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

◆ Authors

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

◆ Compounds

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

◆ Keywords

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

Member Enumeration Documentation

◆ CompoundToken

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

◆ HeaderInformation() [1/2]

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

◆ HeaderInformation() [2/2]

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

◆ ~HeaderInformation()

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

overridedefault

Member Function Documentation

◆ add_author()

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

Add an author to this Title section.

References authors_.

◆ author_in_progress()

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

inline

References author_in_progress_.

Referenced by parse_in_progress().

◆ authors()

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

inline

References authors_.

Referenced by fill_author_records(), and store_authors().

◆ classification()

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

References classification_.

Referenced by fill_header_record(), and store_classification().

◆ clear_authors()

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

inline

References authors_.

◆ clear_compounds()

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

References compounds_.

◆ clear_experimental_techniques()

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

References experimental_techniques_.

◆ clear_keywords()

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

References keywords_.

◆ clear_title()

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

References title_.

◆ compound_in_progress()

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

References compound_in_progress_.

Referenced by parse_in_progress().

◆ compound_token_to_string()

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().

◆ compounds()

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

References compounds_.

◆ deposition_date() [1/2]

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

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

Referenced by fill_header_record().

◆ deposition_date() [2/2]

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_.

◆ experimental_technique_in_progress()

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

References experimental_technique_in_progress_.

Referenced by finalize_experimental_technique_records(), and parse_in_progress().

◆ experimental_techniques()

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

References experimental_techniques_.

◆ fill_author_records()

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

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

Referenced by fill_records().

◆ fill_compound_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().

◆ fill_experimental_technique_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().

◆ fill_header_record()

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().

◆ fill_keyword_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().

◆ 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().

◆ 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().

◆ fill_wrapped_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().

◆ finalize_author_records()

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

inline

References author_in_progress_.

Referenced by finalize_parse().

◆ finalize_compound_records()

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().

◆ finalize_experimental_technique_records()

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().

◆ finalize_keyword_records()

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

References keyword_in_progress_.

Referenced by finalize_parse().

◆ finalize_parse()

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

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

◆ idCode()

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

References idCode_.

Referenced by fill_header_record(), and store_idCode().

◆ is_experimental_technique()

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

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

◆ keyword_in_progress()

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

References keyword_in_progress_.

Referenced by parse_in_progress().

◆ keywords()

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

References keywords_.

Referenced by fill_keyword_records(), and store_keywords().

◆ parse_in_progress()

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().

◆ set_line_continuation()

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().

◆ store_authors()

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

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

Referenced by store_record().

◆ store_classification()

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

References classification(), and classification_.

Referenced by store_record().

◆ store_compound() [1/2]

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

References compounds_.

◆ store_compound() [2/2]

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().

◆ store_deposition_date() [1/2]

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().

◆ store_deposition_date() [2/2]

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().

◆ store_experimental_technique()

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

References experimental_techniques_.

◆ store_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().

◆ store_idCode()

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

References idCode(), and idCode_.

Referenced by store_record().

◆ store_keywords()

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

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

Referenced by store_record().

◆ 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().

◆ 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().

◆ string_to_compound_token()

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

static

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

Referenced by finalize_compound_records(), and store_compound().

◆ title()

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

References title_.

Referenced by store_title().

Member Data Documentation

◆ author_in_progress_

bool core::io::HeaderInformation::author_in_progress_

private

Referenced by author_in_progress(), finalize_author_records(), and store_authors().

◆ authors_

Authors core::io::HeaderInformation::authors_

private

Referenced by add_author(), authors(), clear_authors(), fill_author_records(), and store_authors().

◆ classification_

std::string core::io::HeaderInformation::classification_

private

Possibly abbreviated classification type.

Referenced by classification(), and store_classification().

◆ compound_in_progress_

std::string core::io::HeaderInformation::compound_in_progress_

private

Referenced by compound_in_progress(), finalize_compound_records(), and store_compound().

