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core::chemical::carbohydrates Namespace Reference

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, RootDataread_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

typedef utility::pointer::shared_ptr< CarbohydrateInfo const > core::chemical::carbohydrates::CarbohydrateInfoCOP
typedef std::map< std::pair< std::string, std::string >, utility::vector1< LinkageConformerData > > core::chemical::carbohydrates::LinkageConformers

Function Documentation

void core::chemical::carbohydrates::check_if_applicable ( std::string &  variable)
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)
LinkageConformers core::chemical::carbohydrates::read_linkage_conformers_from_database_file ( std::string const &  filename)
SugarModificationsNomenclatureTable core::chemical::carbohydrates::read_nomenclature_table_from_database_file ( std::string const &  filename)
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)