PDBSystem Class Template Reference

#include <pdb_system.hpp>

Inheritance diagram for PDBSystem:

List of all members.

Public Types
typedef base_type::chemical_type_system	chemical_type_system
typedef base_type::dictionary	dictionary
typedef base_type::id_type	id_type
typedef base_type::value_type	value_type
typedef base_type::iterator	iterator
typedef base_type::const_iterator	const_iterator
typedef base_type::reverse_iterator	reverse_iterator
typedef base_type::const_reverse_iterator	const_reverse_iterator
typedef base_type::reference	reference
typedef base_type::const_reference	const_reference
typedef base_type::pointer	pointer
typedef base_type::const_pointer	const_pointer
typedef base_type::difference_type	difference_type
typedef base_type::size_type	size_type
typedef base_type::chain_type	chain_type
	Type definitions required for all System classes.
typedef base_type::chain_iterator	chain_iterator
typedef base_type::const_chain_iterator	const_chain_iterator
typedef base_type::reverse_chain_iterator	reverse_chain_iterator
typedef base_type::const_reverse_chain_iterator	const_reverse_chain_iterator
typedef base_type::structure_id_type	structure_id_type
typedef base_type::atom_type	atom_type
typedef base_type::atom_iterator	atom_iterator
typedef base_type::const_atom_iterator	const_atom_iterator
typedef base_type::reverse_atom_iterator	reverse_atom_iterator
typedef base_type::const_reverse_atom_iterator	const_reverse_atom_iterator
typedef base_type::monomer_type	monomer_type
typedef base_type::monomer_iterator	monomer_iterator
typedef base_type::const_monomer_iterator	const_monomer_iterator
typedef base_type::reverse_monomer_iterator	reverse_monomer_iterator
typedef base_type::const_reverse_monomer_iterator	const_reverse_monomer_iterator
Public Member Functions
	PDBSystem (PDBSystem const &src)
	Copy a PDBSystem object.
virtual	~PDBSystem ()
	Destructor.
bool	open (std::string filename, int which_model=0)
	Open a new PDB file.
void	close ()
	Close the current PDB file.
std::string const &	header () const
	Get the current PDB file header.
std::string const &	filename () const
	Get the current PDB file name.
bool	get_model (int which, bool load_hetatoms=true)
	Get a MODEL from the current PDB file.
bool	get_next_model (bool load_hetatoms=true)
	Get the next model from the current PDB file.

---

Detailed Description

template<typename PolymerType, typename ChemicalTypeSystemType = typename PolymerType::chemical_type_system, typename StorageStrategy = std::list<PolymerType>>
class BTK::IO::PDBSystem< PolymerType, ChemicalTypeSystemType, StorageStrategy >

Examples:

gyration_radius.cpp.

---

Member Typedef Documentation

typedef base_type ::chemical_type_system chemical_type_system

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::dictionary dictionary

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::id_type id_type

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::value_type value_type

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::iterator iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_iterator const_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::reverse_iterator reverse_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_reverse_iterator const_reverse_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::reference reference

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_reference const_reference

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::pointer pointer

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_pointer const_pointer

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::difference_type difference_type

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::size_type size_type

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::chain_type chain_type

Type definitions required for all System classes.

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::chain_iterator chain_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_chain_iterator const_chain_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::reverse_chain_iterator reverse_chain_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_reverse_chain_iterator const_reverse_chain_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::structure_id_type structure_id_type

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::atom_type atom_type

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::atom_iterator atom_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_atom_iterator const_atom_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::reverse_atom_iterator reverse_atom_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::const_reverse_atom_iterator const_reverse_atom_iterator

Reimplemented from System< PolymerType, ChemicalTypeSystemType, StorageStrategy >.

typedef base_type ::monomer_type monomer_type

Reimplemented from PolymerSystemBase.

typedef base_type ::monomer_iterator monomer_iterator

Reimplemented from PolymerSystemBase.

typedef base_type ::const_monomer_iterator const_monomer_iterator

Reimplemented from PolymerSystemBase.

typedef base_type ::reverse_monomer_iterator reverse_monomer_iterator

Reimplemented from PolymerSystemBase.

typedef base_type ::const_reverse_monomer_iterator const_reverse_monomer_iterator

Reimplemented from PolymerSystemBase.

