Chemical Data Processing Library C++ API - Version 1.1.1
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#include <Bond.hpp>
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... | |
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::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 Atom & | getBegin () const =0 |
Returns a const reference to the start atom of the bond. More... | |
virtual Atom & | getBegin ()=0 |
Returns a non-const reference to the start atom of the bond. More... | |
virtual const Atom & | getEnd () const =0 |
Returns a const reference to the end atom of the bond. More... | |
virtual Atom & | getEnd ()=0 |
Returns a non-const reference to the end atom of the bond. More... | |
virtual const Atom & | getNeighbor (const Atom &atom) const =0 |
Returns a const reference to the connected neighbor of the argument atom. More... | |
virtual Atom & | getNeighbor (const Atom &atom)=0 |
Returns a non-const reference to the connected neighbor of the argument atom. More... | |
virtual std::size_t | getIndex () const =0 |
Returns the index of the bond in its parent molecule. More... | |
virtual std::size_t | getNumAtoms () const =0 |
Returns the number of atoms connected by the bond. More... | |
virtual const Atom & | getAtom (std::size_t idx) const =0 |
Returns a const reference to the atom at index idx. More... | |
virtual Atom & | getAtom (std::size_t idx)=0 |
Returns a non-const reference to the atom at index idx. More... | |
virtual bool | containsAtom (const Atom &atom) const =0 |
Tells whether the bond is incident to the specified atom. More... | |
virtual std::size_t | getAtomIndex (const Atom &atom) const =0 |
Returns the index of the specified atom. More... | |
Bond & | operator= (const Bond &bond) |
Assignment operator that replaces the current set of properties with the properties of bond;. 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... | |
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::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 | ~Bond () |
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::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... | |
Bond.
A mutable random access iterator used to iterate over the connected atoms.
A constant random access iterator used to iterate over the connected atoms.
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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::BasicBond.
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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::BasicBond.
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pure virtual |
Returns a const
reference to the start atom of the bond.
const
reference to the start atom of the bond. Implemented in CDPL::Chem::BasicBond.
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pure virtual |
Returns a non-const
reference to the start atom of the bond.
const
reference to the start atom of the bond. Implemented in CDPL::Chem::BasicBond.
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pure virtual |
Returns a const
reference to the end atom of the bond.
const
reference to the end atom of the bond. Implemented in CDPL::Chem::BasicBond.
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pure virtual |
Returns a non-const
reference to the end atom of the bond.
const
reference to the end atom of the bond. Implemented in CDPL::Chem::BasicBond.
Returns a const
reference to the connected neighbor of the argument atom.
atom | The atom for which to return the connected neighbor atom. |
const
reference to the connected neighbor of the argument atom. Base::ItemNotFound | if the bond is not incident to the specified atom. |
Implemented in CDPL::Chem::BasicBond.
Returns a non-const
reference to the connected neighbor of the argument atom.
atom | The atom for which to return the connected neighbor atom. |
const
reference to the connected neighbor atom of the argument atom. Base::ItemNotFound | if the specified atom is not involved in the bond. |
Implemented in CDPL::Chem::BasicBond.
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pure virtual |
Returns the index of the bond in its parent molecule.
Implemented in CDPL::Chem::BasicBond.
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pure virtual |
Returns the number of atoms connected by the bond.
Since a bond connects exactly two atoms, the return value is always 2.
Implements CDPL::Chem::AtomContainer.
Implemented in CDPL::Chem::BasicBond.
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pure virtual |
Returns a const
reference to the atom at index idx.
The index 0 specifies the start atom (see getBegin() const) and 1 the end atom of the bond (see getEnd() const).
idx | The index of the atom to return. |
const
reference to the atom at index idx. Base::IndexError | if idx is not in the range [0, 1]. |
Implements CDPL::Chem::AtomContainer.
Implemented in CDPL::Chem::BasicBond.
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pure virtual |
Returns a non-const
reference to the atom at index idx.
The index 0 specifies the start atom (see getBegin() const) and 1 the end atom of the bond (see getEnd() const).
idx | The index of the atom to return. |
const
reference to the atom at index idx. Base::IndexError | if idx is not in the range [0, 1]. |
Implements CDPL::Chem::AtomContainer.
Implemented in CDPL::Chem::BasicBond.
Tells whether the bond is incident to the specified atom.
atom | The atom to check. |
true
if the bond is incident to the specified atom, and false
otherwise. Implements CDPL::Chem::AtomContainer.
Implemented in CDPL::Chem::BasicBond.
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pure virtual |
Returns the index of the specified atom.
If the specified atom is the start atom of the bond, the index 0 is returned. For the end atom of the bond, the value 1 will be returned.
atom | The atom for which to return the index. |
Base::ItemNotFound | if the bond is not incident to the specified atom. |
Implements CDPL::Chem::AtomContainer.
Implemented in CDPL::Chem::BasicBond.
Assignment operator that replaces the current set of properties with the properties of bond;.
bond | The bond 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.