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.