Bindings for core::chemical::carbohydrates namespace

Classes
		builtins.object CarbohydrateInfo LinkageConformerData LinkageType SugarModificationsNomenclatureTableRow rosetta.utility.SingletonBase_core_chemical_carbohydrates_CarbohydrateInfoManager_t(builtins.object) CarbohydrateInfoManager   class CarbohydrateInfo(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, residue_type : rosetta.std.weak_ptr_const_core_chemical_ResidueType_t) -> NoneType   2. __init__(self : handle, object_to_copy : rosetta.core.chemical.carbohydrates.CarbohydrateInfo, new_owner : rosetta.std.weak_ptr_const_core_chemical_ResidueType_t) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> str anomer(...) from builtins.PyCapsule anomer(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> str   Get the anomeric form for the monosaccharide.        "alpha", "beta", or ""       "alpha" and "beta" designate the stereochemistry at the anomeric carbon of a cyclic sugar. anomeric_carbon(...) from builtins.PyCapsule anomeric_carbon(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> int   Return the anomeric carbon number.       For linear monosaccharides, this number corresponds to the carbon that is oxidized to the aldehyde  or ketone.  See also:   CarbohydrateInfo.anomeric_carbon_name()   CarbohydrateInfo.anomeric_carbon_index()   CarbohydrateInfo.is_aldose()   CarbohydrateInfo.is_ketose()   CarbohydrateInfo.is_ulose() anomeric_carbon_index(...) from builtins.PyCapsule anomeric_carbon_index(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> int   Return the atom index of the anomeric carbon in this ResidueType.       See also:   CarbohydrateInfo.anomeric_carbon()   CarbohydrateInfo.anomeric_carbon_name()   CarbohydrateInfo.is_aldose()   CarbohydrateInfo.is_ketose()   CarbohydrateInfo.is_ulose() anomeric_carbon_name(...) from builtins.PyCapsule anomeric_carbon_name(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> str   Return the atom name of the anomeric carbon.       See also:   CarbohydrateInfo.anomeric_carbon()   CarbohydrateInfo.anomeric_carbon_index()   CarbohydrateInfo.is_aldose()   CarbohydrateInfo.is_ketose()   CarbohydrateInfo.is_ulose() base_name(...) from builtins.PyCapsule base_name(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> str   Return the standard/common, non-residue, short name of the monosaccharide. branch_point(...) from builtins.PyCapsule branch_point(self : rosetta.core.chemical.carbohydrates.CarbohydrateInfo, i : int) -> int   Return the attachment point of the downstream saccharide residue attached to ith branch off of this  residue. cyclic_oxygen(...) from builtins.PyCapsule cyclic_oxygen(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> int   Return the cyclic oxygen number or 0, if linear.       This atom is used as a reference atom for certain torsion angles.  See also:   CarbohydrateInfo.anomeric_carbon()   CarbohydrateInfo.cyclic_oxygen_name()   CarbohydrateInfo.cyclic_oxygen_index() cyclic_oxygen_index(...) from builtins.PyCapsule cyclic_oxygen_index(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> int   Return the atom index of the cyclic oxygen in this ResidueType or 0, if linear.       This atom is used as a reference atom for certain torsion angles.  See also:   CarbohydrateInfo.cyclic_oxygen()   CarbohydrateInfo.cyclic_oxygen_name()   CarbohydrateInfo.anomeric_carbon_index() cyclic_oxygen_name(...) from builtins.PyCapsule cyclic_oxygen_name(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> str   Return the atom name of the cyclic oxygen.       This atom is used as a reference atom for certain torsion angles.  See also:   CarbohydrateInfo.cyclic_oxygen()   CarbohydrateInfo.anomeric_carbon_name()   CarbohydrateInfo.cyclic_oxygen_index() full_name(...) from builtins.PyCapsule full_name(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> str   Return the full IUPAC name of the monosaccharide. has_exocyclic_linkage_to_child_mainchain(...) from builtins.PyCapsule has_exocyclic_linkage_to_child_mainchain(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the attachment point of the downstream saccharide (N+1) OF THE MAINCHAIN is on an exocyclic carbon.   This residue may still have an exocylic linkage through a branch point.   See core::pose::has_exocylic_carbon_linkage to get more specific exocyclic carbon linkage info. is_D_sugar(...) from builtins.PyCapsule is_D_sugar(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is a D-sugar. is_L_sugar(...) from builtins.PyCapsule is_L_sugar(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is an L-sugar. is_N_acetylated(...) from builtins.PyCapsule is_N_acetylated(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if any hydroxyl group has been modified to an acetylated amino group. is_O_acetylated(...) from builtins.PyCapsule is_O_acetylated(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if any hydroxyl group has been modified by acetylation. is_acetylated(...) from builtins.PyCapsule is_acetylated(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the sugar has been acetylated at any position. is_acyclic(...) from builtins.PyCapsule is_acyclic(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is linear. is_aldose(...) from builtins.PyCapsule is_aldose(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is an aldose.       