PDBFileParser Class Template Reference

#include <pdb_file_parser.hpp>

List of all members.

Public Types
typedef TypeSystem	type_system
typedef type_system::element_dictionary	element_dictionary
typedef type_system::atom_dictionary	atom_dictionary
typedef type_system::monomer_dictionary	monomer_dictionary
typedef element_dictionary::id_type	element_id_type
typedef atom_dictionary::id_type	atom_id_type
typedef monomer_dictionary::id_type	monomer_id_type
Public Member Functions
	PDBFileParser (type_system const &ts=type_system(), bool use_dynamic_types=true)
	Default Constructor.
	PDBFileParser (std::string const &filename, int which_model=0, type_system const &ts=type_system(), bool use_dynamic_types=true)
	Construct a PDBFileParser from a PDB file.
	PDBFileParser (PDBFileParser const &src)
	Copy constructor A new file stream is opened, and a seek performed to find the current model.
virtual	~PDBFileParser ()
bool	open (std::string filename, int which_model=0)
	Open a PDB file.
void	close ()
	Close the current PDB file.
std::string const &	get_header () const
	Get the PDB file header.
std::string const &	get_filename () const
	Get the file name.
template<typename PolymerSystemType>
bool	get_model (int which, PolymerSystemType &model_out, bool load_hetatoms=true)
	Get the specified model from the PDB file.
template<typename PolymerSystemType>
bool	get_current_model (PolymerSystemType &model_out, bool load_hetatoms=true)
	Get the current model from the PDB file.
template<typename PolymerSystemType>
bool	get_next_model (PolymerSystemType &model_out, bool load_hetatoms=true)
	Get the next model from the PDB file.
type_system	dictionary ()
	Get the TypeSystem used to parse the current PDB file.
type_system const	dictionary () const
Protected Member Functions
std::string	eat_whitespace (std::string const &s) const
void	open_file ()
void	rewind_file ()
void	save_header ()
bool	find_model (int which)
bool	find_next_atom (bool find_hetatoms)
template<typename AtomType>
AtomType	parse_atom (std::string const &atom_record, bool is_hetatom=false)
template<typename PolymerSystemType>
void	parse_current_model (PolymerSystemType &model_out, bool load_hetatoms)
template<typename AtomIterator, typename PolymerSystemType>
void	save_hetatoms (AtomIterator het_begin, AtomIterator het_end, PolymerSystemType &model_out)

template<typename TypeSystem = DefaultTypeSystem>
class BTK::IO::PDBFileParser< TypeSystem >

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Member Typedef Documentation

typedef TypeSystem type_system

typedef type_system::element_dictionary element_dictionary

typedef type_system::atom_dictionary atom_dictionary

typedef type_system::monomer_dictionary monomer_dictionary

typedef element_dictionary::id_type element_id_type

typedef atom_dictionary::id_type atom_id_type

typedef monomer_dictionary::id_type monomer_id_type

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Constructor & Destructor Documentation

PDBFileParser	(	type_system const &	ts = type_system(),
		bool	use_dynamic_types = true
	)

Default Constructor.

Does nothing.

PDBFileParser	(	std::string const &	filename,
		int	which_model = 0,
		type_system const &	ts = type_system(),
		bool	use_dynamic_types = true
	)

Construct a PDBFileParser from a PDB file.

Parameters:

	filename	The name of the PDB file.
	which_model	The number of the MODEL to parse (default = first).
	ts	The TypeSystem to use for identifying molecular types (note: this object is always deep-copied).
	use_dynamic_types	If true, try to add new types to the TypeSystem as they are identified in the PDB file (this is only possible for dynamic types).

PDBFileParser

(

PDBFileParser< TypeSystem > const &

src

)

Copy constructor A new file stream is opened, and a seek performed to find the current model.

All other state data is copied.

virtual ~PDBFileParser

(

)

[virtual]

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Member Function Documentation

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

Open a PDB file.

void close

(

)

Close the current PDB file.

std::string const& get_header

(

)

const

Get the PDB file header.

std::string const& get_filename

(

)

const

Get the file name.

bool get_model	(	int	which,
		PolymerSystemType &	model_out,
		bool	load_hetatoms = true
	)

Get the specified model from the PDB file.

bool get_current_model	(	PolymerSystemType &	model_out,
		bool	load_hetatoms = true
	)

Get the current model from the PDB file.

bool get_next_model	(	PolymerSystemType &	model_out,
		bool	load_hetatoms = true
	)

Get the next model from the PDB file.

type_system dictionary

(

)

Get the TypeSystem used to parse the current PDB file.

type_system const dictionary

(

)

const

std::string eat_whitespace

(

std::string const &

s

)

const [protected]

void open_file

(

)

[protected]

void rewind_file

(

)

[protected]

void save_header

(

)

[protected]

bool find_model

(

int

which

)

[protected]

bool find_next_atom

(

bool

find_hetatoms

)

[protected]

AtomType parse_atom	(	std::string const &	atom_record,
		bool	is_hetatom = false
	)			[protected]

void parse_current_model	(	PolymerSystemType &	model_out,
		bool	load_hetatoms
	)			[protected]

void save_hetatoms	(	AtomIterator	het_begin,
		AtomIterator	het_end,
		PolymerSystemType &	model_out
	)			[protected]

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

• pdb_file_parser.hpp

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