<commit_before>Installation
************

In the Sali Lab
===============

If you are working in the Sali lab, you don't need to build and install
AllosMod - it is already set up for you as a module. Just run
``module load allosmod`` to load it.

Dependencies
============

* `MODELLER <https://salilab.org/modeller/>`_. This library expects to be able
  to directly import the Modeller Python package (via ``import modeller``)
  and to run the Modeller binary (e.g. :command:`mod9.15`). If you installed
  Modeller from the ``.tar.gz`` package, you will need to set the
  ``PYTHONPATH``, ``PATH`` and ``LD_LIBRARY_PATH`` environment variables
  to facilitate this.

* `DSSP <http://swift.cmbi.ru.nl/gv/dssp/>`_. It is expected that the
  :command:`mkdssp` binary is in the ``PATH``.
<commit_msg>We also need Python and nose.<commit_after>Installation
************

In the Sali Lab
===============

If you are working in the Sali lab, you don't need to build and install
AllosMod - it is already set up for you as a module. Just run
``module load allosmod`` to load it.

Dependencies
============

* `Python <https://www.python.org>`_ 2.6 or later (Python 3 should also be OK).

* `MODELLER <https://salilab.org/modeller/>`_. This library expects to be able
  to directly import the Modeller Python package (via ``import modeller``)
  and to run the Modeller binary (e.g. :command:`mod9.15`). If you installed
  Modeller from the ``.tar.gz`` package, you will need to set the
  ``PYTHONPATH``, ``PATH`` and ``LD_LIBRARY_PATH`` environment variables
  to facilitate this.

* `DSSP <http://swift.cmbi.ru.nl/gv/dssp/>`_. It is expected that the
  :command:`mkdssp` binary is in the ``PATH``.

* `nose <https://nose.readthedocs.io/en/latest/>`_ is also needed to run the
  test suite (recommended but not essential).

{'fraction_non_alphanumeric': 0.15388858246001103, 'fraction_numerical': 0.004964147821290678, 'mean_word_length': 4.124293785310734, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 9, 'https://': 4, 'lorem ipsum': 0, 'www.': 1, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7350262', 'n_tokens_mistral': 593, 'n_tokens_neox': 573, 'n_words': 234}