Installing

pip

atomium can be installed using pip:

$ pip3 install atomium

atomium is written for Python 3, and does not support Python 2.

If you get permission errors, try using sudo:

$ sudo pip3 install atomium

Development

The repository for atomium, containing the most recent iteration, can be found here. To clone the atomium repository directly from there, use:

$ git clone git://github.com/samirelanduk/atomium.git

Requirements

atomium requires requests for fetching structures from the RCSB, paramiko for fetching structures over SSH, msgpack for parsing .mmtf files, and valerius for dealing with sequences.

Testing

To test a local version of atomium, cd to the atomium directory and run:

$ python -m unittest discover tests

You can opt to only run unit tests or integration tests:

$ python -m unittest discover tests.unit $ python -m unittest discover tests.integration

You can run the ‘big test’ to get a random 1000 structures, parse them all, and report any problems:

$ python tests/big.py

Finally, to perform speed profiles you can run:

$ python tests/time/time.py

…which creates various profiles that SnakeViz can visualise.