An aldose sugar is an aldehyde derivative.  See also:   CarbohydrateInfo.is_ketose()   CarbohydrateInfo.is_ulose()   CarbohydrateInfo.anomeric_carbon() is_alpha_sugar(...) from builtins.PyCapsule is_alpha_sugar(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the cyclic monosaccharide is an alpha sugar.       "alpha" and "beta" designate the stereochemistry at the anomeric carbon of a cyclic sugar. is_amino_sugar(...) from builtins.PyCapsule is_amino_sugar(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if any hydroxyl group has been modified to an amino group or an acetylated amino group. is_beta_sugar(...) from builtins.PyCapsule is_beta_sugar(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the cyclic monosaccharide is a beta sugar.       "alpha" and "beta" designate the stereochemistry at the anomeric carbon of a cyclic sugar. is_cyclic(...) from builtins.PyCapsule is_cyclic(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is a ring. is_furanose(...) from builtins.PyCapsule is_furanose(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is a furanose.       A furanose has a five-membered ring (like furan). is_glycoside(...) from builtins.PyCapsule is_glycoside(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is attached to something at the anomeric carbon. is_heptose(...) from builtins.PyCapsule is_heptose(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is a heptose. is_hexose(...) from builtins.PyCapsule is_hexose(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is a hexose. is_ketose(...) from builtins.PyCapsule is_ketose(*args, **kwargs) Overloaded function.   1. is_ketose(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is a ketose.       A ketose sugar is a ketone derivative.  Does not distinguish between 2-ketoses (uloses) and 3-ketoses.    See also:   CarbohydrateInfo.is_aldose()   CarbohydrateInfo.is_ulose()   CarbohydrateInfo.anomeric_carbon()   2. is_ketose(self : rosetta.core.chemical.carbohydrates.CarbohydrateInfo, n : int) -> bool   Return true if the monosaccharide is an n-ketose.       A ketose sugar is a ketone derivative.  See also:   CarbohydrateInfo.is_aldose()   CarbohydrateInfo.is_ulose()   CarbohydrateInfo.anomeric_carbon() is_nonose(...) from builtins.PyCapsule is_nonose(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is a nonose. is_octose(...) from builtins.PyCapsule is_octose(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is an octose. is_pentose(...) from builtins.PyCapsule is_pentose(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is a pentose. is_pyranose(...) from builtins.PyCapsule is_pyranose(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is a pyranose.       A pyranose has a six-membered ring (like pyran). is_septanose(...) from builtins.PyCapsule is_septanose(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is a septanose.       A septanose has a seven-membered ring. is_tetrose(...) from builtins.PyCapsule is_tetrose(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is a tetrose. is_triose(...) from builtins.PyCapsule is_triose(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is a triose. is_ulose(...) from builtins.PyCapsule is_ulose(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the monosaccharide is a 2-ketose.       See also:   CarbohydrateInfo.is_aldose()   CarbohydrateInfo.is_ketose()   CarbohydrateInfo.anomeric_carbon() is_uronic_acid(...) from builtins.PyCapsule is_uronic_acid(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> bool   Return true if the primary hydroxyl group is oxidized to the acid. last_carbon_in_ring(...) from builtins.PyCapsule last_carbon_in_ring(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> int   Get the last carbon of the ring.  Varies with ketose or aldose. mainchain_glycosidic_bond_acceptor(...) from builtins.PyCapsule mainchain_glycosidic_bond_acceptor(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> int   Return the attachment point of the downstream saccharide residue of the main chain.        an integer n of (1->n) of polysaccharide nomenclature, where n specifies the attachment point on the  upstream monosaccharide residue; e.g., 4 specifies O4; n = 0 specifies an upper terminus       A monosaccharide with a group linked to it at one position is a distinct residue type from the same  monosaccharide with the same group linked to it at another position.  For example, Rosetta treats (1->4)-beta-  D-glucopyranose as an entirely distinct residue type from (1->3)-beta-D-glucopyranose, with separate .params  files for each.    See also:   CarbohydrateInfo.n_branches()   CarbohydrateInfo.branch_point() n_branches(...) from builtins.PyCapsule n_branches(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> int   Return the number of branches off of this residue.       