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Rosetta
2020.50
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#include <CarbohydrateInfoManager.hh>
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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 > |
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.
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Default constructor.
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Does this sugar modification affix have an inherent/defined position?
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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().
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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().
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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.
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Get the path to the codes_to_root.map database file.
References protocols::abinitio::filename().
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Get the default position for this sugar modification affix.
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Get the default stereochemistry from the given Rosetta/IUPAC 3-letter code.
Referenced by core::chemical::carbohydrates::CarbohydrateInfo::determine_IUPAC_names().
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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().
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Is the given short affix valid for designating a sugar modification?
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Is the given 1-letter code valid for designating carbohydrate ring size?
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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(), and core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized().
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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().
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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().
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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().
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Get the Rosetta patch name for this sugar modification affix.
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Get the 1-letter affix for designating a carbohydrate ring of this size.
Referenced by core::chemical::carbohydrates::CarbohydrateInfo::determine_IUPAC_names().
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Get the path to the ring_size_to_morphemes.map database file.
References protocols::abinitio::filename().
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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().
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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().
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Get the path to the sugar_modifications.table database file.
References protocols::abinitio::filename().
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