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typedef boost::indirect_iterator< FragmentList::const_iterator, const HierarchyViewFragment > | ConstFragmentIterator |
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typedef std::shared_ptr< Fragment > | SharedPointer |
| A reference-counted smart pointer [SHPTR] for dynamically allocated Fragment instances. More...
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typedef boost::indirect_iterator< AtomList::const_iterator, const Atom > | ConstAtomIterator |
| A constant random access iterator used to iterate over the stored const Chem::Atom objects. More...
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typedef boost::indirect_iterator< AtomList::iterator, Atom > | AtomIterator |
| A mutable random access iterator used to iterate over the stored const Chem::Atom objects. More...
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typedef boost::indirect_iterator< BondList::const_iterator, const Bond > | ConstBondIterator |
| A constant random access iterator used to iterate over the stored const Chem::Bond objects. More...
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typedef boost::indirect_iterator< BondList::iterator, Bond > | BondIterator |
| A mutable random access iterator used to iterate over the stored const Chem::Bond objects. More...
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typedef std::shared_ptr< MolecularGraph > | SharedPointer |
| A reference-counted smart pointer [SHPTR] for dynamically allocated MolecularGraph instances. More...
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typedef Util::IndexedElementIterator< const Atom, ConstAtomAccessor > | ConstAtomIterator |
| A constant random access iterator used to iterate over the stored const Chem::Atom objects. More...
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typedef Util::IndexedElementIterator< Atom, AtomAccessor > | AtomIterator |
| A mutable random access iterator used to iterate over the stored Chem::Atom objects. More...
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typedef Util::IndexedElementIterator< const Entity3D, ConstEntityAccessor > | ConstEntityIterator |
| A constant random access iterator used to iterate over the stored const Chem::Entity3D objects. More...
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typedef Util::IndexedElementIterator< Entity3D, EntityAccessor > | EntityIterator |
| A mutable random access iterator used to iterate over the stored Chem::Entity3D objects. More...
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typedef Util::IndexedElementIterator< const Bond, ConstBondAccessor > | ConstBondIterator |
| A constant random access iterator used to iterate over the stored const Chem::Bond objects. More...
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typedef Util::IndexedElementIterator< Bond, BondAccessor > | BondIterator |
| A mutable random access iterator used to iterate over the stored Chem::Bond objects. More...
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typedef PropertyMap::value_type | PropertyEntry |
| A Base::LookupKey / Base::Any pair that stores the property value for a given property key. More...
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typedef PropertyMap::const_iterator | ConstPropertyIterator |
| A constant iterator used to iterate over the property entries. More...
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std::size_t | getNumFragments () const |
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const HierarchyViewFragment & | getFragment (std::size_t idx) const |
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ConstFragmentIterator | getFragmentsBegin () const |
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ConstFragmentIterator | getFragmentsEnd () const |
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ConstFragmentIterator | begin () const |
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ConstFragmentIterator | end () const |
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const ResidueList & | getResidues () const |
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| Fragment () |
| Constructs an empty Fragment instance. More...
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| Fragment (const Fragment &frag) |
| Constructs a copy of the Fragment instance frag. More...
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| Fragment (const MolecularGraph &molgraph) |
| Constructs a Fragment instance storing the atoms, bonds and properties of the molecular graph molgraph. More...
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| ~Fragment () |
| Destructor. More...
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std::size_t | getNumAtoms () const |
| Returns the number of atoms. More...
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std::size_t | getNumBonds () const |
| Returns the number of bonds. More...
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bool | containsAtom (const Atom &atom) const |
| Tells whether the specified atom is part of this fragment. More...
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bool | containsBond (const Bond &bond) const |
| Tells whether the specified bond is part of this fragment. More...
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std::size_t | getAtomIndex (const Atom &atom) const |
| Returns the index of the specified atom. More...
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std::size_t | getBondIndex (const Bond &bond) const |
| Returns the index of the specified bond. More...
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ConstAtomIterator | getAtomsBegin () const |
| Returns a constant iterator pointing to the beginning of the stored const Chem::Atom objects. More...
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AtomIterator | getAtomsBegin () |
| Returns a mutable iterator pointing to the beginning of the stored const Chem::Atom objects. More...
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ConstAtomIterator | getAtomsEnd () const |
| Returns a constant iterator pointing to the end of the stored const Chem::Atom objects. More...
