Chemical Data Processing Library C++ API - Version 1.1.1
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CDPL::Biomol::HierarchyViewFragment Class Reference

HierarchyViewFragment. More...

#include <HierarchyViewFragment.hpp>

+ Inheritance diagram for CDPL::Biomol::HierarchyViewFragment:

Friends

class HierarchyViewChain
 

Additional Inherited Members

- Public Types inherited from CDPL::Chem::Fragment
typedef std::shared_ptr< FragmentSharedPointer
 A reference-counted smart pointer [SHPTR] for dynamically allocated Fragment instances. More...
 
typedef boost::indirect_iterator< AtomList::const_iterator, const AtomConstAtomIterator
 A constant random access iterator used to iterate over the stored const Chem::Atom objects. More...
 
typedef boost::indirect_iterator< AtomList::iterator, AtomAtomIterator
 A mutable random access iterator used to iterate over the stored const Chem::Atom objects. More...
 
typedef boost::indirect_iterator< BondList::const_iterator, const BondConstBondIterator
 A constant random access iterator used to iterate over the stored const Chem::Bond objects. More...
 
typedef boost::indirect_iterator< BondList::iterator, BondBondIterator
 A mutable random access iterator used to iterate over the stored const Chem::Bond objects. More...
 
- Public Types inherited from CDPL::Chem::MolecularGraph
typedef std::shared_ptr< MolecularGraphSharedPointer
 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 inherited from CDPL::Biomol::HierarchyViewNode
const ResidueListgetResidues () const
 
- Public Member Functions inherited from CDPL::Chem::Fragment
 Fragment ()
 Constructs an empty Fragment instance. More...
 
 Fragment (const Fragment &frag)
 Constructs a copy of the Fragment instance frag. More...
 
 Fragment (const MolecularGraph &molgraph)
 Constructs a Fragment instance storing the atoms, bonds and properties of the molecular graph molgraph. More...
 
 ~Fragment ()
 Destructor. More...
 
std::size_t getNumAtoms () const
 Returns the number of atoms. More...
 
std::size_t getNumBonds () const
 Returns the number of bonds. More...
 
bool containsAtom (const Atom &atom) const
 Tells whether the specified atom is part of this fragment. More...
 
bool containsBond (const Bond &bond) const
 Tells whether the specified bond is part of this fragment. More...
 
std::size_t getAtomIndex (const Atom &atom) const
 Returns the index of the specified atom. More...
 
std::size_t getBondIndex (const Bond &bond) const
 Returns the index of the specified 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 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 getAtomsEnd ()
 Returns a mutable iterator pointing to the end of the stored const 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 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 getBondsEnd ()
 Returns a mutable iterator pointing to the end of the stored const Chem::Bond objects. More...
 
const AtomgetAtom (std::size_t idx) const
 Returns a const reference to the atom at index idx. More...
 
AtomgetAtom (std::size_t idx)
 Returns a non-const reference to the atom at index idx. More...
 
const BondgetBond (std::size_t idx) const
 Returns a const reference to the bond at index idx. More...
 
BondgetBond (std::size_t idx)
 Returns a non-const reference to the bond at index idx. More...
 
bool addAtom (const Atom &atom)
 Extends the fragment by the specified atom. More...
 
bool addBond (const Bond &bond)
 Extends the fragment by the specified bond. More...
 
void removeAtom (std::size_t idx)
 Removes the atom at the specified index. More...
 
AtomIterator removeAtom (const AtomIterator &it)
 Removes the atom specified by the iterator it. More...
 
bool removeAtom (const Atom &atom)
 Removes the specified atom. More...
 
void removeBond (std::size_t idx)
 Removes the bond at the specified index. More...
 
BondIterator removeBond (const BondIterator &it)
 Removes the bond specified by the iterator it. More...
 
bool removeBond (const Bond &bond)
 Removes the specified bond. More...
 
void clear ()
 Removes all atoms and bonds. More...
 
void swap (Fragment &frag)
 Exchanges the atoms, bonds and properties of this fragment with the atoms, bonds and properties of the fragment frag. More...
 
void orderAtoms (const AtomCompareFunction &func)
 Orders the stored atoms according to criteria implemented by the provided atom comparison function. More...
 
void orderBonds (const BondCompareFunction &func)
 Orders the stored bonds according to criteria implemented by the provided bond comparison function. More...
 
Fragmentoperator= (const Fragment &frag)
 Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the fragment frag. More...
 
Fragmentoperator= (const MolecularGraph &molgraph)
 Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the molecular graph molgraph. More...
 
Fragmentoperator+= (const MolecularGraph &molgraph)
 Extends the current set of atoms and bonds by the atoms and bonds in the molecular graph molgraph. More...
 
Fragmentoperator-= (const MolecularGraph &molgraph)
 Removes the atoms and bonds referenced by the molecular graph molgraph from this Fragment instance. More...
 
MolecularGraph::SharedPointer clone () const
 Creates a copy of the molecular graph. More...
 
void reserveMemoryForAtoms (std::size_t num_atoms)
 
void reserveMemoryForBonds (std::size_t num_bonds)
 
- Public Member Functions inherited from CDPL::Chem::MolecularGraph
virtual ~MolecularGraph ()
 Virtual destructor. 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 Entity3DgetEntity (std::size_t idx) const
 Returns a const reference to the Chem::Entity3D instance at index idx. More...
 
virtual Entity3DgetEntity (std::size_t idx)
 Returns a non-const reference to the entity at index idx. More...
 
const AtomContainergetAtoms () const
 Returns a const reference to itself. More...
 
AtomContainergetAtoms ()
 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 Entity3DContainergetEntities () const
 Returns a const reference to itself. More...
 
Entity3DContainergetEntities ()
 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 BondContainergetBonds () const
 Returns a const reference to itself. More...
 
BondContainergetBonds ()
 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 AnygetProperty (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 PropertyContainergetProperties () const
 Returns a const reference to itself. More...
 
- Protected Member Functions inherited from CDPL::Biomol::HierarchyViewNode
 HierarchyViewNode ()
 
 ~HierarchyViewNode ()
 
std::mutex & getMutex () const
 
- Protected Member Functions inherited from CDPL::Chem::MolecularGraph
MolecularGraphoperator= (const MolecularGraph &molgraph)
 Assignment operator. More...
 
- Protected Member Functions inherited from CDPL::Chem::AtomContainer
virtual ~AtomContainer ()
 Virtual destructor. More...
 
AtomContaineroperator= (const AtomContainer &cntnr)
 Assignment operator. More...
 
- Protected Member Functions inherited from CDPL::Chem::Entity3DContainer
virtual ~Entity3DContainer ()
 Virtual destructor. More...
 
Entity3DContaineroperator= (const Entity3DContainer &cntnr)
 Assignment operator. More...
 
- Protected Member Functions inherited from CDPL::Chem::BondContainer
virtual ~BondContainer ()
 Virtual destructor. More...
 
BondContaineroperator= (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...
 
PropertyContaineroperator= (const PropertyContainer &cntnr)
 Assignment operator. More...
 

Detailed Description

HierarchyViewFragment.

Friends And Related Function Documentation

◆ HierarchyViewChain

friend class HierarchyViewChain
friend

The documentation for this class was generated from the following file: