carbohydrates

Bindings for core::chemical::carbohydrates namespace

class pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo

Bases: pybind11_object

anomer(self: pyrosetta.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.

C++: core::chemical::carbohydrates::CarbohydrateInfo::anomer() const –> std::string

anomeric_carbon(self: pyrosetta.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()

C++: core::chemical::carbohydrates::CarbohydrateInfo::anomeric_carbon() const –> unsigned long

anomeric_carbon_index(self: pyrosetta.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()

C++: core::chemical::carbohydrates::CarbohydrateInfo::anomeric_carbon_index() const –> unsigned long

anomeric_carbon_name(self: pyrosetta.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()

C++: core::chemical::carbohydrates::CarbohydrateInfo::anomeric_carbon_name() const –> std::string

anomeric_pseudotorsion(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → float

Get pseudotorsion of anomeric carbon from ideal residue: defined as the out-of-plane angle

of the anomeric O with respect to the Oring-Canomeric-Cadjacent plane w/i the ring

C++: core::chemical::carbohydrates::CarbohydrateInfo::anomeric_pseudotorsion() const –> double

anomeric_sidechain_index(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → int

Get the index of the non-ring atom bound to the anomeric carbon

C++: core::chemical::carbohydrates::CarbohydrateInfo::anomeric_sidechain_index() const –> unsigned long

basic_name(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → str

Return the standard/common, non-residue, short name of the monosaccharide.

C++: core::chemical::carbohydrates::CarbohydrateInfo::basic_name() const –> std::string

branch_point(self: pyrosetta.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.

C++: core::chemical::carbohydrates::CarbohydrateInfo::branch_point(const unsigned long) const –> unsigned long

cyclic_oxygen(self: pyrosetta.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()

C++: core::chemical::carbohydrates::CarbohydrateInfo::cyclic_oxygen() const –> unsigned long

cyclic_oxygen_index(self: pyrosetta.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()

C++: core::chemical::carbohydrates::CarbohydrateInfo::cyclic_oxygen_index() const –> unsigned long

cyclic_oxygen_name(self: pyrosetta.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()

C++: core::chemical::carbohydrates::CarbohydrateInfo::cyclic_oxygen_name() const –> std::string

full_name(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → str

Return the full IUPAC name of the monosaccharide.

C++: core::chemical::carbohydrates::CarbohydrateInfo::full_name() const –> std::string

has_mainchain_bidirectional_linkage_to_child(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the attachment point of the downstream saccharide (N+1) is a bidirectional linkage.

C++: core::chemical::carbohydrates::CarbohydrateInfo::has_mainchain_bidirectional_linkage_to_child() const –> bool

has_mainchain_exocyclic_linkage_to_child(self: pyrosetta.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.

C++: core::chemical::carbohydrates::CarbohydrateInfo::has_mainchain_exocyclic_linkage_to_child() const –> bool

is_D_sugar(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is a D-sugar.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_D_sugar() const –> bool

is_L_sugar(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is an L-sugar.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_L_sugar() const –> bool

is_N_acetylated(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if any hydroxyl group has been modified to an acetylated amino group.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_N_acetylated() const –> bool

is_O_acetylated(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if any hydroxyl group has been modified by acetylation.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_O_acetylated() const –> bool

is_acetylated(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the sugar has been acetylated at any position.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_acetylated() const –> bool

is_acyclic(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is linear.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_acyclic() const –> bool

is_aldose(self: pyrosetta.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()

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_aldose() const –> bool

is_alpha_sugar(self: pyrosetta.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.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_alpha_sugar() const –> bool

is_amino_sugar(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if any hydroxyl group has been modified to an amino group or an acetylated amino group.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_amino_sugar() const –> bool

is_beta_sugar(self: pyrosetta.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.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_beta_sugar() const –> bool

is_cyclic(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is a ring.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_cyclic() const –> bool

is_furanose(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is a furanose.

A furanose has a five-membered ring (like furan).

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_furanose() const –> bool

is_glycoside(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is attached to something at the anomeric carbon.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_glycoside() const –> bool

is_heptose(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is a heptose.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_heptose() const –> bool

is_hexose(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is a hexose.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_hexose() const –> bool

is_ketose(*args, **kwargs)

Overloaded function.

1. is_ketose(self: pyrosetta.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()

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_ketose() const –> bool

2. is_ketose(self: pyrosetta.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()

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_ketose(const unsigned long) const –> bool

is_nonose(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is a nonose.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_nonose() const –> bool

is_octose(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is an octose.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_octose() const –> bool

is_pentose(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is a pentose.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_pentose() const –> bool

is_pyranose(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is a pyranose.

