Information stored in the header records http://www.wwpdb.org/documentation/format32/sect2.html HEADER PEPTIDASE 13-JAN-98 1A2Z. More...

#include <HeaderInformation.hh>

Inheritance diagram for core::io::pdb::HeaderInformation:

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Collaboration diagram for core::io::pdb::HeaderInformation:

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Public Types
enum	CompoundToken { MOL_ID =1, MOLECULE, CHAIN, FRAGMENT, SYNONYM, EC, ENGINEERED, MUTATION, OTHER_DETAILS, CompoundToken_max = OTHER_DETAILS }

enum	ExperimentalTechnique { X_RAY_DIFFRACTION = 1, FIBER_DIFFRACTION, NEUTRON_DIFFRACTION, ELECTRON_CRYSTALLOGRAPHY, ELECTRON_MICROSCOPY, SOLID_STATE_NMR, SOLUTION_NMR, SOLUTION_SCATTERING, THEORETICAL_MODEL, ExperimentalTechnique_max_current = THEORETICAL_MODEL, ELECTRON_DEFRACTION, CRYO_ELECTRON_MICROSCOPY, SOLUTION_SCATTERING_THEORETICAL_MODEL, FLORECENCE_TRANSFER, NMR, ExperimentalTechnique_max = NMR }
	Fields for the EXPDTA Record. More...

typedef std::list< std::string >	Keywords

typedef utility::vector1 < std::pair< CompoundToken, std::string > >	Compounds

typedef std::list < ExperimentalTechnique >	ExperimentalTechniques

Public Member Functions
	HeaderInformation ()

	HeaderInformation (HeaderInformation const &src)

	~HeaderInformation ()

void	store_record (Record &R)

void	finalize_parse ()

bool	parse_in_progress () const

void	fill_records (std::vector< Record > &VR) const

void	store_classification (std::string const &classification)

std::string	classification () const

void	store_deposition_date (std::string const &deposition_date)
	Store the deposition date using the format like "84-DEC-18". More...

void	store_deposition_date (Size yy, Size mm, Size dd)
	Store the deposition date using the format of two digit numbers for the year, month and day of the month. More...

std::string	deposition_date () const

void	deposition_date (Size &yy, Size &mm, Size &dd) const
	get the deposition date using the format of two digit numbers for the year, month and day of the month More...

std::string	idCode () const

void	store_idCode (std::string const &id_code)

void	fill_header_record (std::vector< Record > &VR) const

void	store_title (std::string const &title)
	Append title record onto current title string. More...

void	clear_title ()

std::string const &	title () const

void	fill_title_records (std::vector< Record > &VR) const

void	store_keywords (std::string const &keywords)

void	finalize_keyword_records ()

bool	keyword_in_progress () const

void	clear_keywords ()

Keywords const &	keywords () const

void	fill_keyword_records (std::vector< Record > &VR) const

void	store_compound (std::string const &compound)

void	store_compound (CompoundToken token, std::string const &value)

Compounds const &	compounds () const

void	finalize_compound_records ()

bool	compound_in_progress () const

void	clear_compounds ()

void	fill_compound_records (std::vector< Record > &VR) const

void	store_experimental_techniques (std::string const &exp)

void	store_experimental_technique (ExperimentalTechnique technique)

ExperimentalTechniques const &	experimental_techniques () const

void	finalize_experimental_technique_records ()

bool	experimental_technique_in_progress () const

void	clear_experimental_techniques ()

bool	is_experimental_technique (ExperimentalTechnique technique) const

void	fill_experimental_technique_records (std::vector< Record > &VR) const

Static Public Member Functions
static std::string	compound_token_to_string (CompoundToken token)

static CompoundToken	string_to_compound_token (std::string const &token)

static std::string	experimental_technique_to_string (ExperimentalTechnique technique)

static ExperimentalTechnique	string_to_experimental_technique (std::string const &technique)

Private Member Functions
void	fill_wrapped_records (std::string const &record_type, std::string const &field_name, std::string const &contents, Size &line_no, std::vector< Record > &VR) const
	create enough records of <record_type> to express the <contents> string and save them into the Records vector More...

void	set_line_continuation (Record &R, Size const line_no) const

Private Attributes
std::string	classification_
	Possibly abbreviated classification type. More...

