CDPL::Biomol::HierarchyViewModel Class Reference

HierarchyViewModel. More...

#include <HierarchyViewModel.hpp>

Inheritance diagram for CDPL::Biomol::HierarchyViewModel:

Public Types
typedef boost::indirect_iterator< ChainList::const_iterator, const HierarchyViewChain >	ConstChainIterator
Public Types inherited from CDPL::Chem::Fragment
typedef std::shared_ptr< Fragment >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated Fragment instances. More...
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...
typedef boost::indirect_iterator< AtomList::iterator, Atom >	AtomIterator
	A mutable random access iterator used to iterate over the stored const Chem::Atom objects. More...
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...
typedef boost::indirect_iterator< BondList::iterator, Bond >	BondIterator
	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< MolecularGraph >	SharedPointer
	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
std::size_t	getNumChains () const
const HierarchyViewChain &	getChain (std::size_t idx) const
bool	hasChainWithID (const std::string &id) const
const HierarchyViewChain &	getChainByID (const std::string &id) const
ConstChainIterator	getChainsBegin () const
ConstChainIterator	getChainsEnd () const
ConstChainIterator	begin () const
ConstChainIterator	end () const
Public Member Functions inherited from CDPL::Biomol::HierarchyViewNode
const ResidueList &	getResidues () 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 Atom &	getAtom (std::size_t idx) const
	Returns a const reference to the atom at index idx. More...
Atom &	getAtom (std::size_t idx)
	Returns a non-const reference to the atom at index idx. More...
const Bond &	getBond (std::size_t idx) const
	Returns a const reference to the bond at index idx. More...
Bond &	getBond (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...
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...
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...
Fragment &	operator+= (const MolecularGraph &molgraph)
	Extends the current set of atoms and bonds by the atoms and bonds in the molecular graph molgraph. More...
Fragment &	operator-= (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 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...
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	HierarchyView

Additional Inherited Members
Protected Member Functions inherited from CDPL::Biomol::HierarchyViewNode
	HierarchyViewNode ()
	~HierarchyViewNode ()
std::mutex &	getMutex () const
Protected Member Functions inherited from CDPL::Chem::MolecularGraph
MolecularGraph &	operator= (const MolecularGraph &molgraph)
	Assignment operator. 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::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...

Detailed Description

HierarchyViewModel.

Member Typedef Documentation

ConstChainIterator

typedef boost::indirect_iterator<ChainList::const_iterator, const HierarchyViewChain> CDPL::Biomol::HierarchyViewModel::ConstChainIterator

Member Function Documentation

getNumChains()

std::size_t CDPL::Biomol::HierarchyViewModel::getNumChains

(

)

const

getChain()

const HierarchyViewChain& CDPL::Biomol::HierarchyViewModel::getChain

(

std::size_t

idx

)

const

hasChainWithID()

bool CDPL::Biomol::HierarchyViewModel::hasChainWithID

(

const std::string &

id

)

const

getChainByID()

const HierarchyViewChain& CDPL::Biomol::HierarchyViewModel::getChainByID

(

const std::string &

id

)

const

getChainsBegin()

ConstChainIterator CDPL::Biomol::HierarchyViewModel::getChainsBegin

(

)

const

getChainsEnd()

ConstChainIterator CDPL::Biomol::HierarchyViewModel::getChainsEnd

(

)

const

begin()

ConstChainIterator CDPL::Biomol::HierarchyViewModel::begin

(

)

const

end()

ConstChainIterator CDPL::Biomol::HierarchyViewModel::end

(

)

const

Friends And Related Function Documentation

HierarchyView

friend class HierarchyView

friend

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

• HierarchyViewModel.hpp