Installing

Note

We are assuming you have a working mamba installation in your computer. If this is not the case, please refer to their official documentation.

If you installed mamba into an existing conda installation, also make sure that the conda-forge channel is configured by running conda config --add channels conda-forge.

Install from the conda package

Create a new conda environment called opencadd with the opencadd package and all its dependencies installed:
```
mamba create -n opencadd opencadd
```
Activate the new conda environment:
```
conda activate opencadd
```

Install from the latest development snapshot

Install the latest development snapshot from the GitHub repository’s master branch.

Create a new conda environment called opencadd:

mamba env create -f https://raw.githubusercontent.com/volkamerlab/opencadd/master/devtools/conda-envs/user_env.yaml

Activate the new conda environment:
```
conda activate opencadd
```

Install opencadd package via pip:

pip install https://github.com/volkamerlab/opencadd/archive/master.tar.gz

Development version

To install the development version of OpenCADD, you can run:

# Install development environment (incl. packages for testing and documentation)
mamba env create -f https://raw.githubusercontent.com/volkamerlab/opencadd/master/devtools/conda-envs/test_env.yaml -n opencadd-dev
conda activate opencadd-dev

# Download repository and install `opencadd` package in editable mode
git clone git@github.com:volkamerlab/opencadd.git
pip install -e opencadd

# Let's change into the repo's folder
cd opencadd

# Run tests like this
pytest -v opencadd/tests/

# Before you push changes to GitHub, lint and style-check your code
pylint opencadd
black --check -l 99 opencadd

# Check how the documentation renders
cd docs
make html

Note: If you add new dependencies to opencadd, please update the test and user environment, and leave a note in the dependencies section.

Dependencies

opencadd is supported for at least Python 3.7 and needs the following modules:

Package	Minimal supported version	Used by submodules
`pandas`	1.3.4	1, 2, 4
`biopandas`	0.2.9	1, 2
`bravado`	11.0.3	1
`rdkit`	2021.09.2	1
`tqdm`	4.62.3	1
`biopython`	= 1.77	2
`mdanalysis`	2.0.0	3
`biotite`	0.31.0	3
`mmligner`	1.0.2	3
`muscle`	3.8.1551	3
`theseus`	3.3.0	3
`matplotlib-base`	3.5.0	4
`nglview`	3.0.3	4

Some packages are only needed for a subset of the following modules: [1] opencadd.databases.klifs, [2] opencadd.io, [3] opencadd.structure.superposition, [4] opencadd.structure.pocket

This list of minimal supported versions is based on this CI run.