Size	dep_year_
	Deposition date DD-MON-YY. More...

Size	dep_month_

Size	dep_day_

std::string	idCode_
	4-character PDB unique identifier More...

std::string	title_

Keywords	keywords_

bool	keyword_in_progress_

Compounds	compounds_

bool	compound_in_progress_

ExperimentalTechniques	experimental_techniques_

std::string	experimental_technique_in_progress_

Detailed Description

Information stored in the header records http://www.wwpdb.org/documentation/format32/sect2.html HEADER PEPTIDASE 13-JAN-98 1A2Z.

Definition at line 42 of file HeaderInformation.hh.

Member Typedef Documentation

typedef utility::vector1< std::pair< CompoundToken, std::string > > core::io::pdb::HeaderInformation::Compounds

Definition at line 223 of file HeaderInformation.hh.

typedef std::list< ExperimentalTechnique > core::io::pdb::HeaderInformation::ExperimentalTechniques

Definition at line 277 of file HeaderInformation.hh.

typedef std::list< std::string > core::io::pdb::HeaderInformation::Keywords

Definition at line 117 of file HeaderInformation.hh.

Member Enumeration Documentation

enum core::io::pdb::HeaderInformation::CompoundToken

Enumerator
MOL_ID
MOLECULE
CHAIN
FRAGMENT
SYNONYM
EC
ENGINEERED
MUTATION
OTHER_DETAILS
CompoundToken_max

Definition at line 189 of file HeaderInformation.hh.

enum core::io::pdb::HeaderInformation::ExperimentalTechnique

Fields for the EXPDTA Record.

Enumerator
X_RAY_DIFFRACTION
FIBER_DIFFRACTION
NEUTRON_DIFFRACTION
ELECTRON_CRYSTALLOGRAPHY
ELECTRON_MICROSCOPY
SOLID_STATE_NMR
SOLUTION_NMR
SOLUTION_SCATTERING
THEORETICAL_MODEL
ExperimentalTechnique_max_current
ELECTRON_DEFRACTION
CRYO_ELECTRON_MICROSCOPY
SOLUTION_SCATTERING_THEORETICAL_MODEL
FLORECENCE_TRANSFER
NMR
ExperimentalTechnique_max

Definition at line 254 of file HeaderInformation.hh.

Constructor & Destructor Documentation

core::io::pdb::HeaderInformation::HeaderInformation ( )

Definition at line 59 of file HeaderInformation.cc.

core::io::pdb::HeaderInformation::HeaderInformation ( HeaderInformation const & src)

Definition at line 74 of file HeaderInformation.cc.

core::io::pdb::HeaderInformation::~HeaderInformation ( )

Definition at line 90 of file HeaderInformation.cc.

Member Function Documentation

string core::io::pdb::HeaderInformation::classification ( ) const

Definition at line 156 of file HeaderInformation.cc.

References classification_.

Referenced by fill_header_record(), and store_classification().

void core::io::pdb::HeaderInformation::clear_compounds ( )

Definition at line 493 of file HeaderInformation.cc.

References compounds_.

void core::io::pdb::HeaderInformation::clear_experimental_techniques ( )

Definition at line 694 of file HeaderInformation.cc.

References experimental_techniques_.

void core::io::pdb::HeaderInformation::clear_keywords ( )

Definition at line 367 of file HeaderInformation.cc.

References keywords_.

void core::io::pdb::HeaderInformation::clear_title ( )

Definition at line 302 of file HeaderInformation.cc.

