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.