Classes
class	CarbohydrateInfo

struct	RootData

class	CarbohydrateInfoManager

struct	LinkageConformerData
	Holds conformer data for glycan torsional sampling used by the LinkageConformerMover. More...

struct	SugarModificationsNomenclatureTableRow
	A structure for storing information related to the nomenclature of modified sugars. More...

Typedefs
typedef utility::pointer::shared_ptr< CarbohydrateInfo >	CarbohydrateInfoOP

typedef utility::pointer::shared_ptr< CarbohydrateInfo const >	CarbohydrateInfoCOP

typedef std::map< std::pair< std::string, std::string >, utility::vector1< LinkageConformerData > >	LinkageConformers

typedef std::map< std::string, SugarModificationsNomenclatureTableRow >	SugarModificationsNomenclatureTable

Functions
std::ostream &	operator<< (std::ostream &output, CarbohydrateInfo const &object_to_output)

std::pair< std::string, std::string >	convert_residue_names_into_linkage_map_key (std::string const &name1, std::string const &name2)

std::string	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	read_glycan_sequence_file (std::string filename)
	Read a single-line glycan sequence file. More...

void	check_if_applicable (std::string &variable)

void	replace_underscores_with_spaces (std::string &phrase)

std::map< std::string, RootData >	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 > >	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	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	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 >	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...

Typedef Documentation

◆ CarbohydrateInfoCOP

typedef utility::pointer::shared_ptr< CarbohydrateInfo const > core::chemical::carbohydrates::CarbohydrateInfoCOP

◆ CarbohydrateInfoOP

typedef utility::pointer::shared_ptr< CarbohydrateInfo > core::chemical::carbohydrates::CarbohydrateInfoOP

◆ LinkageConformers

typedef std::map< std::pair< std::string, std::string >, utility::vector1< LinkageConformerData > > core::chemical::carbohydrates::LinkageConformers

◆ SugarModificationsNomenclatureTable

typedef std::map< std::string, SugarModificationsNomenclatureTableRow > core::chemical::carbohydrates::SugarModificationsNomenclatureTable

Function Documentation

◆ check_if_applicable()

void core::chemical::carbohydrates::check_if_applicable ( std::string & variable )

Referenced by read_nomenclature_table_from_database_file().

◆ convert_residue_names_into_linkage_map_key()

std::pair< std::string, std::string > core::chemical::carbohydrates::convert_residue_names_into_linkage_map_key	(	std::string const &	name1,
		std::string const &	name2
	)

Referenced by core::chemical::carbohydrates::CarbohydrateInfoManager::linkages_from_pair(), and core::chemical::carbohydrates::CarbohydrateInfoManager::pair_has_linkage_statistics().

◆ find_glycan_sequence_file()

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.

The default directory to search is: database/chemical/carbohydrates/common_glycans/
The default file extension is: .iupac

References protocols::abinitio::filename().

Referenced by core::pose::carbohydrates::glycosylate_pose_by_file().

◆ operator<<()

std::ostream & core::chemical::carbohydrates::operator<<	(	std::ostream &	output,
		CarbohydrateInfo const &	object_to_output
	)

References core::chemical::carbohydrates::CarbohydrateInfo::show().

◆ read_codes_and_roots_from_database_file()

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.

References protocols::abinitio::filename(), and core::chemical::TR().

Referenced by core::chemical::carbohydrates::CarbohydrateInfoManager::code_to_root_map().

◆ read_glycan_sequence_file()

std::string core::chemical::carbohydrates::read_glycan_sequence_file ( std::string filename )

Read a single-line glycan sequence file.

References protocols::abinitio::filename().

Referenced by core::pose::carbohydrates::glycosylate_pose_by_file(), read_short_names_to_iupac_format_string(), and protocols::carbohydrates::SimpleGlycosylateMover::setup_and_load_iupac_sequences().

◆ read_linkage_conformers_from_database_file()

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.

Author: Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)

References core::chemical::carbohydrates::LinkageConformerData::conformer_bins, protocols::abinitio::filename(), core::chemical::carbohydrates::LinkageConformerData::mean_sd, core::chemical::carbohydrates::LinkageConformerData::omega_mean_sd, core::chemical::carbohydrates::LinkageConformerData::population, core::id::to_string(), and core::chemical::TR().

Referenced by core::chemical::carbohydrates::CarbohydrateInfoManager::linkage_conformers_map().

◆ read_nomenclature_table_from_database_file()

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.

References check_if_applicable(), core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow::default_position, protocols::abinitio::filename(), core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow::has_inherent_position, core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow::implies, core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow::patch_name, replace_underscores_with_spaces(), core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow::short_affix, core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow::substituent_full_name, and core::chemical::TR().

Referenced by core::chemical::carbohydrates::CarbohydrateInfoManager::nomenclature_table().

◆ read_ring_sizes_and_morphemes_from_database_file()

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.

References protocols::abinitio::filename(), and core::chemical::TR().

Referenced by core::chemical::carbohydrates::CarbohydrateInfoManager::ring_size_to_morphemes_map().

◆ read_short_names_to_iupac_format_string()

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.

References read_glycan_sequence_file(), update_ResidueType_enum_files::short_name, and core::chemical::TR().

Referenced by core::chemical::carbohydrates::CarbohydrateInfoManager::short_name_to_iupac_strings_map().

◆ replace_underscores_with_spaces()

void core::chemical::carbohydrates::replace_underscores_with_spaces ( std::string & phrase )

References protocols::forge::methods::replace().