System Class Template Reference

A class for representing systems of molecules. More...

#include <system.hpp>

Inheritance diagram for System:

List of all members.

Public Types
typedef cto_type::chemical_type_system	chemical_type_system
typedef cto_type::dictionary	dictionary
typedef cto_type::id_type	id_type
typedef btk_seq_type::value_type	value_type
typedef btk_seq_type::iterator	iterator
typedef btk_seq_type::const_iterator	const_iterator
typedef btk_seq_type::reverse_iterator	reverse_iterator
typedef btk_seq_type::const_reverse_iterator	const_reverse_iterator
typedef btk_seq_type::reference	reference
typedef btk_seq_type::const_reference	const_reference
typedef btk_seq_type::pointer	pointer
typedef btk_seq_type::const_pointer	const_pointer
typedef btk_seq_type::difference_type	difference_type
typedef btk_seq_type::size_type	size_type
typedef value_type	chain_type
	Type definitions required for all System classes.
typedef iterator	chain_iterator
	Type definitions required for all System classes.
typedef const_iterator	const_chain_iterator
	Type definitions required for all System classes.
typedef reverse_iterator	reverse_chain_iterator
	Type definitions required for all System classes.
typedef const_reverse_iterator	const_reverse_chain_iterator
	Type definitions required for all System classes.
typedef id_type	structure_id_type
	Type definitions required for all System classes.
typedef chain_type::atom_type	atom_type
typedef BTK::UTILITY::GroupedElementIterator< chain_iterator, typename chain_type::atom_iterator, chain_type, atom_type >	atom_iterator
typedef BTK::UTILITY::GroupedElementIterator< const_chain_iterator, typename chain_type::const_atom_iterator, chain_type const, atom_type const >	const_atom_iterator
typedef boost::reverse_iterator< atom_iterator >	reverse_atom_iterator
typedef boost::reverse_iterator< const_atom_iterator >	const_reverse_atom_iterator
Public Member Functions
	System (chemical_type_system const &cts, id_type type=id_type())
	Create an empty System with a given instance of a ChemicalTypeSystem.
virtual	~System ()
virtual dictionary const &	get_dictionary () const
virtual dictionary &	get_dictionary ()
virtual void	set_chemical_type_system (chemical_type_system const &cts)
	Set the TypeSystem object associated with this System.
size_type	num_chains () const
	Methods required for all System objects.
iterator	system_begin ()
	Methods required for all System objects.
const_iterator	system_begin () const
	Methods required for all System objects.
reverse_iterator	system_rbegin ()
	Methods required for all System objects.
const_reverse_iterator	system_rbegin () const
	Methods required for all System objects.
iterator	system_end ()
	Methods required for all System objects.
const_iterator	system_end () const
	Methods required for all System objects.
reverse_iterator	system_rend ()
	Methods required for all System objects.
const_reverse_iterator	system_rend () const
	Methods required for all System objects.
virtual std::ostream &	print (std::ostream &os, size_type first_atom_num=1) const
	Methods required for all System objects.
chain_type::size_type	num_atoms () const
	Methods required by the AtomIterableConcept.
atom_iterator	structure_begin ()
	Methods required by the AtomIterableConcept.
atom_iterator	structure_end ()
	Methods required by the AtomIterableConcept.
reverse_atom_iterator	structure_rbegin ()
	Methods required by the AtomIterableConcept.
reverse_atom_iterator	structure_rend ()
	Methods required by the AtomIterableConcept.
const_atom_iterator	structure_begin () const
	Methods required by the AtomIterableConcept.
const_atom_iterator	structure_end () const
	Methods required by the AtomIterableConcept.
const_reverse_atom_iterator	structure_rbegin () const
	Methods required by the AtomIterableConcept.
const_reverse_atom_iterator	structure_rend () const
	Methods required by the AtomIterableConcept.
virtual void	swap (self_type &b)
	Methods required for STL Reversible containers.
self_type const &	operator= (self_type const &rhs)
	Methods required for STL Reversible containers.
bool	operator== (self_type const &rhs) const
	Methods required for STL Reversible containers.
bool	operator!= (self_type const &rhs) const
	Methods required for STL Reversible containers.
bool	operator< (self_type const &rhs) const
	Methods required for STL Reversible containers.