A pyranose has a six-membered ring (like pyran).

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_pyranose() const –> bool

is_reducing_sugar(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is a reducing sugar.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_reducing_sugar() const –> bool

is_septanose(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is a septanose.

A septanose has a seven-membered ring.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_septanose() const –> bool

is_tetrose(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is a tetrose.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_tetrose() const –> bool

is_triose(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the monosaccharide is a triose.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_triose() const –> bool

is_ulose(self: pyrosetta.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()

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_ulose() const –> bool

is_uronic_acid(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → bool

Return true if the primary hydroxyl group is oxidized to the acid.

C++: core::chemical::carbohydrates::CarbohydrateInfo::is_uronic_acid() const –> bool

last_carbon_in_ring(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → int

Get the last carbon of the ring. Varies with ketose or aldose.

C++: core::chemical::carbohydrates::CarbohydrateInfo::last_carbon_in_ring() const –> unsigned long

linkage_notation(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → str

Return the main-chain IUPAC linkage notation for this monosaccharide

(for use in polysaccharide sequences).

C++: core::chemical::carbohydrates::CarbohydrateInfo::linkage_notation() const –> std::string

mainchain_glycosidic_bond_acceptor(self: pyrosetta.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()

C++: core::chemical::carbohydrates::CarbohydrateInfo::mainchain_glycosidic_bond_acceptor() const –> unsigned long

n_branches(self: pyrosetta.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()

C++: core::chemical::carbohydrates::CarbohydrateInfo::n_branches() const –> unsigned long

n_carbons(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → int

Get the number of carbons in the monosaccharide.

This ignores carbons found in modifications to the base sugar.

C++: core::chemical::carbohydrates::CarbohydrateInfo::n_carbons() const –> unsigned long

n_ring_carbons(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → int

Get the number of carbons in the ring.

C++: core::chemical::carbohydrates::CarbohydrateInfo::n_ring_carbons() const –> unsigned long

ring_size(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → int

Get the size of the carbohydrate ring.

A linear monosaccharide has a ring size of zero.

C++: core::chemical::carbohydrates::CarbohydrateInfo::ring_size() const –> unsigned long

short_name(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → str

Return the abbreviated IUPAC name of the monosaccharide (for use in polysaccharide sequences).

C++: core::chemical::carbohydrates::CarbohydrateInfo::short_name() const –> std::string

short_name_w_linkage_notation(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → str

Return the abbreviated IUPAC name of the monosaccharide, including main-chain linkage notation

(for use in polysaccharide sequences).

C++: core::chemical::carbohydrates::CarbohydrateInfo::short_name_w_linkage_notation() const –> std::string

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) -> None

2. show(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of CarbohydrateInfo for debugging purposes.

C++: core::chemical::carbohydrates::CarbohydrateInfo::show(std::ostream &) const –> void

stereochem(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → str

Get the stereochemical designation for the monosaccharide.

‘L’ or ‘D’

C++: core::chemical::carbohydrates::CarbohydrateInfo::stereochem() const –> char

virtual_anomeric_carbon_index(self: pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo) → int

Return the atom index of the virtual atom that superimposes with the anomeric carbon in this

ResidueType or 0, if linear.

This atom is used as a reference atom for certain torsion angles.

See also:

CarbohydrateInfo.anomeric_carbon_index()

C++: core::chemical::carbohydrates::CarbohydrateInfo::virtual_anomeric_carbon_index() const –> unsigned long

virtual_cyclic_oxygen_index(self: pyrosetta.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()

C++: core::chemical::carbohydrates::CarbohydrateInfo::virtual_cyclic_oxygen_index() const –> unsigned long

class pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager

Bases: SingletonBase_core_chemical_carbohydrates_CarbohydrateInfoManager_t

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.

static affix_has_inherent_position(affix: str) → bool

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

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::affix_has_inherent_position(const std::string &) –> bool

static anomeric_position_from_code(code: str) → str

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

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::anomeric_position_from_code(const std::string &) –> char

static branch_variant_type_from_atom_name(atom_name: str) → pyrosetta.rosetta.core.chemical.VariantType

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

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::branch_variant_type_from_atom_name(const std::string &) –> enum core::chemical::VariantType

static branch_variant_type_from_position(position: int) → pyrosetta.rosetta.core.chemical.VariantType

Get the Cn_BRANCH_POINT VariantType for this position (n).

