Installation

The default installations from PyPI and conda-forge don’t include any of the optional dependencies required for visualization (see below). This is done to avoid potential conflicts with user defined PyMOL installations.

Installation via conda

ConservedWaterSearch is available through conda-forge using conda (or mamba) and this is the recommended way to install it:

conda install -c conda-forge ConservedWaterSearch

Installation via PyPI

ConservedWaterSearch can be installed via pip from PyPI:

pip install ConservedWaterSearch

Optional visualization dependencies

PyMOL is required for visualization only, if so desired. If not, it’s installation can be skipped. PyMOL is not available via PyPI (pip), but can be installed from conda-forge. If PyMOL is already installed in your current python environment it can be used with CWS. If not, the free (open-source) version can be installed from conda-forge via conda (or mamba):

conda install -c conda-forge pymol-open-source

and paid (licensed version) from schrodinger channel (see here for more details) via conda (or mamba):

conda install -c conda-forge -c schrodinger pymol-bundle

Optional dependencies for visualization can be installed through PyPI (pip) except for PyMOL. To install CWS through pip with nglview use:

pip install ConservedWaterSearch[nglview]

To install with matplotlib for clustering plots use:

pip install ConservedWaterSearch[debug]

To install with both nglview and matplotlib use:

pip install ConservedWaterSearch[all]

Known Issues

AttributeError: 'super' object has no attribute '_ipython_display_' Some versions of Jupyter notebook are incpompatible with ipython (see here). To resolve install version of ipywidgets<8 using conda:

conda install "ipywidgets <8" -c conda-forge

or pip:

pip install ipywidgets==7.6.0

Tests

ConservedWaterSearch (CWS) uses pytest for running unit tests. It can be installed via conda:

conda install -c conda-forge pytest

Or via PyPI (using pip):

pip install pytest

Unit tests can be run from the root directory:

python -m pytest

Documentation

To build the documentation following dependencies have to be installed, either using conda:

conda install -c conda-forge sphinx sphinx_rtd_theme sphinxcontrib-bibtex

or pip:

pip install sphinx sphinx_rtd_theme sphinxcontrib-bibtex

The documentation can be build from the docs folder:

cd docs/
make html
open build/html/index.html