glyles 0.0.4

A tool to convert IUPAC representation of glycans into SMILES strings

GlyLES

A tool to convert IUPAC representation of Glycans into SMILES representation. This repo is still in the development phase; so, feel free to report any errors in the issues section.

Specification and (current) Limitations

The exact specification, we're refering to when talking about "IUPAC representations of glycan", is given in the "Notes" section of this website. But as this package is still in the development phase, not everything of the specification is implemented yet (especially not all monomers and side chains you can attach to monomers).

This implementation currently only works for glycans that fulfil certain properties:

• All monomers are given in D-Enantiomer, except fucose (Fuc) which has L-Enantiomer
• Linkages have to be explicit, i.e. (a1-4)
• The structure of the glycan can be represented as tree of the monomers with maximal branching factor 3.
• Only the 23 implemented monomers may participate in the glycan (see below)

For an overview of the implemented monomers, please look at the README in the grammar folder. You can get a python-readable list of the currently included monomers with the following code

from glyles.glycans.factory import MonomerFactory

MonomerFactory.monomers()

Installation

So far, this package can only be downloaded from the python package index. So the installation with pip is very easy. Just type

pip install glyles

and you're ready to use it as described below.

Workflow

Convert the IUPAC into a SMILES representation using the handy convert method

from glyles.converter import convert

convert(glycan="Man(a1-2)Man", output_file="./test.txt")

You can also use the convert_generator method to get generator over all SMILES:

from glyles.converter import convert_generator

for smiles in convert_generator(glycan_list=["Man(a1-2)Man a", "Man(a1-2)Man b"]):
    print(smiles)

In general, the convert and convert_generator methods supports the same for types of input. The samples are shown for convert but it's the same for convert_generator.

• single glycan, e.g. convert(glycan="Man(a1-2)Man)",
• a list of glycans, e.g. convert(glycan_list=["Man(a1-2)Man a", "Man(a1-2)Man"]), and
• a file of glycans, e.g. convert(glycan_file="./glycans.txt"). Here its important that the file many only contain one IUPAC per line.
• for better runtime one can also provide a generator as input, e.g. convert(glycan_generator=some_generator)

The output for convert can be manifold as well. For convert_generator there is one output. convert supports

• stdout when specifying no output-related argument, or
• returned as list of tuples if returning=true is set, or
• writing to an output_file, e.g. convert(glycan="Man(a1-2)Man", output_file="./out.csv").

Here each line of the output will state the input IUPAC and the output SMILES. In case of written output separated with a comma.

Poetry

To develop this package I used the poetry package manager (see here for a detailed instruction). It has basically the same functionality as conda but supports the package management better and also supports distinguishing packages into those that are needed to use the package and those that are needed in the development of the package. In order to enable others to work on this repository, we also publish the exact specifications of out poetry environment.