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Rosetta
2020.50
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Classes | |
class | CarbohydrateInfo |
class | CarbohydrateInfoManager |
struct | LinkageConformerData |
Holds conformer data for glycan torsional sampling used by the LinkageConformerMover. More... | |
struct | RootData |
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 utility::pointer::shared_ptr< CarbohydrateInfo const > core::chemical::carbohydrates::CarbohydrateInfoCOP |
typedef utility::pointer::shared_ptr< CarbohydrateInfo > core::chemical::carbohydrates::CarbohydrateInfoOP |
typedef std::map< std::pair< std::string, std::string >, utility::vector1< LinkageConformerData > > core::chemical::carbohydrates::LinkageConformers |
typedef std::map< std::string, SugarModificationsNomenclatureTableRow > core::chemical::carbohydrates::SugarModificationsNomenclatureTable |
void core::chemical::carbohydrates::check_if_applicable | ( | std::string & | variable | ) |
Referenced by read_nomenclature_table_from_database_file().
std::pair< std::string, std::string > core::chemical::carbohydrates::convert_residue_names_into_linkage_map_key | ( | std::string const & | name1, |
std::string const & | name2 | ||
) |
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
Referenced by core::pose::carbohydrates::glycosylate_pose_by_file().
std::ostream & core::chemical::carbohydrates::operator<< | ( | std::ostream & | output, |
CarbohydrateInfo const & | object_to_output | ||
) |
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 core::chemical::TR().
Referenced by core::chemical::carbohydrates::CarbohydrateInfoManager::code_to_root_map().
std::string core::chemical::carbohydrates::read_glycan_sequence_file | ( | std::string | filename | ) |
Read a single-line glycan sequence file.
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().
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.
References core::chemical::carbohydrates::LinkageConformerData::conformer_bins, 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().
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, 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().
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 core::chemical::TR().
Referenced by core::chemical::carbohydrates::CarbohydrateInfoManager::ring_size_to_morphemes_map().
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(), and core::chemical::TR().
Referenced by core::chemical::carbohydrates::CarbohydrateInfoManager::short_name_to_iupac_strings_map().
void core::chemical::carbohydrates::replace_underscores_with_spaces | ( | std::string & | phrase | ) |
References protocols::forge::methods::replace().
Referenced by read_nomenclature_table_from_database_file().