◆ compounds_

Compounds core::io::HeaderInformation::compounds_

private

Referenced by clear_compounds(), compounds(), fill_compound_records(), finalize_compound_records(), and store_compound().

◆ dep_day_

Size core::io::HeaderInformation::dep_day_

private

Referenced by deposition_date(), and store_deposition_date().

◆ dep_month_

Size core::io::HeaderInformation::dep_month_

private

Referenced by deposition_date(), and store_deposition_date().

◆ dep_year_

Size core::io::HeaderInformation::dep_year_

private

Deposition date DD-MON-YY.

Referenced by deposition_date(), and store_deposition_date().

◆ experimental_technique_in_progress_

std::string core::io::HeaderInformation::experimental_technique_in_progress_

private

Referenced by experimental_technique_in_progress(), finalize_experimental_technique_records(), and store_experimental_techniques().

◆ experimental_techniques_

rcsb::ExperimentalTechniques core::io::HeaderInformation::experimental_techniques_

private

Referenced by clear_experimental_techniques(), experimental_techniques(), fill_experimental_technique_records(), finalize_experimental_technique_records(), is_experimental_technique(), store_experimental_technique(), and store_experimental_techniques().

◆ idCode_

std::string core::io::HeaderInformation::idCode_

private

4-character PDB unique identifier

Referenced by idCode(), and store_idCode().

◆ keyword_in_progress_

bool core::io::HeaderInformation::keyword_in_progress_

private

Referenced by finalize_keyword_records(), keyword_in_progress(), and store_keywords().

◆ keywords_

Keywords core::io::HeaderInformation::keywords_

private

Referenced by clear_keywords(), fill_keyword_records(), keywords(), and store_keywords().

◆ title_

std::string core::io::HeaderInformation::title_

private

Referenced by clear_title(), fill_title_records(), store_title(), and title().

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

src/core/io/HeaderInformation.hh
src/core/io/HeaderInformation.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ Authors

◆ Compounds

◆ Keywords

Member Enumeration Documentation

◆ CompoundToken

Constructor & Destructor Documentation

◆ HeaderInformation() [1/2]

◆ HeaderInformation() [2/2]

◆ ~HeaderInformation()

Member Function Documentation

◆ add_author()

◆ author_in_progress()

◆ authors()

◆ classification()

◆ clear_authors()

◆ clear_compounds()

◆ clear_experimental_techniques()

◆ clear_keywords()

◆ clear_title()

◆ compound_in_progress()

◆ compound_token_to_string()

◆ compounds()

◆ deposition_date() [1/2]

◆ deposition_date() [2/2]

◆ experimental_technique_in_progress()

◆ experimental_techniques()

◆ fill_author_records()

◆ fill_compound_records()

◆ fill_experimental_technique_records()

◆ fill_header_record()

◆ fill_keyword_records()

◆ fill_records()

◆ fill_title_records()

◆ fill_wrapped_records()

◆ finalize_author_records()

◆ finalize_compound_records()

◆ finalize_experimental_technique_records()

◆ finalize_keyword_records()

◆ finalize_parse()

◆ idCode()

◆ is_experimental_technique()

◆ keyword_in_progress()

◆ keywords()

◆ parse_in_progress()

◆ set_line_continuation()

◆ store_authors()

◆ store_classification()

◆ store_compound() [1/2]

◆ store_compound() [2/2]

◆ store_deposition_date() [1/2]

◆ store_deposition_date() [2/2]

◆ store_experimental_technique()

◆ store_experimental_techniques()

◆ store_idCode()

◆ store_keywords()

◆ store_record()

◆ store_title()

◆ string_to_compound_token()

◆ title()

Member Data Documentation

◆ author_in_progress_

◆ authors_

◆ classification_

◆ compound_in_progress_

◆ compounds_

◆ dep_day_

◆ dep_month_

◆ dep_year_

◆ experimental_technique_in_progress_

◆ experimental_techniques_

◆ idCode_

◆ keyword_in_progress_

◆ keywords_