A monosaccharide with a group linked to it at one position is a distinct residue type from the same  monosaccharide with the same group linked to it at another position.  For example, Rosetta treats (1->4)-beta-  D-glucopyranose as an entirely distinct residue type from (1->3)-beta-D-glucopyranose, with separate .params  files for each.    See also:   CarbohydrateInfo.mainchain_glycosidic_bond_acceptor()   CarbohydrateInfo.branch_point() n_carbons(...) from builtins.PyCapsule n_carbons(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> int   Get the number of carbons in the monosaccharide.       This ignores carbons found in modifications to the base sugar. n_ring_carbons(...) from builtins.PyCapsule n_ring_carbons(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> int   Get the number of carbons in the ring. ring_size(...) from builtins.PyCapsule ring_size(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> int   Get the size of the carbohydrate ring.       A linear monosaccharide has a ring size of zero. short_name(...) from builtins.PyCapsule short_name(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> str   Return the abbreviated IUPAC name of the monosaccharide (for use in polysaccharide sequences). stereochem(...) from builtins.PyCapsule stereochem(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> str   Get the stereochemical designation for the monosaccharide.       'L' or 'D' virtual_cyclic_oxygen_index(...) from builtins.PyCapsule virtual_cyclic_oxygen_index(rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> int   Return the atom index of the virtual atom that superimposes with the cyclic oxygen in this  ResidueType or 0, if linear.       This atom is used as a reference atom for certain torsion angles.  See also:   CarbohydrateInfo.cyclic_oxygen_index()   class CarbohydrateInfoManager(rosetta.utility.SingletonBase_core_chemical_carbohydrates_CarbohydrateInfoManager_t)     This class is a singleton and manages CarbohydratesInfo data that should only be read from the database one time and shared among all instances of CarbohydrateInfo.     Method resolution order: CarbohydrateInfoManager rosetta.utility.SingletonBase_core_chemical_carbohydrates_CarbohydrateInfoManager_t builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. branch_variant_type_from_atom_name(...) from builtins.PyCapsule branch_variant_type_from_atom_name(atom_name : str) -> rosetta.core.chemical.VariantType   Get the Cn_BRANCH_POINT VariantType for this atom name, e.g., On. branch_variant_type_from_position(...) from builtins.PyCapsule branch_variant_type_from_position(position : int) -> rosetta.core.chemical.VariantType   Get the Cn_BRANCH_POINT VariantType for this position (n). default_position_from_affix(...) from builtins.PyCapsule default_position_from_affix(affix : str) -> int   Get the default position for this sugar modification affix. get_short_name_to_iupac_strings_map(...) from builtins.PyCapsule get_short_name_to_iupac_strings_map() -> rosetta.std.map_std_string_std_string   Get a map of short names to the full iupac glycan sequence for common glycosylations. is_valid_modification_affix(...) from builtins.PyCapsule is_valid_modification_affix(affix : str) -> bool   Is the given short affix valid for designating a sugar modification? is_valid_ring_affix(...) from builtins.PyCapsule is_valid_ring_affix(affix : str) -> bool   Is the given 1-letter code valid for designating carbohydrate ring size? is_valid_sugar_code(...) from builtins.PyCapsule is_valid_sugar_code(code : str) -> bool   Is the given 3-letter code a valid Rosetta/IUPAC code for carbohydrates? morpheme_from_ring_size(...) from builtins.PyCapsule morpheme_from_ring_size(ring_size : int) -> str   Get the morpheme for designating a carbohydrate ring of this size. pair_has_linkage_statistics(...) from builtins.PyCapsule pair_has_linkage_statistics(res1 : str, res2 : str) -> bool   Does the linkage between the given pair of monosaccharide residues have statistics in the database? patch_name_from_affix(...) from builtins.PyCapsule patch_name_from_affix(affix : str) -> str   Get the Rosetta patch name for this sugar modification affix. ring_affix_from_ring_size(...) from builtins.PyCapsule ring_affix_from_ring_size(ring_size : int) -> str   Get the 1-letter affix for designating a carbohydrate ring of this size. root_from_code(...) from builtins.PyCapsule root_from_code(code : str) -> str   Get the monosaccharide root name from the given Rosetta/IUPAC 3-letter code. Methods inherited from rosetta.utility.SingletonBase_core_chemical_carbohydrates_CarbohydrateInfoManager_t: get_instance(...) from builtins.PyCapsule get_instance() -> core::chemical::carbohydrates::CarbohydrateInfoManager   class LinkageConformerData(builtins.object)     Holds original conformer data from GlycanRelax     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.chemical.carbohydrates.LinkageConformerData) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. get_torsion_mean(...) from builtins.PyCapsule get_torsion_mean(*args, **kwargs) Overloaded function.   