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AtomIterator | getAtomsEnd () |
| Returns a mutable iterator pointing to the end of the stored const Chem::Atom objects. More...
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ConstBondIterator | getBondsBegin () const |
| Returns a constant iterator pointing to the beginning of the stored const Chem::Bond objects. More...
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BondIterator | getBondsBegin () |
| Returns a mutable iterator pointing to the beginning of the stored const Chem::Bond objects. More...
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ConstBondIterator | getBondsEnd () const |
| Returns a constant iterator pointing to the end of the stored const Chem::Bond objects. More...
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BondIterator | getBondsEnd () |
| Returns a mutable iterator pointing to the end of the stored const Chem::Bond objects. More...
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const Atom & | getAtom (std::size_t idx) const |
| Returns a const reference to the atom at index idx. More...
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Atom & | getAtom (std::size_t idx) |
| Returns a non-const reference to the atom at index idx. More...
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const Bond & | getBond (std::size_t idx) const |
| Returns a const reference to the bond at index idx. More...
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Bond & | getBond (std::size_t idx) |
| Returns a non-const reference to the bond at index idx. More...
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bool | addAtom (const Atom &atom) |
| Extends the fragment by the specified atom. More...
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bool | addBond (const Bond &bond) |
| Extends the fragment by the specified bond. More...
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void | removeAtom (std::size_t idx) |
| Removes the atom at the specified index. More...
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AtomIterator | removeAtom (const AtomIterator &it) |
| Removes the atom specified by the iterator it. More...
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bool | removeAtom (const Atom &atom) |
| Removes the specified atom. More...
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void | removeBond (std::size_t idx) |
| Removes the bond at the specified index. More...
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BondIterator | removeBond (const BondIterator &it) |
| Removes the bond specified by the iterator it. More...
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bool | removeBond (const Bond &bond) |
| Removes the specified bond. More...
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void | clear () |
| Removes all atoms and bonds. More...
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void | swap (Fragment &frag) |
| Exchanges the atoms, bonds and properties of this fragment with the atoms, bonds and properties of the fragment frag. More...
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void | orderAtoms (const AtomCompareFunction &func) |
| Orders the stored atoms according to criteria implemented by the provided atom comparison function. More...
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void | orderBonds (const BondCompareFunction &func) |
| Orders the stored bonds according to criteria implemented by the provided bond comparison function. More...
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Fragment & | operator= (const Fragment &frag) |
| Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the fragment frag. More...
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Fragment & | operator= (const MolecularGraph &molgraph) |
| Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the molecular graph molgraph. More...
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Fragment & | operator+= (const MolecularGraph &molgraph) |
| Extends the current set of atoms and bonds by the atoms and bonds in the molecular graph molgraph. More...
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Fragment & | operator-= (const MolecularGraph &molgraph) |
| Removes the atoms and bonds referenced by the molecular graph molgraph from this Fragment instance. More...
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MolecularGraph::SharedPointer | clone () const |
| Creates a copy of the molecular graph. More...
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void | reserveMemoryForAtoms (std::size_t num_atoms) |
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void | reserveMemoryForBonds (std::size_t num_bonds) |
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virtual | ~MolecularGraph () |
| Virtual destructor. More...
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ConstAtomIterator | getAtomsBegin () const |
| Returns a constant iterator pointing to the beginning of the stored const Chem::Atom objects. More...
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ConstAtomIterator | getAtomsEnd () const |
| Returns a constant iterator pointing to the end of the stored const Chem::Atom objects. More...
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AtomIterator | getAtomsBegin () |
| Returns a mutable iterator pointing to the beginning of the stored Chem::Atom objects. More...
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AtomIterator | getAtomsEnd () |
| Returns a mutable iterator pointing to the end of the stored Chem::Atom objects. More...
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ConstAtomIterator | begin () const |
| Returns a constant iterator pointing to the beginning of the stored const Chem::Atom objects. More...
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ConstAtomIterator | end () const |
| Returns a constant iterator pointing to the end of the stored const Chem::Atom objects. More...
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AtomIterator | begin () |
| Returns a mutable iterator pointing to the beginning of the stored Chem::Atom objects. More...
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AtomIterator | end () |
| Returns a mutable iterator pointing to the end of the stored Chem::Atom objects. More...
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virtual std::size_t | getNumEntities () const |
| Returns the number of stored Chem::Entity3D objects. More...
