Linear Code

A module for operating on GlycoMinds Linear Code

Assumes that the structure’s root is the right-most residue, as shown in A Novel Linear Code Nomenclature for Complex Carbohydrates, Banin et al..

Currently does not handle the sigils indicating deviation from the common forms.

glypy.io.linear_code.dumps(structure)

Common alias for to_linear_code()

glypy.io.linear_code.get_relevant_substituents(residue)

Retrieve the set of substituents not implicitly included in the base type’s symbol name.

glypy.io.linear_code.glycan_to_linear_code(structure=None, max_tolerance=3)

Translate a Glycan structure into Linear Code. Called from to_linear_code(). Recursively operates on branches.

Parameters:

structure: Glycan or Monosaccharide

The glycan to be translated. Translation starts from glycan.root if structure is a Glycan.

max_tolerance: int

The maximum amount of deviance to allow when translating Monosaccharide objects into nomenclature symbols

Returns:

deque

glypy.io.linear_code.loads(text)

Common alias for parse_linear_code()

glypy.io.linear_code.monosaccharide_from_linear_code(residue_str, parent=None)

Helper function for parse_linear_code(). Given a residue string of the form “(base_type)(anomer)(outedge?)([substituents]?)”, construct a Monosaccharide object. If parent is not None, connect the resulting Monosaccharide to parent at outedge.

glypy.io.linear_code.monosaccharide_to_linear_code(monosaccharide, max_tolerance=3)

Perform iteratively permissive attempts to translate monosaccharide into a nomenclature symbol.

Note

Uses a multi-pass approach. Could alternatively do a single pass and keep the best match.

Parameters:

monosaccharide: Monosaccharide

The residue to be translated

max_tolerance: int

The maximum error tolerance to allow while looking for a match

Returns:

str

Raises:

ValueError:

When no suitable translation can be found

KeyError:

When an unknown symbol is encountered

glypy.io.linear_code.monosaccharides_from = {'A': 'Gal', 'NJ': 'NeuGc', 'B': 'Rib', 'E': 'Fru', 'NN': 'NeuAc', 'G': 'Glc', 'F': 'Fuc', 'I': 'IdoA', 'H': 'Rha', 'K': 'KDN', 'M': 'Man', 'L': 'GalA', 'O': 'All', 'N': 'Neu', 'P': 'Api', 'R': 'Ara', 'U': 'GlcA', 'W': 'Kdo', 'GN': 'GlcNAc', 'X': 'Xyl', 'AN': 'GalNAc'}

A mapping from symbol to common monosaccharide name

glypy.io.linear_code.monosaccharides_to = OrderedDict([('Glc', 'G'), ('Gal', 'A'), ('GlcNAc', 'GN'), ('GalNAc', 'AN'), ('Man', 'M'), ('Neu', 'N'), ('NeuAc', 'NN'), ('NeuGc', 'NJ'), ('KDN', 'K'), ('Kdo', 'W'), ('GalA', 'L'), ('IdoA', 'I'), ('Rha', 'H'), ('Fuc', 'F'), ('Xyl', 'X'), ('Rib', 'B'), ('Ara', 'R'), ('GlcA', 'U'), ('All', 'O'), ('Api', 'P'), ('Fru', 'E')])

A mapping from common monosaccharide names to their symbol, ordered by priority

glypy.io.linear_code.parse_linear_code(text)

Parse the character string text, extracting GlycoMinds Linear Code-format carbohydrate structures, converting them into a Glycan object.

Note

Assumes that the structure’s root is the right-most residue

Supports only concrete structures.

Parameters:

text: str

The string to be parsed

Returns:

Glycan

Raises:

LinearCodeError:

When an error is encountered while parsing resulting from malformed syntax or structure

ValueError:

When a symbol is encountered for which no suitable translation could be found

KeyError:

When an unknown symbol is encountered

glypy.io.linear_code.priority(sym)

Calculate the branching priority for a given symbol or Monosaccharide. Used when deciding when a residue is considered branch or backbone.

Parameters:sym: str or Monosaccharide Returns:int

glypy.io.linear_code.substituent_to_linear_code(substituent, position=None)

Translate a Substituent to Linear Code. Include’s the substituent’s position if it is known.

Parameters:

substituents: Substituent or str

The structure or the name to translate

position:

The position of the structure to try including

Returns:

str

Raises:

KeyError:

When an unknown symbol is encountered

glypy.io.linear_code.substituents_from = {'ME': 'methyl', 'P': 'phosphate', 'PYR': 'pyruvate', 'PE': 'ethanolominephosphate', 'N': 'n_acetyl', 'Q': 'amino', 'PC': 'phosphocholine', 'S': 'sulfate', 'SH': 'sulfide', 'T': 'o_acetyl', 'IN': 'inositol', 'EP': '2-aminoethylphosphonic acid'}

A mapping from symbol to common substituent names

glypy.io.linear_code.substituents_to = {'methyl': 'ME', 'pyruvate': 'PYR', 'n_acetyl': 'N', 'sulfide': 'SH', 'o_acetyl': 'T', 'inositol': 'IN', 'amino': 'Q', 'phosphocholine': 'PC', 'ethanolominephosphate': 'PE', 'sulfate': 'S', '2-aminoethylphosphonic acid': 'EP', 'phosphate': 'P'}

A mapping from common substituent names to symbol

glypy.io.linear_code.to_linear_code(structure)

Translates structure to Linear Code.

Parameters:structure: Monosaccharide or Glycan Returns:str