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

#include <HeaderInformation.hh>

Inheritance diagram for core::io::HeaderInformation:

[legend]

Public Types
enum	CompoundToken { UNKNOWN_CMPD =0, MOL_ID =1, MOLECULE, BIOLOGICAL_UNIT, CHAIN, FRAGMENT, SYNONYM, EC, ENGINEERED, MUTATION, OTHER_DETAILS, CompoundToken_max = OTHER_DETAILS }

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

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

typedef std::list< std::string >	Authors

Public Member Functions
	HeaderInformation ()

	HeaderInformation (HeaderInformation const &src)

	~HeaderInformation () override

void	store_record (pdb::Record &R)

void	finalize_parse ()

bool	parse_in_progress () const

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

void	store_experimental_techniques (std::string const &exp)
	Parse the list of techniques string following the technique field in the EXPDTA record of the pdb format and store the techniques. More...

void	store_experimental_technique (rcsb::ExperimentalTechnique technique)

rcsb::ExperimentalTechniques const &	experimental_techniques () const

void	finalize_experimental_technique_records ()

bool	experimental_technique_in_progress () const

void	clear_experimental_techniques ()

bool	is_experimental_technique (rcsb::ExperimentalTechnique technique) const

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

Authors const &	authors () const

void	clear_authors ()

bool	author_in_progress () const

void	finalize_author_records ()

void	store_authors (std::string const &authors)

void	add_author (std::string const &author)
	Add an author to this Title section. More...

void	fill_author_records (std::vector< pdb::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, bool warn_on_unrecognized=true)

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< pdb::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 (pdb::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_

std::string	compound_in_progress_

rcsb::ExperimentalTechniques	experimental_techniques_

std::string	experimental_technique_in_progress_

Authors	authors_

bool	author_in_progress_

Detailed Description

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

Member Typedef Documentation

typedef std::list< std::string > core::io::HeaderInformation::Authors

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

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

Member Enumeration Documentation

enum core::io::HeaderInformation::CompoundToken

Enumerator
UNKNOWN_CMPD
MOL_ID
MOLECULE
BIOLOGICAL_UNIT
CHAIN
FRAGMENT
SYNONYM
EC
ENGINEERED
MUTATION
OTHER_DETAILS
CompoundToken_max

Constructor & Destructor Documentation

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

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

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

overridedefault

Member Function Documentation

void core::io::HeaderInformation::add_author ( std::string const & author )

Add an author to this Title section.

References authors_.

bool core::io::HeaderInformation::author_in_progress ( ) const

inline

References author_in_progress_.

Referenced by parse_in_progress().

Authors const& core::io::HeaderInformation::authors ( ) const

inline

References authors_.

Referenced by fill_author_records().

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

References classification_.

Referenced by fill_header_record(), and store_classification().

void core::io::HeaderInformation::clear_authors ( )

inline

References authors_.

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

References compounds_.

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

References experimental_techniques_.

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

References keywords_.

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

References title_.

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

References compound_in_progress_.

Referenced by parse_in_progress().

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

static

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

Referenced by fill_compound_records().

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

References compounds_.

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

References dep_day_, dep_month_, dep_year_, and core::id::to_string().

Referenced by fill_header_record().

void core::io::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

References dep_day_, dep_month_, and dep_year_.

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

References experimental_technique_in_progress_.

Referenced by finalize_experimental_technique_records(), and parse_in_progress().

rcsb::ExperimentalTechniques const & core::io::HeaderInformation::experimental_techniques ( ) const

References experimental_techniques_.

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

References authors(), authors_, and fill_wrapped_records().

Referenced by fill_records().

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

References compound_token_to_string(), compounds_, fill_wrapped_records(), and protocols::hybridization::t.

Referenced by fill_records().

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

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

Referenced by fill_records().

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

References classification(), deposition_date(), core::io::pdb::HEADER, idCode(), and core::io::pdb::RecordCollection::record_from_record_type().

Referenced by fill_records().

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

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

Referenced by fill_records().

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

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

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

References fill_wrapped_records(), and title_.

Referenced by fill_records().

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

private

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

References core::io::pdb::RecordCollection::record_from_record_type(), set_line_continuation(), and core::io::TR().

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

void core::io::HeaderInformation::finalize_author_records ( )

inline

References author_in_progress_.

Referenced by finalize_parse().

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

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

Referenced by finalize_parse(), and store_compound().

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

References experimental_technique_in_progress(), experimental_technique_in_progress_, experimental_techniques_, and core::io::rcsb::string_to_experimental_technique().

Referenced by finalize_parse().

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

References keyword_in_progress_.

Referenced by finalize_parse().

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

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

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

References idCode_.

Referenced by fill_header_record(), and store_idCode().

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

References experimental_techniques_, and protocols::hybridization::t.

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

References keyword_in_progress_.

Referenced by parse_in_progress().

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

References keywords_.

Referenced by fill_keyword_records().

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

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

Referenced by fill_experimental_technique_records().

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

private

References core::io::TR().

Referenced by fill_wrapped_records().

void core::io::HeaderInformation::store_authors ( std::string const & authors )

References author_in_progress_, authors_, and core::io::TR().

Referenced by store_record().

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

References classification(), and classification_.

Referenced by store_record().

void core::io::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.

References compound_in_progress_, finalize_compound_records(), string_to_compound_token(), and UNKNOWN_CMPD.

Referenced by store_record().

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

References compounds_.

void core::io::HeaderInformation::store_deposition_date ( std::string const & deposition_date )

Store the deposition date using the format like "84-DEC-18".

References dep_day_, dep_month_, dep_year_, and core::io::TR().

Referenced by store_record().

void core::io::HeaderInformation::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.

Note: These parameters are listed in the opposite order that they are given in a .pdb file!

References dep_day_, dep_month_, dep_year_, and core::io::TR().

void core::io::HeaderInformation::store_experimental_technique ( rcsb::ExperimentalTechnique technique )

References experimental_techniques_.

void core::io::HeaderInformation::store_experimental_techniques ( std::string const & exp )

Parse the list of techniques string following the technique field in the EXPDTA record of the pdb format and store the techniques.

References experimental_technique_in_progress_, experimental_techniques_, core::io::rcsb::string_to_experimental_technique(), and core::io::TR().

Referenced by store_record().

void core::io::HeaderInformation::store_idCode ( std::string const & id_code )

References idCode(), and idCode_.

Referenced by store_record().

void core::io::HeaderInformation::store_keywords ( std::string const & keywords )

References keyword_in_progress_, keywords_, and core::io::TR().

Referenced by store_record().

void core::io::HeaderInformation::store_record ( pdb::Record & R )

References store_authors(), store_classification(), store_compound(), store_deposition_date(), store_experimental_techniques(), store_idCode(), store_keywords(), and store_title().

void core::io::HeaderInformation::store_title ( std::string const & title )

Append title record onto current title string.

Append title, strip off white space on the left for the first record and on the right for all records.

References core::chemical::orbitals::strip_whitespace(), title(), title_, and core::io::TR().

Referenced by store_record().

HeaderInformation::CompoundToken core::io::HeaderInformation::string_to_compound_token	(	std::string const &	token,
		bool	warn_on_unrecognized = `true`
	)