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::branch_variant_type_from_position(const unsigned long) –> enum core::chemical::VariantType

static codes_to_root_map_file() → str

Get the path to the codes_to_root.map database file

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::codes_to_root_map_file() –> const std::string &

static default_position_from_affix(affix: str) → int

Get the default position for this sugar modification affix.

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::default_position_from_affix(const std::string &) –> unsigned long

static default_stereochem_from_code(code: str) → str

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

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::default_stereochem_from_code(const std::string &) –> char

static get_instance() → core::chemical::carbohydrates::CarbohydrateInfoManager

C++: utility::SingletonBase<core::chemical::carbohydrates::CarbohydrateInfoManager>::get_instance() –> class core::chemical::carbohydrates::CarbohydrateInfoManager *

static get_short_name_to_iupac_strings_map() → pyrosetta.rosetta.std.map_std_string_std_string

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

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::get_short_name_to_iupac_strings_map() –> const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

static is_valid_modification_affix(affix: str) → bool

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

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::is_valid_modification_affix(const std::string &) –> bool

static is_valid_ring_affix(affix: str) → bool

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

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::is_valid_ring_affix(char) –> bool

static is_valid_sugar_code(code: str) → bool

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

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::is_valid_sugar_code(const std::string &) –> bool

static morpheme_from_ring_size(ring_size: int) → str

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

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::morpheme_from_ring_size(unsigned long) –> const std::string &

static pair_has_linkage_statistics(res1: str, res2: str) → bool

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

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::pair_has_linkage_statistics(const std::string &, const std::string &) –> bool

static patch_name_from_affix(affix: str) → str

Get the Rosetta patch name for this sugar modification affix.

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::patch_name_from_affix(const std::string &) –> const std::string &

static ring_affix_from_ring_size(ring_size: int) → str

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

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::ring_affix_from_ring_size(unsigned long) –> char

static ring_size_to_morphemes_map_file() → str

Get the path to the ring_size_to_morphemes.map database file

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::ring_size_to_morphemes_map_file() –> const std::string &

static root_from_code(code: str) → str

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

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::root_from_code(const std::string &) –> const std::string &

static sugar_modifications_table_file() → str

Get the path to the sugar_modifications.table database file

C++: core::chemical::carbohydrates::CarbohydrateInfoManager::sugar_modifications_table_file() –> const std::string &

class pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData

Bases: pybind11_object

Holds conformer data for glycan torsional sampling used by the LinkageConformerMover.

assign(self: pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData, : pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData) → pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData

C++: core::chemical::carbohydrates::LinkageConformerData::operator=(const struct core::chemical::carbohydrates::LinkageConformerData &) –> struct core::chemical::carbohydrates::LinkageConformerData &

property conformer_bins

get_torsion_mean(*args, **kwargs)

Overloaded function.

1. get_torsion_mean(self: pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData, torsion: pyrosetta.rosetta.core.id.MainchainTorsionType) -> float

C++: core::chemical::carbohydrates::LinkageConformerData::get_torsion_mean(enum core::id::MainchainTorsionType) const –> double

2. get_torsion_mean(self: pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData, torsion: pyrosetta.rosetta.core.id.MainchainTorsionType, torsion_num: int) -> float

C++: core::chemical::carbohydrates::LinkageConformerData::get_torsion_mean(enum core::id::MainchainTorsionType, unsigned long) const –> double

get_torsion_sd(*args, **kwargs)

Overloaded function.

1. get_torsion_sd(self: pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData, torsion: pyrosetta.rosetta.core.id.MainchainTorsionType) -> float

C++: core::chemical::carbohydrates::LinkageConformerData::get_torsion_sd(enum core::id::MainchainTorsionType) const –> double

2. get_torsion_sd(self: pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData, torsion: pyrosetta.rosetta.core.id.MainchainTorsionType, torsion_num: int) -> float

C++: core::chemical::carbohydrates::LinkageConformerData::get_torsion_sd(enum core::id::MainchainTorsionType, unsigned long) const –> double

has_omega(self: pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData) → bool

C++: core::chemical::carbohydrates::LinkageConformerData::has_omega() const –> bool

property mean_sd

n_omega(self: pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData) → int

C++: core::chemical::carbohydrates::LinkageConformerData::n_omega() const –> unsigned long

n_torsions(self: pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData) → int

C++: core::chemical::carbohydrates::LinkageConformerData::n_torsions() const –> unsigned long

property omega_mean_sd

property population

class pyrosetta.rosetta.core.chemical.carbohydrates.RootData

Bases: pybind11_object

property DL

property anomeric

assign(self: pyrosetta.rosetta.core.chemical.carbohydrates.RootData, : pyrosetta.rosetta.core.chemical.carbohydrates.RootData) → pyrosetta.rosetta.core.chemical.carbohydrates.RootData

