |
| virtual const Entity3D & | getEntity (std::size_t idx) const |
Returns a const reference to the Chem::Entity3D instance at index idx (equivalent to getAtom(idx)). More... | |
| virtual Entity3D & | getEntity (std::size_t idx) |
Returns a non-const reference to the Chem::Entity3D instance at index idx (equivalent to getAtom(idx)). 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... | |
| 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... | |
Friends | |
| class | BasicMolecule |
Additional Inherited Members | |
Protected Member Functions inherited from CDPL::Chem::Atom | |
| 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... | |
Concrete Chem::Atom implementation used as the atom type of Chem::BasicMolecule.
Stores its own incident-bond list and provides constant-time access to neighbor atoms and bonds via the inherited Chem::Atom interface. BasicAtom instances are owned by a Chem::BasicMolecule and are not constructed directly by client code; use Chem::BasicMolecule::addAtom() instead.
| typedef boost::transform_iterator<AtomAccessor<BasicAtom>, NeighborList::iterator> CDPL::Chem::BasicAtom::AtomIterator |
Mutable random-access iterator over the connected (neighbor) atoms.
| typedef boost::transform_iterator<AtomAccessor<const BasicAtom>, NeighborList::const_iterator> CDPL::Chem::BasicAtom::ConstAtomIterator |
Constant random-access iterator over the connected (neighbor) atoms.
| typedef boost::transform_iterator<BondAccessor<BasicBond>, NeighborList::iterator> CDPL::Chem::BasicAtom::BondIterator |
Mutable random-access iterator over the incident bonds.
| typedef boost::transform_iterator<BondAccessor<const BasicBond>, NeighborList::const_iterator> CDPL::Chem::BasicAtom::ConstBondIterator |
Constant random-access iterator over the incident bonds.
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Returns a const reference to the molecule owning this atom.
const reference to the owning molecule. Implements CDPL::Chem::Atom.
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Returns a mutable reference to the molecule owning this atom.
Implements CDPL::Chem::Atom.
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Returns the number of connected (neighbor) atoms.
Implements CDPL::Chem::Atom.
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Returns the number of incident bonds (equal to getNumAtoms()).
Implements CDPL::Chem::Atom.
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Returns a const reference to the incident bond at index idx.
| idx | The zero-based index of the bond. |
const reference to the bond. | Base::IndexError | if idx is not less than getNumBonds(). |
Implements CDPL::Chem::Atom.
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Returns a mutable reference to the incident bond at index idx.
| idx | The zero-based index of the bond. |
| Base::IndexError | if idx is not less than getNumBonds(). |
Implements CDPL::Chem::Atom.
Returns the incident bond that connects this atom with atom.
| atom | The other end-atom of the requested bond. |
const reference to the connecting bond. | Base::ItemNotFound | if there is no such bond. |
Implements CDPL::Chem::Atom.
Returns the incident bond that connects this atom with atom.
| atom | The other end-atom of the requested bond. |
| Base::ItemNotFound | if there is no such bond. |
Implements CDPL::Chem::Atom.
Looks up the incident bond that connects this atom with atom without throwing.
| atom | The other end-atom of the requested bond. |
nullptr if no such bond exists. Implements CDPL::Chem::Atom.
Looks up the incident bond that connects this atom with atom without throwing.
| atom | The other end-atom of the requested bond. |
nullptr if no such bond exists. Implements CDPL::Chem::Atom.
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Returns a const reference to the connected (neighbor) atom at index idx.
| idx | The zero-based index of the neighbor atom. |
const reference to the neighbor atom. | Base::IndexError | if idx is not less than getNumAtoms(). |
Implements CDPL::Chem::Atom.
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Returns a mutable reference to the connected (neighbor) atom at index idx.
| idx | The zero-based index of the neighbor atom. |
| Base::IndexError | if idx is not less than getNumAtoms(). |
Implements CDPL::Chem::Atom.
| ConstAtomIterator CDPL::Chem::BasicAtom::getAtomsBegin | ( | ) | const |
Returns a constant iterator pointing to the beginning of the connected atoms.
| AtomIterator CDPL::Chem::BasicAtom::getAtomsBegin | ( | ) |
Returns a mutable iterator pointing to the beginning of the connected atoms.
| ConstAtomIterator CDPL::Chem::BasicAtom::getAtomsEnd | ( | ) | const |
Returns a constant iterator pointing to the end of the connected atoms.
| AtomIterator CDPL::Chem::BasicAtom::getAtomsEnd | ( | ) |
Returns a mutable iterator pointing to the end of the connected atoms.
| ConstBondIterator CDPL::Chem::BasicAtom::getBondsBegin | ( | ) | const |
Returns a constant iterator pointing to the beginning of the incident bonds.
| BondIterator CDPL::Chem::BasicAtom::getBondsBegin | ( | ) |
Returns a mutable iterator pointing to the beginning of the incident bonds.
| ConstBondIterator CDPL::Chem::BasicAtom::getBondsEnd | ( | ) | const |
Returns a constant iterator pointing to the end of the incident bonds.
| BondIterator CDPL::Chem::BasicAtom::getBondsEnd | ( | ) |
Returns a mutable iterator pointing to the end of the incident bonds.
Tells whether atom is a neighbor of this atom.
| atom | The atom to look up. |
true if atom is in the neighbor list, and false otherwise. Implements CDPL::Chem::Atom.
Tells whether bond is an incident bond of this atom.
| bond | The bond to look up. |
true if bond is in the incident-bond list, and false otherwise. Implements CDPL::Chem::Atom.
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Returns the index of the neighbor atom atom in the connected-atoms list.
| atom | The neighbor atom to look up. |
| Base::ItemNotFound | if atom is not a neighbor. |
Implements CDPL::Chem::Atom.
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Returns the index of the incident bond bond.
| bond | The bond to look up. |
| Base::ItemNotFound | if bond is not incident. |
Implements CDPL::Chem::Atom.
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Returns the index of this atom in its owning molecule's atom list.
Implements CDPL::Chem::Atom.
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Reorders the connected (neighbor) atom list using the binary comparator func.
| func | The strict-weak-ordering comparator used to sort the neighbor list. |
Implements CDPL::Chem::AtomContainer.
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Reorders the incident bond list using the binary comparator func.
| func | The strict-weak-ordering comparator used to sort the bond list. |
Implements CDPL::Chem::BondContainer.
Assignment operator that replaces the current set of properties with the properties of atom;.
| atom | The atom whose properties get copied. |
| Atom& CDPL::Chem::Atom::operator= |
Assignment operator that replaces the current set of properties with the properties of atom;.
| atom | The atom whose properties get copied. |
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friend |