#include <CarbohydrateInfoManager.hh>

Inheritance diagram for core::chemical::carbohydrates::CarbohydrateInfoManager:

Static Public Member Functions
static std::string const &	codes_to_root_map_file ()
	Get the path to the codes_to_root.map database file. More...

static std::string const &	sugar_modifications_table_file ()
	Get the path to the sugar_modifications.table database file. More...

static std::string const &	ring_size_to_morphemes_map_file ()
	Get the path to the ring_size_to_morphemes.map database file. More...

static bool	is_valid_sugar_code (std::string const &code)
	Is the given 3-letter code a valid Rosetta/IUPAC code for carbohydrates? More...

static std::string const &	root_from_code (std::string const &code)
	Get the monosaccharide root name from the given Rosetta/IUPAC 3-letter code. More...

static char	default_stereochem_from_code (std::string const &code)
	Get the default stereochemistry from the given Rosetta/IUPAC 3-letter code. More...

static char	anomeric_position_from_code (std::string const &code)
	Get the position of the anomeric carbon from the given Rosetta/IUPAC 3-letter code. More...

static bool	is_valid_ring_affix (char affix)
	Is the given 1-letter code valid for designating carbohydrate ring size? More...

static char	ring_affix_from_ring_size (core::Size ring_size)
	Get the 1-letter affix for designating a carbohydrate ring of this size. More...

static std::string const &	morpheme_from_ring_size (core::Size ring_size)
	Get the morpheme for designating a carbohydrate ring of this size. More...

static bool	is_valid_modification_affix (std::string const &affix)
	Is the given short affix valid for designating a sugar modification? More...

static std::string const &	patch_name_from_affix (std::string const &affix)
	Get the Rosetta patch name for this sugar modification affix. More...

static core::uint	default_position_from_affix (std::string const &affix)
	Get the default position for this sugar modification affix. More...

static bool	affix_has_inherent_position (std::string const &affix)
	Does this sugar modification affix have an inherent/defined position? More...

static VariantType	branch_variant_type_from_atom_name (std::string const &atom_name)
	Get the Cn_BRANCH_POINT VariantType for this atom name, e.g., On. More...

static VariantType	branch_variant_type_from_position (core::uint const position)
	Get the Cn_BRANCH_POINT VariantType for this position (n). More...

static bool	pair_has_linkage_statistics (std::string const &res1, std::string const &res2)
	Does the linkage between the given pair of monosaccharide residues have statistics in the database? More...

static utility::vector1< LinkageConformerData >	linkages_from_pair (std::string const &res1, std::string const &res2)
	Get the "linkage conformer" statistical data from a given pair of monosaccharide residues. More...

static std::map< std::string, std::string > const &	get_short_name_to_iupac_strings_map ()
	Get a map of short names to the full iupac glycan sequence for common glycosylations. More...

Private Member Functions
	CarbohydrateInfoManager ()
	Default constructor. More...

std::map< std::string, RootData > const &	code_to_root_map ()

std::map< core::Size, std::pair< char, std::string > > const &	ring_size_to_morphemes_map ()

utility::vector1< char > const &	ring_affixes ()

SugarModificationsNomenclatureTable const &	nomenclature_table ()

std::map< std::string, std::string > const &	affix_to_patch_map ()

std::map< std::string, core::uint > const &	affix_to_position_map ()

std::map< std::string, bool > const &	affix_to_position_inherency_map ()

LinkageConformers const &	linkage_conformers_map ()

std::string	find_linkage_conformer_data_file (std::string filename)

std::map< std::string, std::string > const &	short_name_to_iupac_strings_map ()
	Get a map of short names to the full iupac glycan sequence for common glycosylations. More...

Private Attributes
std::map< std::string, RootData >	code_to_root_map_

std::map< core::Size, std::pair< char, std::string > >	ring_size_to_morphemes_map_

utility::vector1< char >	ring_affixes_

SugarModificationsNomenclatureTable	nomenclature_table_

std::map< std::string, std::string >	affix_to_patch_map_

std::map< std::string, core::uint >	affix_to_position_map_

std::map< std::string, std::string >	short_name_to_iupac_strings_map_

std::map< std::string, bool >	affix_to_position_inherency_map_

std::map< std::pair< std::string, std::string >, utility::vector1< LinkageConformerData > >	linkage_conformers_map_

Friends
class	utility::SingletonBase< CarbohydrateInfoManager >

Detailed Description

This class is a singleton and manages CarbohydrateInfo data that should only be read from the database one time and shared among all instances of CarbohydrateInfo.

