Installation

WaterNetworkAnalysis can be installed as a python package or as a PyMOL plugin.

Installation of the Python package

The easiest ways to install WaterNetworkAnalysis is using conda from conda-forge:

conda install -c conda-forge WaterNetworkAnalysis

Alternatively, WNA is also available on PyPi via pip:

pip install WaterNetworkAnalysis

Pymol is an optional dependency for visualisation and is not present on PyPi, however WNA can be installed and used without it (bar pymol visualisation features). Pymol can be installed using conda:

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

For more information on CWS dependencies also see CWS installation guide.

Python package installation

The easiest ways to install WaterNetworkAnalysis is using conda from conda-forge:

conda install -c conda-forge WaterNetworkAnalysis

Alternatively, WNA is also available on PyPi via pip:

pip install WaterNetworkAnalysis

Pymol is an optional dependency for visualisation and is not present on PyPi, however WNA can be installed and used without it (bar pymol visualisation features). Pymol can be installed using conda:

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

For more information on CWS dependencies also see CWS installation guide.

PyMOL plugin installation

This guide provides detailed installation instructions for Linux, Mac, and Windows users. We recommend using conda or mamba to create a new environment with at least Python 3.9.

Note that PyMOL which can be downloaded from the PyMOL website comes with python 3.7 which is not supported by WaterNetworkAnalysis or ConservedWaterSearch. For this reason users will have to install mamba/conda and create a new environment with python version greater or equal to 3.9 and install PyMOL in that environment. The plugin has been tested with PyMOL version > 2.5.0.

Prerequisites

Ensure you have conda or mamba installed. If not, download and install miniforge , or miniconda or Anaconda.
For users who wish to use the paid version of PyMOL, ensure you have a valid license.
Once conda/mamba has been installed, make sure you activate the installation by either sourcing your .bashrc or restarting your terminal.

Installation Steps

Create a new conda environment (use mamba instead of conda if you opted for mamba):
conda create -n myenv python=3.9
Replace myenv with your preferred environment name.
Activate the environment:
- Linux & Mac:
```
conda activate myenv
```
- Windows:
```
activate myenv
```
Install PyMOL:
- Open-source version:
```
conda install -c conda-forge pymol-open-source
```
- Paid version:
```
conda install -c schrodinger pymol-bundle
```
macOS users may need to install the extra packages. For more information see PyMOL documentation. To test if the installation was successful users should just be able to type the following in their terminal:
pymol
Users with a license should download their license file from the PyMOL website and activate it by going to Help -> Install new License File in main PyMOL window.
Install dependencies:

WaterNetworkAnalysis is the main dependency and can be installed via:
conda install -c conda-forge WaterNetworkAnalysis

Install the WaterNetworkAnalysis plugin in PyMOL:

The plugin is a single file located here. In PyMOL, go to Plugin > Plugin Manager > Install New Plugin and select the WNA_PyMOL_plugin.py file from the WNA_PyMOL folder. The plugin can then be accessed from the plugin drop-down menu.

Troubleshooting

If you encounter any issues, ensure you’re using the correct Python version and that all packages are installed with their specified versions.

Known Issues with dependencies

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