README.rst

isoenum

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 isoenum

Install on Windows

py -3 -m pip install isoenum

Dependencies

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:

• Follow the instructions to install docker on your system: https://docs.docker.com/engine/installation

  • Ubuntu
  • Debian
  • CentOS
  • Fedora
  • Mac
  • Windows

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.git

Install development version on Windows

py -3 -m pip install git+git://github.com/MoseleyBioinformaticsLab/isoenum.git

License

This package is distributed under the BSD license.