References title_.

bool core::io::pdb::HeaderInformation::compound_in_progress ( ) const

Definition at line 488 of file HeaderInformation.cc.

References compound_in_progress_.

Referenced by parse_in_progress().

std::string core::io::pdb::HeaderInformation::compound_token_to_string ( CompoundToken token)

static

Definition at line 390 of file HeaderInformation.cc.

References CHAIN, EC, ENGINEERED, FRAGMENT, MOL_ID, MOLECULE, MUTATION, OTHER_DETAILS, SYNONYM, and core::io::pdb::TR().

Referenced by fill_compound_records().

utility::vector1< pair< HeaderInformation::CompoundToken, string > > const & core::io::pdb::HeaderInformation::compounds ( ) const

Definition at line 478 of file HeaderInformation.cc.

References compounds_.

string core::io::pdb::HeaderInformation::deposition_date ( ) const

Definition at line 214 of file HeaderInformation.cc.

References dep_day_, dep_month_, and dep_year_.

Referenced by fill_header_record().

void core::io::pdb::HeaderInformation::deposition_date	(	Size &	yy,
		Size &	mm,
		Size &	dd
	)		const

get the deposition date using the format of two digit numbers for the year, month and day of the month

Definition at line 245 of file HeaderInformation.cc.

References dep_day_, dep_month_, and dep_year_.

bool core::io::pdb::HeaderInformation::experimental_technique_in_progress ( ) const

Definition at line 689 of file HeaderInformation.cc.

References experimental_technique_in_progress_.

Referenced by finalize_experimental_technique_records(), and parse_in_progress().

string core::io::pdb::HeaderInformation::experimental_technique_to_string ( ExperimentalTechnique technique)

static

Definition at line 524 of file HeaderInformation.cc.

References CRYO_ELECTRON_MICROSCOPY, ELECTRON_CRYSTALLOGRAPHY, ELECTRON_DEFRACTION, ELECTRON_MICROSCOPY, FIBER_DIFFRACTION, FLORECENCE_TRANSFER, NEUTRON_DIFFRACTION, NMR, SOLID_STATE_NMR, SOLUTION_NMR, SOLUTION_SCATTERING, SOLUTION_SCATTERING_THEORETICAL_MODEL, core::scoring::hbonds::t(), THEORETICAL_MODEL, core::io::pdb::TR(), and X_RAY_DIFFRACTION.

Referenced by fill_experimental_technique_records().

list< HeaderInformation::ExperimentalTechnique > const & core::io::pdb::HeaderInformation::experimental_techniques ( ) const

Definition at line 675 of file HeaderInformation.cc.

References experimental_techniques_.

void core::io::pdb::HeaderInformation::fill_compound_records ( std::vector< Record > & VR) const

Definition at line 498 of file HeaderInformation.cc.

References compound_token_to_string(), compounds_, fill_wrapped_records(), and core::scoring::hbonds::t().

Referenced by fill_records().

void core::io::pdb::HeaderInformation::fill_experimental_technique_records ( std::vector< Record > & VR) const

Definition at line 710 of file HeaderInformation.cc.

References experimental_technique_to_string(), experimental_techniques_, fill_wrapped_records(), parse_in_progress(), and core::io::pdb::TR().

Referenced by fill_records().

void core::io::pdb::HeaderInformation::fill_header_record ( std::vector< Record > & VR) const

Definition at line 266 of file HeaderInformation.cc.

References classification(), classification_, dep_day_, dep_month_, dep_year_, deposition_date(), core::io::pdb::Field::getRecordCollection(), idCode(), and idCode_.

Referenced by fill_records().

void core::io::pdb::HeaderInformation::fill_keyword_records ( std::vector< Record > & VR) const

Definition at line 372 of file HeaderInformation.cc.

References fill_wrapped_records(), keywords(), and keywords_.