---

Constructor & Destructor Documentation

PDBSystem	(	std::string const &	filename,
		int	which_model,
		bool	load_hetatoms = true,
		bool	dynamic_types = true,
		chemical_type_system const &	cts = chemical_type_system()
	)

A model-aware constructor.

Creates a PDBSystem using the specified MODEL from a PDB file.

Parameters:

	filename	Name of PDB file to parse.
	which_model	The number of the MODEL to parse from the PDB file.
	load_hetatoms	If true, HETATM records are parsed as atoms. If false, HETATM records are skipped.
	dynamic_types	If true, unknown atom types/names are added to the specified type system. If the type system does not support dynamic types, this option has no effect.

PDBSystem	(	std::string const &	filename,
		bool	load_hetatoms = true,
		bool	dynamic_types = true,
		chemical_type_system const &	cts = chemical_type_system()
	)

Construct from a PDB file.

Creates a PDBSystem from the specified PDB file.

Parameters:

	filename	Name of PDB file to parse.
	load_hetatoms	If true, HETATM records are parsed as atoms. If false, HETATM records are skipped.
	dynamic_types	If true, unknown atom types/names are added to the specified type system. If the type system does not support dynamic types, this option has no effect.

PDBSystem	(	size_type	n = 0,
		const_reference	t = chain_type()
	)

Create a PDBSystem from 0 or more Chain objects.

Because no PDB file is specified with these constructors, subsequent calls to get_model() and get_next_model() will fail, unless a call is made to open().

PDBSystem	(	ChainIterator	begin,
		ChainIterator	end
	)

Create a PDBSystem from a range of Chain objects.

PDBSystem

(

PDBSystem< PolymerType, ChemicalTypeSystemType, StorageStrategy > const &

src

)

Copy a PDBSystem object.

virtual ~PDBSystem

(

)

[virtual]

Destructor.

PDBSystem	(	std::string const &	filename,
		int	which_model,
		bool	load_hetatoms = true,
		bool	dynamic_types = true,
		chemical_type_system const &	cts = chemical_type_system()
	)

A model-aware constructor.

Creates a PDBSystem using the specified MODEL from a PDB file.

Parameters:

	filename	Name of PDB file to parse.
	which_model	The number of the MODEL to parse from the PDB file.
	load_hetatoms	If true, HETATM records are parsed as atoms. If false, HETATM records are skipped.
	dynamic_types	If true, unknown atom types/names are added to the specified type system. If the type system does not support dynamic types, this option has no effect.

PDBSystem	(	std::string const &	filename,
		bool	load_hetatoms = true,
		bool	dynamic_types = true,
		chemical_type_system const &	cts = chemical_type_system()
	)

Construct from a PDB file.

Creates a PDBSystem from the specified PDB file.

Parameters:

	filename	Name of PDB file to parse.
	load_hetatoms	If true, HETATM records are parsed as atoms. If false, HETATM records are skipped.
	dynamic_types	If true, unknown atom types/names are added to the specified type system. If the type system does not support dynamic types, this option has no effect.

PDBSystem	(	size_type	n = 0,
		const_reference	t = chain_type()
	)

Create a PDBSystem from 0 or more Chain objects.

Because no PDB file is specified with these constructors, subsequent calls to get_model() and get_next_model() will fail, unless a call is made to open().

PDBSystem	(	ChainIterator	begin,
		ChainIterator	end
	)

Create a PDBSystem from a range of Chain objects.

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Member Function Documentation

bool open	(	std::string	filename,
		int	which_model = 0
	)

Open a new PDB file.

Any previously loaded structures will be destroyed.

void close

(

)

Close the current PDB file.

Structures in memory are unaffected.

std::string const& header

(

)

const

Get the current PDB file header.

std::string const& filename

(

)

const

Get the current PDB file name.

bool get_model	(	int	which,
		bool	load_hetatoms = true
	)

Get a MODEL from the current PDB file.

Any previously loaded structures/models will be destroyed.

bool get_next_model

(

bool

load_hetatoms = true

)

Get the next model from the current PDB file.

Any previously loaded structures/models will be destroyed.

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

• pdb_system.hpp

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