1. get_torsion_mean(self : rosetta.core.chemical.carbohydrates.LinkageConformerData, torsion : rosetta.core.id.MainchainTorsionType) -> float   ///////////////////////////////////////////////////////////////   2. get_torsion_mean(self : rosetta.core.chemical.carbohydrates.LinkageConformerData, torsion : rosetta.core.id.MainchainTorsionType, torsion_num : int) -> float get_torsion_sd(...) from builtins.PyCapsule get_torsion_sd(*args, **kwargs) Overloaded function.   1. get_torsion_sd(self : rosetta.core.chemical.carbohydrates.LinkageConformerData, torsion : rosetta.core.id.MainchainTorsionType) -> float   2. get_torsion_sd(self : rosetta.core.chemical.carbohydrates.LinkageConformerData, torsion : rosetta.core.id.MainchainTorsionType, torsion_num : int) -> float has_omega(...) from builtins.PyCapsule has_omega(rosetta.core.chemical.carbohydrates.LinkageConformerData) -> bool n_omega(...) from builtins.PyCapsule n_omega(rosetta.core.chemical.carbohydrates.LinkageConformerData) -> int n_torsions(...) from builtins.PyCapsule n_torsions(rosetta.core.chemical.carbohydrates.LinkageConformerData) -> int Data descriptors defined here: mean_sd omega_mean_sd population   class LinkageType(builtins.object)     Labels for the linkage type of the carbohydrate phi or psi angle.      The CHI energy functions depend on the type of linkage. Parameters for the Gaussian functions that compose the CHI energy functions are stored in a vector indexed by these labels.     Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.chemical.carbohydrates.LinkageType, rosetta.core.chemical.carbohydrates.LinkageType) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.chemical.carbohydrates.LinkageType) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.chemical.carbohydrates.LinkageType, int) -> NoneType   2. __init__(rosetta.core.chemical.carbohydrates.LinkageType, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.chemical.carbohydrates.LinkageType) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.chemical.carbohydrates.LinkageType, rosetta.core.chemical.carbohydrates.LinkageType) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.core.chemical.carbohydrates.LinkageType) -> str Data and other attributes defined here: ALPHA_LINKS = LinkageType.ALPHA_LINKS BETA_LINKS = LinkageType.BETA_LINKS FIRST_LINK_TYPE = LinkageType.ALPHA_LINKS LINKAGE_NA = LinkageType.LINKAGE_NA N_LINK_TYPES = LinkageType.N_LINK_TYPES   class SugarModificationsNomenclatureTableRow(builtins.object)     A structure for storing information related to the nomenclature of modified sugars.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow) -> NoneType   2. __init__(self : rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow,  : rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow,  : rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow) -> rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow Data descriptors defined here: default_position implies patch_name short_affix substituent_full_name

Functions
		convert_residue_names_into_linkage_map_key(...) method of builtins.PyCapsule instance convert_residue_names_into_linkage_map_key(name1 : str, name2 : str) -> (str, str) find_glycan_sequence_file(...) method of builtins.PyCapsule instance find_glycan_sequence_file(filename : str) -> str   Try various combinations to locate the specific glycan sequence file being requested by the user. read_codes_and_roots_from_database_file(...) method of builtins.PyCapsule instance read_codes_and_roots_from_database_file(filename : str) -> rosetta.std.map_std_string_std_string   Return a map of strings to strings, which are saccharide-specific 3-letter codes mapped to IUPAC roots, read  from a database file. read_glycan_sequence_file(...) method of builtins.PyCapsule instance read_glycan_sequence_file(filename : str) -> str   Read a single-line glycan sequence file. read_nomenclature_table_from_database_file(...) method of builtins.PyCapsule instance read_nomenclature_table_from_database_file(filename : str) -> rosetta.std.map_std_string_core_chemical_carbohydrates_SugarModificationsNomenclatureTableRow   Return a table of nomenclature data for sugar modifications, read from a database file. read_ring_sizes_and_morphemes_from_database_file(...) method of builtins.PyCapsule instance read_ring_sizes_and_morphemes_from_database_file(filename : str) -> rosetta.std.map_unsigned_long_std_pair_char_std_string_t   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. read_short_names_to_iupac_format_string(...) method of builtins.PyCapsule instance read_short_names_to_iupac_format_string(dir : str, common_mapping_path : str) -> rosetta.std.map_std_string_std_string   Return a map of short names to IUPAC formatted strings.   Reads from db_dir/common_names.txt, and loads the IUPAC files as strings.

Data
		ALPHA_LINKS = LinkageType.ALPHA_LINKS BETA_LINKS = LinkageType.BETA_LINKS FIRST_LINK_TYPE = LinkageType.ALPHA_LINKS LINKAGE_NA = LinkageType.LINKAGE_NA N_LINK_TYPES = LinkageType.N_LINK_TYPES