---

Detailed Description

template<typename ChainType, typename ChemicalTypeSystemType = typename ChainType::chemical_type_system, typename StorageStrategy = std::list<ChainType>>
class BTK::MOLECULES::System< ChainType, ChemicalTypeSystemType, StorageStrategy >

A class for representing systems of molecules.

Parameters:

	ChainType	The type of chain/molecule stored in the system (must be a model of the BTK ChainConcept).
	StorageStrategy	The underlying storage method (must be a model of the STL Sequence concept).

A System stores molecules (or more strictly, chains of atoms). It is a BTKSequence of ChainType objects, and therefore, a model of the BTKMutableContainerConcept (with a value_type equivalent to the ChainType).

This class requires that its ChainType be a model of the ChainConcept, but beyond that, no further requirements are imposed on the type of the object used to instantiate the class. If the ChainType is also a model of the MonomerIterableConcept, the resulting System type will be a model of the MonomerIterableConcept.

---

Member Typedef Documentation

typedef cto_type ::chemical_type_system chemical_type_system

Reimplemented from ChemicallyTypedObject< ChemicalTypeSystemType, ChemicalTypeSystemType::structure_dictionary >.

Reimplemented in PDBSystem.

typedef cto_type ::dictionary dictionary

Reimplemented from ChemicallyTypedObject< ChemicalTypeSystemType, ChemicalTypeSystemType::structure_dictionary >.

Reimplemented in PDBSystem.

typedef cto_type ::id_type id_type

Reimplemented from ChemicallyTypedObject< ChemicalTypeSystemType, ChemicalTypeSystemType::structure_dictionary >.

Reimplemented in PDBSystem.

typedef btk_seq_type ::value_type value_type

Reimplemented from BTKSequence< ChainType, StorageStrategy >.

Reimplemented in PDBSystem.

typedef btk_seq_type ::iterator iterator

Reimplemented from BTKSequence< ChainType, StorageStrategy >.

Reimplemented in PDBSystem.

typedef btk_seq_type ::const_iterator const_iterator

Reimplemented from BTKSequence< ChainType, StorageStrategy >.

Reimplemented in PDBSystem.

typedef btk_seq_type ::reverse_iterator reverse_iterator

Reimplemented from BTKSequence< ChainType, StorageStrategy >.

Reimplemented in PDBSystem.

typedef btk_seq_type ::const_reverse_iterator const_reverse_iterator

Reimplemented from BTKSequence< ChainType, StorageStrategy >.

Reimplemented in PDBSystem.

typedef btk_seq_type ::reference reference

Reimplemented from BTKSequence< ChainType, StorageStrategy >.

Reimplemented in PDBSystem.

typedef btk_seq_type ::const_reference const_reference

Reimplemented from BTKSequence< ChainType, StorageStrategy >.

Reimplemented in PDBSystem.

typedef btk_seq_type ::pointer pointer

Reimplemented from BTKSequence< ChainType, StorageStrategy >.

Reimplemented in PDBSystem.

typedef btk_seq_type ::const_pointer const_pointer

Reimplemented from BTKSequence< ChainType, StorageStrategy >.

Reimplemented in PDBSystem.

typedef btk_seq_type ::difference_type difference_type

Reimplemented from BTKSequence< ChainType, StorageStrategy >.

Reimplemented in PDBSystem.

typedef btk_seq_type ::size_type size_type

Reimplemented from BTKSequence< ChainType, StorageStrategy >.

Reimplemented in PDBSystem.

typedef value_type chain_type

Type definitions required for all System classes.

Reimplemented in PDBSystem.

typedef iterator chain_iterator

Type definitions required for all System classes.

Reimplemented in PDBSystem.

typedef const_iterator const_chain_iterator

Type definitions required for all System classes.

Reimplemented in PDBSystem.

typedef reverse_iterator reverse_chain_iterator

Type definitions required for all System classes.

Reimplemented in PDBSystem.

typedef const_reverse_iterator const_reverse_chain_iterator

Type definitions required for all System classes.

Reimplemented in PDBSystem.

typedef id_type structure_id_type

Type definitions required for all System classes.

