Packages and webservers used in TeachOpenCADD
=============================================

TeachOpenCADD uses several external packages and webservers as listed below. 
If we are using your resource and forgot to add it here, please let us know, thank you!

Python packages
---------------

- Cheminformatics and structural bioinformatics:

  - ``rdkit``: http://rdkit.org/
  - ``openbabel``: https://openbabel.org/
  - ``mdanalysis``: https://www.mdanalysis.org/
  - ``biopython``: https://biopython.org/
  - ``biopandas``: https://biopandas.github.io/biopandas/
  - ``opencadd``: https://opencadd.readthedocs.io/en/latest/
  - ``plip``: https://github.com/pharmai/plip
  - ``openff``: https://github.com/openforcefield/openff-toolkit
  - ``openff-toolkit``: https://github.com/openforcefield/openff-toolkit
  - ``openmmforcefields``: https://github.com/openmm/openmmforcefields
  - ``pdbfixer``: https://github.com/openmm/pdbfixer
  - ``mdanalysis``: https://www.mdanalysis.org/
  - ``biotite``: https://www.biotite-python.org/
  - ``smina``: https://sourceforge.net/p/smina/discussion/

- Deep learning: 

  - ``pytorch``: https://pytorch.org/
  - ``pyg``: https://pyg.org/

- Data science (PyData stack):

  - ``numpy``: https://numpy.org/
  - ``pandas``: https://pandas.pydata.org/
  - ``scikit-learn``: https://scikit-learn.org/
  - ``keras``: https://keras.io/
  - ``jupyter``: https://jupyter.org/
  - ``ipywidgets``: https://ipywidgets.readthedocs.io

- Data visualization:

  - ``matplotlib``: https://matplotlib.org/ 
  - ``mpl_toolkits``: https://matplotlib.org/stable/api/toolkits/mplot3d.html
  - ``matplotlib_venn``: https://github.com/konstantint/matplotlib-venn
  - ``seaborn``: https://seaborn.pydata.org/
  - ``nglview``: http://nglviewer.org/nglview/latest/

- Web services clients:

  - ``pypdb``: https://github.com/williamgilpin/pypdb
  - ``chembl_webresource_client``: https://github.com/chembl/chembl_webresource_client
  - ``requests``: https://requests.readthedocs.io/en/latest/
  - ``bravado``: https://bravado.readthedocs.io/en/stable/
  - ``beautifulsoup4``: https://www.crummy.com/software/BeautifulSoup/bs4/doc/

- Utilities:

  - ``tqdm``: https://tqdm.github.io/
  - ``requests_cache``: https://requests-cache.readthedocs.io
  - ``redo``: https://github.com/mozilla-releng/redo
  - ``google-colab``: https://pypi.org/project/google-colab/
  - ``condacolab``: https://pypi.org/project/condacolab/

- Continuous integration:

  - ``pytest``: https://docs.pytest.org
  - ``nbval``: https://nbval.readthedocs.io

- Documentation:

  - ``sphinx``: https://www.sphinx-doc.org
  - ``nbsphinx``: https://nbsphinx.readthedocs.io

- Code style:

  - ``black-nb``: https://github.com/tomcatling/black-nb

Databases and webservers
------------------------

- ChEMBL: https://www.ebi.ac.uk/chembl/
- RCSB PDB: https://www.rcsb.org/
- KLIFS: https://klifs.net/
- PubMed: https://pubchem.ncbi.nlm.nih.gov/
- ProteinsPlus: https://proteins.plus/