Isotopic (iso) enumerator (enum) - enumerates isotopically resolved InChI (International Chemical Identifier) for metabolites.
The isoenum Python package provides command-line interface that allows you to enumerate the possible isotopically-resolved InChI from one of the Chemical Table file (CTfile) formats (i.e. molfile, SDfile) used to describe chemical molecules and reactions as well as from InChI itself.
See Tutorial documentation for usage examples of isoenum Python package as well as isoenum docker container.
Links
isoenum @ GitHub
isoenum @ PyPI
isoenum @ DockerHub
isoenum @ ReadTheDocs
Installation
The isoenum package runs under Python 2.7 and Python 3.4+. Use pip to install.
Install on Linux, Mac OS X
python3 -m pip install isoenumInstall on Windows
py -3 -m pip install isoenumDependencies
The isoenum Python package requires a non-pip-installable dependency: the Open Babel chemistry library version 2.3.90 or later, which relies on InChI library version 1.0.4 or later to perform InChI conversions.
Refer to the official documentation to install Open Babel on your system:
Official Installation Instructions: http://openbabel.org/wiki/Category:Installation
Docker
In addition to PyPI package, Dockerfile and the automatically built DockerHub container, which contains the isoenum Python package and all its dependencies, are also provided.
To use the isoenum Python package, you will need to setup docker for your system and pull or build the docker container.
Install docker
Install docker:
Setup container
Setup the isoenum container:
pull the built image from the DockerHub:
# docker pull moseleybioinformaticslab/isoenum # docker tag moseleybioinformaticslab/isoenum:latest isoenum:latest # retag docker image # docker rmi moseleybioinformaticslab/isoenum # remove after you have retagged it
or build an image using Dockerfile at the root of this repo by running docker build from the directory containing Dockerfile:
# docker build -t isoenum .
Development version installation
Install development version on Linux, Mac OS X
python3 -m pip install git+git://github.com/MoseleyBioinformaticsLab/isoenum.gitInstall development version on Windows
py -3 -m pip install git+git://github.com/MoseleyBioinformaticsLab/isoenum.gitLicense
This package is distributed under the BSD license.
2 maintainers
Metadata
2 maintainers
Release files for isoenum 0.4.1
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| isoenum-0.4.1.tar.gz | 280.9 kB | Without provenance | Details |
Release files / isoenum-0.4.1.tar.gz
| Download URL | isoenum-0.4.1.tar.gz |
|---|---|
| Size | 280.9 kB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
05ef4e924934fb103ac1daa4728a80566e9c7947313bb61fd94d63083a2cb0f4
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BLAKE2b-256 checksum How to use checksums |
cc9924a578d68d4b439d69705e2143f7be93aff2942d747c445053392ca2b535
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twine/1.13.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/40.8.0 requests-toolbelt/0.9.1 tqdm/4.32.2 CPython/3.7.4
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Security for isoenum 0.4.1
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