Constructor & Destructor Documentation

◆ CarbohydrateInfoManager()

core::chemical::carbohydrates::CarbohydrateInfoManager::CarbohydrateInfoManager ( )

private

Default constructor.

Member Function Documentation

◆ affix_has_inherent_position()

bool core::chemical::carbohydrates::CarbohydrateInfoManager::affix_has_inherent_position ( std::string const & affix )

static

Does this sugar modification affix have an inherent/defined position?

◆ affix_to_patch_map()

std::map< std::string, std::string > const & core::chemical::carbohydrates::CarbohydrateInfoManager::affix_to_patch_map ( )

private

◆ affix_to_position_inherency_map()

std::map< std::string, bool > const & core::chemical::carbohydrates::CarbohydrateInfoManager::affix_to_position_inherency_map ( )

private

◆ affix_to_position_map()

std::map< std::string, core::uint > const & core::chemical::carbohydrates::CarbohydrateInfoManager::affix_to_position_map ( )

private

◆ anomeric_position_from_code()

char core::chemical::carbohydrates::CarbohydrateInfoManager::anomeric_position_from_code ( std::string const & code )

static

Get the position of the anomeric carbon from the given Rosetta/IUPAC 3-letter code.

Referenced by core::io::determine_glycan_links(), and core::io::pose_from_sfr::PoseFromSFRBuilder::determine_residue_branching_info().

◆ branch_variant_type_from_atom_name()

VariantType core::chemical::carbohydrates::CarbohydrateInfoManager::branch_variant_type_from_atom_name ( std::string const & atom_name )

static

Get the Cn_BRANCH_POINT VariantType for this atom name, e.g., On.

References core::chemical::C1_BRANCH_POINT, core::chemical::C2_BRANCH_POINT, core::chemical::C3_BRANCH_POINT, core::chemical::C4_BRANCH_POINT, core::chemical::C5_BRANCH_POINT, core::chemical::C6_BRANCH_POINT, core::chemical::C7_BRANCH_POINT, core::chemical::C8_BRANCH_POINT, core::chemical::C9_BRANCH_POINT, and core::chemical::NO_VARIANT.

Referenced by core::pose::carbohydrates::glycosylate_pose(), and core::pose::carbohydrates::setup_existing_glycans().

◆ branch_variant_type_from_position()

VariantType core::chemical::carbohydrates::CarbohydrateInfoManager::branch_variant_type_from_position ( core::uint const position )

static

Get the Cn_BRANCH_POINT VariantType for this position (n).

References core::chemical::C1_BRANCH_POINT, core::chemical::C2_BRANCH_POINT, core::chemical::C3_BRANCH_POINT, core::chemical::C4_BRANCH_POINT, core::chemical::C5_BRANCH_POINT, core::chemical::C6_BRANCH_POINT, core::chemical::C7_BRANCH_POINT, core::chemical::C8_BRANCH_POINT, core::chemical::C9_BRANCH_POINT, and core::chemical::NO_VARIANT.

◆ code_to_root_map()

std::map< std::string, RootData > const & core::chemical::carbohydrates::CarbohydrateInfoManager::code_to_root_map ( )

private

References core::chemical::carbohydrates::read_codes_and_roots_from_database_file().

◆ codes_to_root_map_file()

std::string const & core::chemical::carbohydrates::CarbohydrateInfoManager::codes_to_root_map_file ( )

static

Get the path to the codes_to_root.map database file.

References protocols::abinitio::filename().

◆ default_position_from_affix()

core::uint core::chemical::carbohydrates::CarbohydrateInfoManager::default_position_from_affix ( std::string const & affix )

static

Get the default position for this sugar modification affix.

Returns: A position from 1 to 9 or 0 if there is no default value.

◆ default_stereochem_from_code()

char core::chemical::carbohydrates::CarbohydrateInfoManager::default_stereochem_from_code ( std::string const & code )

static

Get the default stereochemistry from the given Rosetta/IUPAC 3-letter code.

Returns: L, D, or *, where * indicates that the stereochemistry is inherent to the name.

Referenced by core::chemical::carbohydrates::CarbohydrateInfo::determine_IUPAC_names().

◆ find_linkage_conformer_data_file()

std::string core::chemical::carbohydrates::CarbohydrateInfoManager::find_linkage_conformer_data_file ( std::string filename )

private

References protocols::abinitio::filename().

◆ get_short_name_to_iupac_strings_map()

std::map< std::string, std::string > const & core::chemical::carbohydrates::CarbohydrateInfoManager::get_short_name_to_iupac_strings_map ( )

static

Get a map of short names to the full iupac glycan sequence for common glycosylations.

