Add documentation for the command-line scripts #228
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env setup in tutorials; remove TOC from tutorials for heading formatting
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Preview of the edited documentations: https://rwxmeeko.readthedocs.io/en/latest/cli_rec_prep.html#
Please consider the added documentations a basic version for the command-line scripts.
For each command-line .py scripts, the documentation has three main sections:
(1) A very brief summary and a code block as the
Basic usage(2) An
Aboutsection that allows us to explain the design and the importance, like the Templates, Write flag and the Residue selection and assignment language for mk_prepare_receptor.py(3) An exhaustive list of
Options. This list is generated not manually written. could add some more details and example usage for the most commonly used options.@diogomart Please let me know if you like the layout, and I could add more details to the description pages of the command line scripts! Thanks
Some other changes included in this PR:
Deleted the redundant Table of Content in the body of tutorials
Deleted installation of Meeko from tutorials
Added the Covalent (Tethered) Docking Colab back. The two Colab notebooks now use a better (complied from develop) version of AD-GPU
Some other small fixes