IUPAC Three Letter Code

A reader and writer for the ubiquitious trivial IUPAC notation for glycan structures. This notation will be familiar to biologists and biochemists, and the parser attempts to recognize common shorthand and special cases that may be inconsistent with the grammmar used to describe the format.

High Level Functions

glypy.io.iupac.dumps(structure, dialect=None)

Translate structure into its textual representation using IUPAC Three Letter Code

Parameters:

• structure (Glycan or Monosaccharide) – The structure to be translated

• dialect (str) – One of “extended” or “simple”, controlling whether the long-form linkage and monosaccharide notation is used, or the more compact simplified form is used. Defaults to “extended”.

Return type:

str

See also

GlycanSerializer

glypy.io.iupac.loads(text, structure_class=<class 'glypy.structure.glycan.Glycan'>, resolve_default_positions=True, dialect=None, **kwargs)

Parse the given text into an instance of Glycan. If there is only a single monosaccharide in the output, just the Monosaccharide instance is returned.

Parameters:

• text (str) – The text to parser

• resolve_default_positions (bool) – Whether to assume default positions for common monosaccharide modifiers that are omitted for brevity, such as the postion of n-acetyl on HexNAc.

• dialect (str) – One of “extended” or “simple”, controlling whether the long-form linkage and monosaccharide notation is used, or the more compact simplified form is used. Defaults to “extended”.

• **kwargs – Forwarded to glycan_from_iupac()

Returns:

If the resulting structure is just a single monosaccharide, the returned value is a Monosaccharide.

Return type:

Glycan or Monosaccharide

exception glypy.io.iupac.IUPACError

There are multiple dialects of IUPAC, affecting how monosaccharides are written and how linkages are denoted. The dialect parameter in these functions control which dialect is expected or generated.

The simple dialect: Neu5Gc(a2-3)Gal(b1-4)[Fuc(a1-3)]Glc2NAc

The extended dialect: a-D-Neup5Gc-(2-3)-b-D-Galp-(1-4)-[a-L-Fucp-(1-3)]b-D-Glcp2NAc

Example

>>> from glypy.io import iupac
>>> iupac.loads('a-L-Fucp-(1-6)-[a-D-Neup5Ac-(2-3)-b-D-Galp-(1-4)-[a-L-Fucp-(1-3)]b-D-Glcp2NAc-(1-6)-[a-D-Neup5Gc-(2-3)-b-D-Galp-(1-4)-[a-L-Fucp-(1-3)]b-D-Glcp2NAc-(1-2)]a-D-Manp-(1-6)-[b-D-Glcp2NAc-(1-4)][b-D-Galp2NAc-(1-4)-b-D-Glcp2NAc-(1-4)-[a-D-Neup5Gc-(2-3)-b-D-Galp-(1-4)-[a-L-Fucp-(1-3)]b-D-Glcp2NAc-(1-2)]a-D-Manp-(1-3)]b-D-Manp-(1-4)-b-D-Glcp2NAc-(1-4)]?-D-Glcp2NAc')
>>>

(Source code, svg, png, hires.png, pdf)

Object-Oriented Interface

The high-level API is implemented using a set of cooperating types for converting between glypy’s objects and IUPAC text formats. All of these objects provide these behaviors by calling them on the appropriate argument

Serialization

class glypy.io.iupac.SubstituentSerializer(monosaccharides=None, substitution_rules=None, substituent_map=None)

Build the textual encoding for the relevant substituents for a provided monosaccharide.

Variables:

monosaccharide_reference (dict) – Map base type to Monosaccharide

class glypy.io.iupac.ModificationSerializer

Build the textual encoding for the relevant modifications for a provided monosaccharide base type.

class glypy.io.iupac.MonosaccharideSerializer(monosaccharides=None, substituent_resolver=None, modification_extractor=None)

Serialize a Monosaccharide object to IUPAC text

Variables:

• modification_extractor (ModificationSerializer) – Convert modifications to a text list

• monosaccharide_reference (dict) – Map base type to Monosaccharide

• substituent_resolver (SubstituentSerializer) – Convert substituents to a text list

class glypy.io.iupac.LinkageSerializer(open_edge='-(', close_edge=')-', open_branch='[', close_branch=']')

class glypy.io.iupac.GlycanSerializer(monosaccharide_serializer=None, linkage_serializer=None)

Converts a Glycan structure to IUPAC format.

Also works on individual Monosaccharide objects, but will traverse any links they have to other nodes.

Variables:

• linkage_serializer (LinkageSerializer) – An object that converts a Link object into text

• monosaccharide_serializer (MonosaccharideSerializer) – An object that converts a Monosaccharide object into text

Deserialization

class glypy.io.iupac.SubstituentDeserializer(substituents_map=None, error_on_missing=True)

class glypy.io.iupac.ModificationDeserializer(modification_map=None)

Parses modification signifiers from text into position, Modification pairs

Variables:

modification_map (dict) – Mapping from text representation to Modification to provide additional names for the existing modification name mapping.

class glypy.io.iupac.MonosaccharideDeserializer(modification_parser=None, substituent_parser=None)

class glypy.io.iupac.GlycanDeserializer(monosaccharide_deserializer=None, set_default_positions=True)

Derivatization

class glypy.io.iupac.DerivatizationAwareMonosaccharideSerializer(monosaccharides=None, substituent_resolver=None, modification_extractor=None)

A derivatization aware version of MonosaccharideSerializer which deviates from the standard IUPAC code to encode derivatization.

If a Monosaccharide object has a derivatizing substituent attached to it, as detected by has_derivatization(), those substituent groups will normally be ignored. With this subclass, a single entry will be appended to the monosaccharide encoding joined by an “^” character. For example a permethylated hexose would be written “Hex^Me”.

class glypy.io.iupac.DerivatizationAwareMonosaccharideDeserializer(modification_parser=None, substituent_parser=None)

Simplified Format

class glypy.io.iupac.SimpleMonosaccharideSerializer(monosaccharides=None, substituent_resolver=None, modification_extractor=None)

class glypy.io.iupac.SimpleLinkageSerializer(open_edge='(', close_edge=')', open_branch='[', close_branch=']')

class glypy.io.iupac.SimpleMonosaccharideDeserializer(modification_parser=None, substituent_parser=None)

class glypy.io.iupac.SimpleLinkageDeserializer