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virtual const Entity3D & | getEntity (std::size_t idx) const |
| Returns a const reference to the Chem::Entity3D instance at index idx. More...
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virtual Entity3D & | getEntity (std::size_t idx) |
| Returns a non-const reference to the entity at index idx. More...
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const AtomContainer & | getAtoms () const |
| Returns a const reference to itself. More...
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AtomContainer & | getAtoms () |
| Returns a reference to itself. More...
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ConstEntityIterator | getEntitiesBegin () const |
| Returns a constant iterator pointing to the beginning of the stored const Chem::Entity3D objects. More...
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ConstEntityIterator | getEntitiesEnd () const |
| Returns a constant iterator pointing to the end of the stored const Chem::Entity3D objects. More...
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EntityIterator | getEntitiesBegin () |
| Returns a mutable iterator pointing to the beginning of the stored Chem::Entity3D objects. More...
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EntityIterator | getEntitiesEnd () |
| Returns a mutable iterator pointing to the end of the stored Chem::Entity3D objects. More...
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ConstEntityIterator | begin () const |
| Returns a constant iterator pointing to the beginning of the stored const Chem::Entity3D objects. More...
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ConstEntityIterator | end () const |
| Returns a constant iterator pointing to the end of the stored const Chem::Entity3D objects. More...
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EntityIterator | begin () |
| Returns a mutable iterator pointing to the beginning of the stored Chem::Entity3D objects. More...
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EntityIterator | end () |
| Returns a mutable iterator pointing to the end of the stored Chem::Entity3D objects. More...
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const Entity3DContainer & | getEntities () const |
| Returns a const reference to itself. More...
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Entity3DContainer & | getEntities () |
| Returns a reference to itself. More...
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ConstBondIterator | getBondsBegin () const |
| Returns a constant iterator pointing to the beginning of the stored const Chem::Bond objects. More...
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ConstBondIterator | getBondsEnd () const |
| Returns a constant iterator pointing to the end of the stored const Chem::Bond objects. More...
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BondIterator | getBondsBegin () |
| Returns a mutable iterator pointing to the beginning of the stored Chem::Bond objects. More...
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BondIterator | getBondsEnd () |
| Returns a mutable iterator pointing to the end of the stored Chem::Bond objects. More...
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ConstBondIterator | begin () const |
| Returns a constant iterator pointing to the beginning of the stored const Chem::Bond objects. More...
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ConstBondIterator | end () const |
| Returns a constant iterator pointing to the end of the stored const Chem::Bond objects. More...
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BondIterator | begin () |
| Returns a mutable iterator pointing to the beginning of the stored Chem::Bond objects. More...
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BondIterator | end () |
| Returns a mutable iterator pointing to the end of the stored Chem::Bond objects. More...
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const BondContainer & | getBonds () const |
| Returns a const reference to itself. More...
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BondContainer & | getBonds () |
| Returns a reference to itself. More...
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std::size_t | getNumProperties () const |
| Returns the number of property entries. More...
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template<typename T > |
void | setProperty (const LookupKey &key, T &&val) |
| Sets the value of the property specified by key to val. More...
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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...
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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...
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const Any & | getProperty (const LookupKey &key, bool throw_=false) const |
| Returns the value of the property specified by key. More...
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bool | isPropertySet (const LookupKey &key) const |
| Tells whether or not a value has been assigned to the property specified by key. More...
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ConstPropertyIterator | getPropertiesBegin () const |
| Returns a constant iterator pointing to the beginning of the property entries. More...
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ConstPropertyIterator | getPropertiesEnd () const |
| Returns a constant iterator pointing to the end of the property entries. More...
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ConstPropertyIterator | begin () const |
| Returns a constant iterator pointing to the beginning of the property entries. More...
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ConstPropertyIterator | end () const |
| Returns a constant iterator pointing to the end of the property entries. More...
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bool | removeProperty (const LookupKey &key) |
| Clears the value of the property specified by key. More...
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void | clearProperties () |
| Clears all property values. More...
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void | addProperties (const PropertyContainer &cntnr) |
| Adds the property value entries in the PropertyContainer instance cntnr. More...
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void | copyProperties (const PropertyContainer &cntnr) |
| Replaces the current set of properties by a copy of the entries in cntnr. More...
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void | swap (PropertyContainer &cntnr) |
| Exchanges the properties of this container with the properties of the container cntnr. More...
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const PropertyContainer & | getProperties () const |
| Returns a const reference to itself. More...
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