This release has been yanked by its maintainers, and will be ignored by installers, except when explicitly specified.
Consider using release 1.2.2 instead.
Reason given by maintainers: Buggy
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 or issues. The code is available on github and the documentation can be found on ReadTheDocs.
Specification and (current) Limitations
The exact specification we're referring 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 side chains you can attach to monomers). The structure of the glycan can be represented as a tree of the monosaccharides with maximal branching factor 4, i.e., each monomer in the glycan has at most 4 children.
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 src
and you're ready to use it as described below. Use
pip install --upgrade src
to upgrade the glyles package to the most recent version.
Command Line Usage
With IUPAC input
$ src -i Man(a1-2)Man -o ./test_output.txt
With IUPAC inputs
$ src -i Man(a1-2)Man Fuc(a1-6)Glc -o ./test_output.txt
With file input
$ src -i ./input_file.txt -o ./test_output.txt
Basic Usage
Convert the IUPAC into a SMILES representation using the handy convert method
from src import convert
convert(glycan="Man(a1-2)Man", output_file="./test.txt")
You can also use the convert_generator method to get a generator for all SMILES:
from src import convert_generator
for smiles in convert_generator(glycan_list=["Man(a1-2)Man a", "Man(a1-2)Man b"]):
print(smiles)
For more examples of how to use this package, please see the notebooks in the examples folder and checkout the documentation on ReadTheDocs.
Notation of glycans
There are multiple different notations for glycans in IUPAC. So, according to the
SNGF specification, Man(a1-4)Gal, Mana1-4Gal, and Mana4Gal
all describe the same disaccharide. This is also covered in this package as all three notations will be parsed into the
same tree of monosaccharides and result in the same SMILES string.
This is also described more detailed in a section on ReadTheDocs.
Poetry
To develop this package, we use the poetry package manager (see here for 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. To enable others to work on this repository, we also publish the exact specifications of our poetry environment.
2 maintainers
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