The resources package#

Glycosylator comes with a dedicated reference dataset for glycans structures. This dataset is loaded by default and can be accessed using the glycosylator.resources.get_default_compounds() and glycosylator.resources.get_default_topology() functions.

In addition to the dedicated datasets, Glycosylator comes with additional auxiliary resources that are doucumented here.

The sequons module#

Pre-defined sequons for protein glycosylation sites

glycosylator.resources.sequons.SEQUONS = {'N-linked': <glycosylator.resources.sequons.Sequon object>, 'O-linked': <glycosylator.resources.sequons.Sequon object>}#: Default sequons for protein glycosylation sites

class glycosylator.resources.sequons.Sequon(id: str, pattern: str)[source]#

Bases: object

A class representing a sequon pattern for glycosylation

add_linkage(resname: str, linkage: str)[source]#

Add a linkage id that is associated with a given residue

Parameters:

resname (str) – Residue name
linkage (str) – Linkage id

get_linkage(resname: str, _topology=None) → Linkage[source]#

Get the linkage id associated with a given residue

Parameters:

resname (str) – Residue name
_topology (Topology) – A particular topology to use to get the linkage from.

Returns:

The Linkage object

Return type:

Linkage

to_dict()[source]#

Convert the sequon to a dictionary

Returns:: Sequon dictionary
Return type:: dict

glycosylator.resources.sequons.add_sequon(sequon_or_pattern: str | Sequon, key: str = None, overwrite: bool = False)[source]#

Add a sequon to the default sequons

Parameters:

sequon_or_pattern (str) – Sequon object or regex pattern
key (str) – Sequon key, if a regex pattern is provided.
overwrite (bool) – If True, the new sequon is permanently included in the default sequons file.

glycosylator.resources.sequons.available_sequons() → list[source]#

Get the available sequons

Returns:: Sequons
Return type:: list

glycosylator.resources.sequons.get_default_sequons() → dict[source]#

Get the default sequons

Returns:: Sequons
Return type:: dict

glycosylator.resources.sequons.get_sequon(key: str) → Sequon[source]#

Get a sequon regex pattern

Parameters:: key (str) – Sequon key
Return type:: Sequon or None

glycosylator.resources.sequons.load_sequons(filename: str) → dict[source]#

Load a json file with sequons

Parameters:: filename (str) – Path to the json file
Returns:: Sequons
Return type:: dict

glycosylator.resources.sequons.restore_sequons(overwrite: bool = True)[source]#

Restore the default sequon regex patterns

Parameters:: overwrite (bool) – If True, the backup is permanently set as the default again.

glycosylator.resources.sequons.save_sequons(filename: str)[source]#

Save the current sequon regex patterns to a json file

Parameters:: filename (str) – Path to the json file

glycosylator.resources.sequons.set_default_sequons(sequons: dict)[source]#

Set the default sequons

Parameters:: sequons (dict) – Sequons

The icons module#

Icons for drawing glycan structures in 2D

glycosylator.resources.icons.get_base_color(name: str) → str[source]#

Get the only base color of a monosaccharide

Parameters:: name (str) – The name of the monosaccharide
Returns:: The base color of the monosaccharide
Return type:: str

glycosylator.resources.icons.get_icon(name: str) → ndarray[source]#

Get an icon by name

Parameters:: name (str) – The name of the icon
Returns:: The icon image
Return type:: “ndarray”

glycosylator.resources.icons.get_icon_path(name: str) → str[source]#

Get the path to an icon PNG file

Parameters:: name (str)
Return type:: str

The names module#

These are name mappings for glycan residues between their PDB identifiers and IUPAC names.

glycosylator.resources.names.id_to_name(id: str) → str[source]#

Translate a monosaccharide PDB id to a name

Parameters:: id (str) – The PDB id of the monosaccharide
Returns:: The name of the monosaccharide. If the id is not found, it is returned as is.
Return type:: str

glycosylator.resources.names.is_beta(id: str) → bool[source]#

Check if a monosaccharide PDB id is beta-configured.

Parameters:: id (str) – The PDB id of the monosaccharide
Returns:: True if the monosaccharide is beta-configured, False otherwise.
Return type:: bool