A tool to convert IUPAC representation of glycans into SMILES strings
Project description
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.
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 monomers and side chains you can attach to monomers).
This implementation currently only works for glycans that fulfill certain properties:
- Linkages have to be explicit, i.e.
(a1-4)
- The structure of the glycan can be represented as a tree of the monomers with maximal branching factor 2.
- All root monomers (e.g. Glc, but not GlcNAc) from this website (GalNAc is seen as modification of galactose)
- Some modifications can be added to the monomers, please see the README in the grammar folder for more information on this.
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. Use
pip install --upgrade glyles
to upgrade the glyles package to the most recent version.
Usage
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 a generator for 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 support the same 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:
stdout
when specifying no output-related argument, or- return 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")
.
Any output consists of tuples of the form (input_iupac, smiles). The same also holds for convert_generator
which returns
tuples of input and smiles strings.
Poetry
To develop this package, I used 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.
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