C++: core::chemical::carbohydrates::RootData::operator=(const struct core::chemical::carbohydrates::RootData &) –> struct core::chemical::carbohydrates::RootData &

property root

class pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow

Bases: pybind11_object

A structure for storing information related to the nomenclature of modified sugars.

assign(self: pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow, : pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow) → pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow

C++: core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow::operator=(const struct core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow &) –> struct core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow &

property default_position

property has_inherent_position

property implies

property patch_name

property short_affix

property substituent_full_name

pyrosetta.rosetta.core.chemical.carbohydrates.convert_residue_names_into_linkage_map_key(name1: str, name2: str) → Tuple[str, str]

C++: core::chemical::carbohydrates::convert_residue_names_into_linkage_map_key(const std::string &, const std::string &) –> struct std::pair<std::string, std::string >

pyrosetta.rosetta.core.chemical.carbohydrates.find_glycan_sequence_file(filename: str) → str

Try various combinations to locate the specific glycan sequence file being requested by the user.

C++: core::chemical::carbohydrates::find_glycan_sequence_file(std::string) –> std::string

pyrosetta.rosetta.core.chemical.carbohydrates.read_codes_and_roots_from_database_file(filename: str) → pyrosetta.rosetta.std.map_std_string_core_chemical_carbohydrates_RootData

Return a map of strings to strings, which are saccharide-specific 3-letter codes mapped to IUPAC roots, read

from a database file.

C++: core::chemical::carbohydrates::read_codes_and_roots_from_database_file(const std::string &) –> class std::map<std::string, struct core::chemical::carbohydrates::RootData, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::chemical::carbohydrates::RootData> > >

pyrosetta.rosetta.core.chemical.carbohydrates.read_glycan_sequence_file(filename: str) → str

Read a single-line glycan sequence file.

C++: core::chemical::carbohydrates::read_glycan_sequence_file(std::string) –> std::string

pyrosetta.rosetta.core.chemical.carbohydrates.read_linkage_conformers_from_database_file(filename: str) → pyrosetta.rosetta.std.map_std_pair_std_string_std_string_t_utility_vector1_core_chemical_carbohydrates_LinkageConformerData_std_allocator_core_chemical_carbohydrates_LinkageConformerData_t_std_less_std_pair_std_string_std_string_t_std_allocator_std_pair_const_std_pair_std_string_std_string_utility_vector1_core_chemical_carbohydrates_LinkageConformerData_std_allocator_core_chemical_carbohydrates_LinkageConformerData_t

Return a map of linkage conformer data, read from a database file.

C++: core::chemical::carbohydrates::read_linkage_conformers_from_database_file(const std::string &) –> class std::map<struct std::pair<std::string, std::string >, class utility::vector1<struct core::chemical::carbohydrates::LinkageConformerData, class std::allocator<struct core::chemical::carbohydrates::LinkageConformerData> >, struct std::less<struct std::pair<std::string, std::string > >, class std::allocator<struct std::pair<const struct std::pair<std::string, std::string >, class utility::vector1<struct core::chemical::carbohydrates::LinkageConformerData, class std::allocator<struct core::chemical::carbohydrates::LinkageConformerData> > > > >

pyrosetta.rosetta.core.chemical.carbohydrates.read_nomenclature_table_from_database_file(filename: str) → pyrosetta.rosetta.std.map_std_string_core_chemical_carbohydrates_SugarModificationsNomenclatureTableRow

Return a table of nomenclature data for sugar modifications, read from a database file.

C++: core::chemical::carbohydrates::read_nomenclature_table_from_database_file(const std::string &) –> class std::map<std::string, struct core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow> > >

pyrosetta.rosetta.core.chemical.carbohydrates.read_ring_sizes_and_morphemes_from_database_file(filename: str) → pyrosetta.rosetta.std.map_unsigned_long_std_pair_char_std_string_t_std_allocator_std_pair_const_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.

C++: core::chemical::carbohydrates::read_ring_sizes_and_morphemes_from_database_file(const std::string &) –> class std::map<unsigned long, struct std::pair<char, std::string >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, struct std::pair<char, std::string > > > >

pyrosetta.rosetta.core.chemical.carbohydrates.read_short_names_to_iupac_format_string(dir: str, common_mapping_path: str) → pyrosetta.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.

C++: core::chemical::carbohydrates::read_short_names_to_iupac_format_string(const std::string &, std::string) –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >