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core::io::pdb::HeaderInformation Class Reference

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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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.

Member Typedef Documentation

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

Member Enumeration Documentation

Enumerator
MOL_ID 
MOLECULE 
CHAIN 
FRAGMENT 
SYNONYM 
EC 
ENGINEERED 
MUTATION 
OTHER_DETAILS 
CompoundToken_max 

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 

Constructor & Destructor Documentation

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

Member Function Documentation

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

References compounds_.

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

References keywords_.

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

References title_.

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

References compound_in_progress_.

Referenced by parse_in_progress().

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

References compounds_.

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

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

References dep_day_, dep_month_, and dep_year_.

bool core::io::pdb::HeaderInformation::experimental_technique_in_progress ( ) const
string core::io::pdb::HeaderInformation::experimental_technique_to_string ( ExperimentalTechnique  technique)
static
list< HeaderInformation::ExperimentalTechnique > const & core::io::pdb::HeaderInformation::experimental_techniques ( ) const
void core::io::pdb::HeaderInformation::fill_compound_records ( std::vector< Record > &  VR) const
void core::io::pdb::HeaderInformation::fill_experimental_technique_records ( std::vector< Record > &  VR) const
void core::io::pdb::HeaderInformation::fill_header_record ( std::vector< Record > &  VR) const
void core::io::pdb::HeaderInformation::fill_keyword_records ( std::vector< Record > &  VR) const

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

Referenced by fill_records().

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

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

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 ( )

References compound_in_progress_.

Referenced by finalize_parse().

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

References keyword_in_progress_.

Referenced by finalize_parse().

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

References idCode_.

Referenced by fill_header_record(), and store_idCode().

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

References keyword_in_progress_.

Referenced by parse_in_progress().

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

References keywords_.

Referenced by fill_keyword_records().

bool core::io::pdb::HeaderInformation::parse_in_progress ( ) const
void core::io::pdb::HeaderInformation::set_line_continuation ( Record R,
Size const  line_no 
) const
private

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

Referenced by fill_wrapped_records().

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

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.

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

Referenced by store_record().

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

References compounds_.

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

Referenced by store_record().

void core::io::pdb::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.

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

void core::io::pdb::HeaderInformation::store_experimental_technique ( HeaderInformation::ExperimentalTechnique  technique)
void core::io::pdb::HeaderInformation::store_experimental_techniques ( std::string const &  exp)

the list of techniques string following the technqiue field in the EXPDTA record of the pdb format and store the techniques

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

Referenced by store_record().

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

References idCode(), and idCode_.

Referenced by store_record().

void core::io::pdb::HeaderInformation::store_keywords ( std::string const &  keywords)
void core::io::pdb::HeaderInformation::store_record ( Record R)
void core::io::pdb::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 strip_whitespace(), title(), title_, and core::io::pdb::TR().

Referenced by store_record().

HeaderInformation::CompoundToken core::io::pdb::HeaderInformation::string_to_compound_token ( std::string const &  token)
static
HeaderInformation::ExperimentalTechnique core::io::pdb::HeaderInformation::string_to_experimental_technique ( std::string const &  technique)
static
std::string const & core::io::pdb::HeaderInformation::title ( ) const

References title_.

Referenced by store_title().

Member Data Documentation

std::string core::io::pdb::HeaderInformation::classification_
private

Possibly abbreviated classification type.

Referenced by classification(), fill_header_record(), and store_classification().

bool core::io::pdb::HeaderInformation::compound_in_progress_
private
Compounds core::io::pdb::HeaderInformation::compounds_
private
Size core::io::pdb::HeaderInformation::dep_day_
private
Size core::io::pdb::HeaderInformation::dep_month_
private
Size core::io::pdb::HeaderInformation::dep_year_
private

Deposition date DD-MON-YY.

Referenced by deposition_date(), fill_header_record(), and store_deposition_date().

std::string core::io::pdb::HeaderInformation::experimental_technique_in_progress_
private
ExperimentalTechniques core::io::pdb::HeaderInformation::experimental_techniques_
private
std::string core::io::pdb::HeaderInformation::idCode_
private

4-character PDB unique identifier

Referenced by fill_header_record(), idCode(), and store_idCode().

bool core::io::pdb::HeaderInformation::keyword_in_progress_
private
Keywords core::io::pdb::HeaderInformation::keywords_
private
std::string core::io::pdb::HeaderInformation::title_
private

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