Referenced by fill_records().

void core::io::pdb::HeaderInformation::fill_records ( std::vector< Record > & VR) const

Definition at line 133 of file HeaderInformation.cc.

References fill_compound_records(), fill_experimental_technique_records(), fill_header_record(), fill_keyword_records(), and fill_title_records().

void core::io::pdb::HeaderInformation::fill_title_records ( std::vector< Record > & VR) const

Definition at line 312 of file HeaderInformation.cc.

References fill_wrapped_records(), and title_.

Referenced by fill_records().

void core::io::pdb::HeaderInformation::fill_wrapped_records	(	std::string const &	record_type,
		std::string const &	field_name,
		std::string const &	contents,
		Size &	line_no,
		std::vector< Record > &	VR
	)		const

private

create enough records of <record_type> to express the <contents> string and save them into the Records vector

Definition at line 741 of file HeaderInformation.cc.

References core::io::pdb::Field::getRecordCollection(), set_line_continuation(), and core::io::pdb::TR().

Referenced by fill_compound_records(), fill_experimental_technique_records(), fill_keyword_records(), and fill_title_records().

void core::io::pdb::HeaderInformation::finalize_compound_records ( )

Definition at line 483 of file HeaderInformation.cc.

References compound_in_progress_.

Referenced by finalize_parse().

void core::io::pdb::HeaderInformation::finalize_experimental_technique_records ( )

Definition at line 680 of file HeaderInformation.cc.

References experimental_technique_in_progress(), experimental_technique_in_progress_, experimental_techniques_, and string_to_experimental_technique().

Referenced by finalize_parse().

void core::io::pdb::HeaderInformation::finalize_keyword_records ( )

Definition at line 357 of file HeaderInformation.cc.

References keyword_in_progress_.

Referenced by finalize_parse().

void core::io::pdb::HeaderInformation::finalize_parse ( )

Definition at line 118 of file HeaderInformation.cc.

References finalize_compound_records(), finalize_experimental_technique_records(), and finalize_keyword_records().

std::string core::io::pdb::HeaderInformation::idCode ( ) const

Definition at line 256 of file HeaderInformation.cc.

References idCode_.

Referenced by fill_header_record(), and store_idCode().

bool core::io::pdb::HeaderInformation::is_experimental_technique ( HeaderInformation::ExperimentalTechnique technique) const

Definition at line 699 of file HeaderInformation.cc.

References experimental_techniques_, and core::scoring::hbonds::t().

bool core::io::pdb::HeaderInformation::keyword_in_progress ( ) const

Definition at line 362 of file HeaderInformation.cc.

References keyword_in_progress_.

Referenced by parse_in_progress().

list< string > const & core::io::pdb::HeaderInformation::keywords ( ) const

Definition at line 352 of file HeaderInformation.cc.

References keywords_.

Referenced by fill_keyword_records().

bool core::io::pdb::HeaderInformation::parse_in_progress ( ) const

Definition at line 125 of file HeaderInformation.cc.

References compound_in_progress(), experimental_technique_in_progress(), and keyword_in_progress().

Referenced by fill_experimental_technique_records().

void core::io::pdb::HeaderInformation::set_line_continuation	(	Record &	R,
		Size const	line_no
	)		const

private

Definition at line 798 of file HeaderInformation.cc.

References core::io::pdb::TR().

Referenced by fill_wrapped_records().

void core::io::pdb::HeaderInformation::store_classification ( std::string const & classification)

Definition at line 146 of file HeaderInformation.cc.

References classification(), and classification_.

Referenced by store_record().

void core::io::pdb::HeaderInformation::store_compound ( std::string const & compound)

Assume each new compound token/value pair begins on a new line but the value can be multiple lines. So, if a compound record is encountered when "in progress" then append the results to the value of the previous pair.

Definition at line 433 of file HeaderInformation.cc.

References compound_in_progress_, compounds_, string_to_compound_token(), and core::io::pdb::TR().

Referenced by store_record().