Referenced by protocols::carbohydrates::SimpleGlycosylateMover::setup_and_load_iupac_sequences().

◆ is_valid_modification_affix()

bool core::chemical::carbohydrates::CarbohydrateInfoManager::is_valid_modification_affix ( std::string const & affix )

static

Is the given short affix valid for designating a sugar modification?

◆ is_valid_ring_affix()

bool core::chemical::carbohydrates::CarbohydrateInfoManager::is_valid_ring_affix ( char affix )

static

Is the given 1-letter code valid for designating carbohydrate ring size?

◆ is_valid_sugar_code()

bool core::chemical::carbohydrates::CarbohydrateInfoManager::is_valid_sugar_code ( std::string const & code )

static

Is the given 3-letter code a valid Rosetta/IUPAC code for carbohydrates?

Referenced by core::io::determine_glycan_links(), core::io::pose_from_sfr::PoseFromSFRBuilder::determine_residue_branching_info(), core::io::find_carbohydrate_order(), core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_quick_and_dirty_resolve_residue_types(), and core::io::pose_from_sfr::PoseFromSFRBuilder::pre_process_residue_type_information().

◆ linkage_conformers_map()

LinkageConformers const & core::chemical::carbohydrates::CarbohydrateInfoManager::linkage_conformers_map ( )

private

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

◆ linkages_from_pair()

utility::vector1< LinkageConformerData > core::chemical::carbohydrates::CarbohydrateInfoManager::linkages_from_pair	(	std::string const &	res1,
		std::string const &	res2
	)

static

Get the "linkage conformer" statistical data from a given pair of monosaccharide residues.

References core::chemical::carbohydrates::convert_residue_names_into_linkage_map_key().

Referenced by protocols::carbohydrates::LinkageConformerMover::apply(), and core::pose::carbohydrates::idealize_last_n_glycans_in_pose().

◆ morpheme_from_ring_size()

std::string const & core::chemical::carbohydrates::CarbohydrateInfoManager::morpheme_from_ring_size ( core::Size ring_size )

static

Get the morpheme for designating a carbohydrate ring of this size.

Referenced by core::chemical::carbohydrates::CarbohydrateInfo::determine_IUPAC_names(), and core::chemical::carbohydrates::CarbohydrateInfo::show().

◆ nomenclature_table()

SugarModificationsNomenclatureTable const & core::chemical::carbohydrates::CarbohydrateInfoManager::nomenclature_table ( )

private

References core::chemical::carbohydrates::read_nomenclature_table_from_database_file().

◆ pair_has_linkage_statistics()

bool core::chemical::carbohydrates::CarbohydrateInfoManager::pair_has_linkage_statistics	(	std::string const &	res1,
		std::string const &	res2
	)

static

Does the linkage between the given pair of monosaccharide residues have statistics in the database?

References core::chemical::carbohydrates::convert_residue_names_into_linkage_map_key().

Referenced by protocols::carbohydrates::LinkageConformerMover::apply(), and core::pose::carbohydrates::idealize_last_n_glycans_in_pose().

◆ patch_name_from_affix()

std::string const & core::chemical::carbohydrates::CarbohydrateInfoManager::patch_name_from_affix ( std::string const & affix )

static

Get the Rosetta patch name for this sugar modification affix.

◆ ring_affix_from_ring_size()

char core::chemical::carbohydrates::CarbohydrateInfoManager::ring_affix_from_ring_size ( core::Size ring_size )

static

Get the 1-letter affix for designating a carbohydrate ring of this size.

Referenced by core::chemical::carbohydrates::CarbohydrateInfo::determine_IUPAC_names().

◆ ring_affixes()

utility::vector1< char > const & core::chemical::carbohydrates::CarbohydrateInfoManager::ring_affixes ( )

private

◆ ring_size_to_morphemes_map()

std::map< core::Size, std::pair< char, std::string > > const & core::chemical::carbohydrates::CarbohydrateInfoManager::ring_size_to_morphemes_map ( )

private

References core::chemical::carbohydrates::read_ring_sizes_and_morphemes_from_database_file().

◆ ring_size_to_morphemes_map_file()

std::string const & core::chemical::carbohydrates::CarbohydrateInfoManager::ring_size_to_morphemes_map_file ( )

static

Get the path to the ring_size_to_morphemes.map database file.

References protocols::abinitio::filename().

