database_io.cc File Reference

Database input/output function definitions for carbohydrate-specific data. More...

#include <core/chemical/carbohydrates/database_io.hh>
#include <core/types.hh>
#include <utility/io/util.hh>
#include <utility/exit.hh>
#include <utility/string_util.hh>
#include <basic/Tracer.hh>
#include <basic/database/open.hh>
#include <sstream>
#include <utility/stream_util.hh>
#include <core/chemical/carbohydrates/CarbohydrateInfoManager.hh>

Namespaces
	core
	A class for reading in the atom type properties.
	core::chemical
	core::chemical::carbohydrates

Functions
static basic::Tracer	TR ("core.chemical.carbohydrates.database_io")
std::string	core::chemical::carbohydrates::find_glycan_sequence_file (std::string filename)
	Try various combinations to locate the specific glycan sequence file being requested by the user. More...
std::string	core::chemical::carbohydrates::read_glycan_sequence_file (std::string filename)
	Read a single-line glycan sequence file. More...
void	core::chemical::carbohydrates::check_if_applicable (std::string &variable)
void	core::chemical::carbohydrates::replace_underscores_with_spaces (std::string &phrase)
std::map< std::string, RootData >	core::chemical::carbohydrates::read_codes_and_roots_from_database_file (std::string const &filename)
	Return a map of strings to strings, which are saccharide-specific 3-letter codes mapped to IUPAC roots, read from a database file. More...
std::map< core::Size, std::pair< char, std::string > >	core::chemical::carbohydrates::read_ring_sizes_and_morphemes_from_database_file (std::string const &filename)
	Return a map of Sizes to pairs of char and string, which are ring sizes mapped to 1-letter affixes and morphemes, respectively, read from a database file. More...
SugarModificationsNomenclatureTable	core::chemical::carbohydrates::read_nomenclature_table_from_database_file (std::string const &filename)
	Return a table of nomenclature data for sugar modifications, read from a database file. More...
LinkageConformers	core::chemical::carbohydrates::read_linkage_conformers_from_database_file (std::string const &filename)
	Return a map of linkage conformer data, read from a database file. More...
std::map< std::string, std::string >	core::chemical::carbohydrates::read_short_names_to_iupac_format_string (std::string const &dir, std::string common_mapping_path)
	Return a map of short names to IUPAC formatted strings. Reads from db_dir/common_names.txt and loads the IUPAC files as strings. More...

Detailed Description

Database input/output function definitions for carbohydrate-specific data.

Author

Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

Function Documentation

TR()

static basic::Tracer TR ( "core.chemical.carbohydrates.database_io"  )

static