carbohydrates

Bindings for core::chemical::carbohydrates namespace

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

Bases: pyrosetta.rosetta.utility.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.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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 class std::basic_string<char> &) –> bool

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 class std::basic_string<char> &) –> char

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 class std::basic_string<char> &) –> enum core::chemical::VariantType

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

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 class std::basic_string<char> &) –> unsigned long

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 class std::basic_string<char> &) –> char

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

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

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 > > > &

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 class std::basic_string<char> &) –> bool

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

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 class std::basic_string<char> &) –> bool

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 &

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 class std::basic_string<char> &, const class std::basic_string<char> &) –> bool

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 class std::basic_string<char> &) –> const std::string &

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

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 class std::basic_string<char> &) –> const std::string &

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

Bases: pybind11_builtins.pybind11_object

Holds original conformer data from GlycanRelax

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData) -> None
2. __init__(self: pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData, arg0: pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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 &

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

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

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

Bases: pybind11_builtins.pybind11_object

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow) -> None
2. __init__(self: pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow, arg0: pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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 &

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 class std::basic_string<char> &, const class std::basic_string<char> &) –> 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(class std::basic_string<char>) –> 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 class std::basic_string<char> &) –> 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(class std::basic_string<char>) –> std::string

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 class std::basic_string<char> &) –> 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

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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &, class std::basic_string<char>) –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >