Installation

Using Pypi

pip3 install pdb_manip_py

Using Conda

conda install pdb_manip_py -c conda-forge

From source code

The sources for Docking Python can be downloaded from the Github repo.

You can either clone the public repository:

$ git clone git://github.com/samuelmurail/pdb_manip_py

Or download the tarball:

$ curl -OJL https://github.com/samuelmurail/pdb_manip_py/tarball/master

Once you have a copy of the source, you can install it with:

$ python setup.py install

Test installation

Launch test with doctest, will check that module’s docstrings are up-to-date by verifying that all interactive examples still work as documented.

$ pytest
=============================== test session starts ================================
platform darwin -- Python 3.8.2, pytest-5.4.1, py-1.8.1, pluggy-0.13.1
rootdir: /Users/smurail/Documents/Code/pdb_manip_py, inifile: pytest.ini
plugins: cov-2.8.1
collected 40 items

pdb_manip_py/pdb2pqr.py .                                                    [  2%]
pdb_manip_py/pdb_manip.py .......................................            [100%]

================================= warnings summary =================================
pdb_manip_py/pdb_manip.py::pdb_manip_py.pdb_manip.Coor.align_principal_axis
  /Users/smurail/opt/miniconda3/envs/docking/lib/python3.8/site-packages/scipy/spatial/transform/rotation.py:1953: UserWarning: Optimal rotation is not uniquely or poorly defined for the given sets of vectors.
    warnings.warn("Optimal rotation is not uniquely or poorly defined "

-- Docs: https://docs.pytest.org/en/latest/warnings.html
========================== 40 passed, 1 warning in 11.64s ==========================