Reimplemented in PDBSystem.

typedef chain_type::atom_type atom_type

Reimplemented in PDBSystem.

typedef BTK::UTILITY:: GroupedElementIterator<chain_iterator, typename chain_type::atom_iterator, chain_type, atom_type> atom_iterator

Reimplemented in PDBSystem.

typedef BTK::UTILITY:: GroupedElementIterator<const_chain_iterator, typename chain_type::const_atom_iterator, chain_type const, atom_type const> const_atom_iterator

Reimplemented in PDBSystem.

typedef boost::reverse_iterator<atom_iterator> reverse_atom_iterator

Reimplemented in PDBSystem.

typedef boost::reverse_iterator<const_atom_iterator> const_reverse_atom_iterator

Reimplemented in PDBSystem.

---

Constructor & Destructor Documentation

System	(	chemical_type_system const &	cts,
		id_type	type = id_type()
	)

Create an empty System with a given instance of a ChemicalTypeSystem.

System	(	size_type	n = 0,
		const_reference	t = chain_type(),
		id_type	type = id_type()
	)

Constructors required by the STL Sequence concept.

System	(	ChainIterator	i,
		ChainIterator	j,
		id_type	type = id_type()
	)

Constructors required by the STL Sequence concept.

System

(

self_type const &

src

)

Constructors required by the STL Sequence concept.

virtual ~System

(

)

[virtual]

System	(	size_type	n = 0,
		const_reference	t = chain_type(),
		id_type	type = id_type()
	)

Constructors required by the STL Sequence concept.

System	(	ChainIterator	i,
		ChainIterator	j,
		id_type	type = id_type()
	)

Constructors required by the STL Sequence concept.

System

(

self_type const &

src

)

Constructors required by the STL Sequence concept.

---

Member Function Documentation

size_type num_chains

(

)

const

Methods required for all System objects.

iterator system_begin

(

)

Methods required for all System objects.

const_iterator system_begin

(

)

const

Methods required for all System objects.

reverse_iterator system_rbegin

(

)

Methods required for all System objects.

const_reverse_iterator system_rbegin

(

)

const

Methods required for all System objects.

iterator system_end

(

)

Methods required for all System objects.

const_iterator system_end

(

)

const

Methods required for all System objects.

reverse_iterator system_rend

(

)

Methods required for all System objects.

const_reverse_iterator system_rend

(

)

const

Methods required for all System objects.

virtual std::ostream& print	(	std::ostream &	os,
		size_type	first_atom_num = 1
	)			const [virtual]

Methods required for all System objects.

chain_type::size_type num_atoms

(

)

const

Methods required by the AtomIterableConcept.

atom_iterator structure_begin

(

)

Methods required by the AtomIterableConcept.

atom_iterator structure_end

(

)

Methods required by the AtomIterableConcept.

reverse_atom_iterator structure_rbegin

(

)

Methods required by the AtomIterableConcept.

reverse_atom_iterator structure_rend

(

)

Methods required by the AtomIterableConcept.

const_atom_iterator structure_begin

(

)

const

Methods required by the AtomIterableConcept.

const_atom_iterator structure_end

(

)

const

Methods required by the AtomIterableConcept.

const_reverse_atom_iterator structure_rbegin

(

)

const

Methods required by the AtomIterableConcept.

const_reverse_atom_iterator structure_rend

(

)

const

Methods required by the AtomIterableConcept.

virtual dictionary const& get_dictionary

(

)

const [virtual]

Implements ChemicallyTypedObject< ChemicalTypeSystemType, ChemicalTypeSystemType::structure_dictionary >.

virtual dictionary& get_dictionary

(

)

[virtual]

Implements ChemicallyTypedObject< ChemicalTypeSystemType, ChemicalTypeSystemType::structure_dictionary >.

virtual void set_chemical_type_system

(

chemical_type_system const &

cts

)

[virtual]

Set the TypeSystem object associated with this System.

virtual void swap

(

self_type &

b

)

[virtual]

Methods required for STL Reversible containers.

self_type const& operator=

(

self_type const &

rhs

)

Methods required for STL Reversible containers.

bool operator==

(

self_type const &

rhs

)

const

Methods required for STL Reversible containers.

bool operator!=

(

self_type const &

rhs

)

const

Methods required for STL Reversible containers.

bool operator<

(

self_type const &

rhs

)

const

Methods required for STL Reversible containers.

---

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

• system.hpp

---