◆ root_from_code()

std::string const & core::chemical::carbohydrates::CarbohydrateInfoManager::root_from_code ( std::string const & code )

static

Get the monosaccharide root name from the given Rosetta/IUPAC 3-letter code.

Referenced by core::chemical::carbohydrates::CarbohydrateInfo::basic_name(), and core::chemical::carbohydrates::CarbohydrateInfo::determine_IUPAC_names().

◆ short_name_to_iupac_strings_map()

std::map< std::string, std::string > const & core::chemical::carbohydrates::CarbohydrateInfoManager::short_name_to_iupac_strings_map ( )

private

Get a map of short names to the full iupac glycan sequence for common glycosylations.

References protocols::abinitio::filename(), protocols::hybridization::path, and core::chemical::carbohydrates::read_short_names_to_iupac_format_string().

◆ sugar_modifications_table_file()

std::string const & core::chemical::carbohydrates::CarbohydrateInfoManager::sugar_modifications_table_file ( )

static

Get the path to the sugar_modifications.table database file.

References protocols::abinitio::filename().

Friends And Related Function Documentation

◆ utility::SingletonBase< CarbohydrateInfoManager >

friend class utility::SingletonBase< CarbohydrateInfoManager >

friend

Member Data Documentation

◆ affix_to_patch_map_

std::map< std::string, std::string > core::chemical::carbohydrates::CarbohydrateInfoManager::affix_to_patch_map_

private

◆ affix_to_position_inherency_map_

std::map< std::string, bool > core::chemical::carbohydrates::CarbohydrateInfoManager::affix_to_position_inherency_map_

private

◆ affix_to_position_map_

std::map< std::string, core::uint > core::chemical::carbohydrates::CarbohydrateInfoManager::affix_to_position_map_

private

◆ code_to_root_map_

std::map< std::string, RootData > core::chemical::carbohydrates::CarbohydrateInfoManager::code_to_root_map_

private

◆ linkage_conformers_map_

std::map< std::pair< std::string, std::string >, utility::vector1< LinkageConformerData > > core::chemical::carbohydrates::CarbohydrateInfoManager::linkage_conformers_map_

private

◆ nomenclature_table_

SugarModificationsNomenclatureTable core::chemical::carbohydrates::CarbohydrateInfoManager::nomenclature_table_

private

◆ ring_affixes_

utility::vector1< char > core::chemical::carbohydrates::CarbohydrateInfoManager::ring_affixes_

private

◆ ring_size_to_morphemes_map_

std::map< core::Size, std::pair< char, std::string > > core::chemical::carbohydrates::CarbohydrateInfoManager::ring_size_to_morphemes_map_

private

◆ short_name_to_iupac_strings_map_

std::map< std::string, std::string > core::chemical::carbohydrates::CarbohydrateInfoManager::short_name_to_iupac_strings_map_

private

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

src/core/chemical/carbohydrates/CarbohydrateInfoManager.hh
src/core/chemical/carbohydrates/CarbohydrateInfoManager.cc

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ CarbohydrateInfoManager()

Member Function Documentation

◆ affix_has_inherent_position()

◆ affix_to_patch_map()

◆ affix_to_position_inherency_map()

◆ affix_to_position_map()

◆ anomeric_position_from_code()

◆ branch_variant_type_from_atom_name()

◆ branch_variant_type_from_position()

◆ code_to_root_map()

◆ codes_to_root_map_file()

◆ default_position_from_affix()

◆ default_stereochem_from_code()

◆ find_linkage_conformer_data_file()

◆ get_short_name_to_iupac_strings_map()

◆ is_valid_modification_affix()

◆ is_valid_ring_affix()

◆ is_valid_sugar_code()

◆ linkage_conformers_map()

◆ linkages_from_pair()

◆ morpheme_from_ring_size()

◆ nomenclature_table()

◆ pair_has_linkage_statistics()

◆ patch_name_from_affix()

◆ ring_affix_from_ring_size()

◆ ring_affixes()

◆ ring_size_to_morphemes_map()

◆ ring_size_to_morphemes_map_file()

◆ root_from_code()

◆ short_name_to_iupac_strings_map()

◆ sugar_modifications_table_file()

Friends And Related Function Documentation

◆ utility::SingletonBase< CarbohydrateInfoManager >

Member Data Documentation

◆ affix_to_patch_map_

◆ affix_to_position_inherency_map_

◆ affix_to_position_map_

◆ code_to_root_map_

◆ linkage_conformers_map_

◆ nomenclature_table_

◆ ring_affixes_

◆ ring_size_to_morphemes_map_

◆ short_name_to_iupac_strings_map_