Document expected standard residues

[IAlibay]

Apologies if I'm missing something obvious here.

My understanding is that propka expects certain standard residues (defined here) as ATOM entries in the input PDB and that other "non-standard" residues (say ASH coming off an AMBER force field residue definition) will be ignored without warning.

Additionally, it seems that "standard" residues for DNA are usually just automatically set to HETATM (or so it seems to appear this way here).

In part I'm opening this issue to check that this interpretation is correct, but it would be really useful downstream (i.e. for tools like propkatraj) to have this documented (I couldn't find this anywhere, maybe I missed something obvious) somewhere so we can enforce what we pass as ATOM and HETATM entries to propka.

[sobolevnrm]

Hello; you are correct: the list is not documented. This is a good suggestion and we will add it to the "to-do" list. We are also always looking for help with tasks like this if you (or anyone) is interested!

Thank you for the suggestion.

[IAlibay]

Thanks for confirming this @sobolevnrm

We are also always looking for help with tasks like this if you (or anyone) is interested!

Sure can do 😃 I'll probably open two separate PRs, one to add to the API docs, and one to add an "I/O" section to the main docs.

[sobolevnrm]

That sounds awesome, @IAlibay. Thank you very much!

[sobolevnrm]

Per your comment in #104, I'm not sure that we'd document standard residue types in the API docs. Can you clarify this request?

[IAlibay]

@sobolevnrm apologies for the confusion, my proposal here is to do two things:

1. Document I/O in detail as a new entry in the main docs.
2. Add extra docstring details (probably through notes) to protein_precheck / set_properties / anything related (also maybe looking to add type hints, f-strings if/where appropriate).

[sobolevnrm]

That sounds very reasonable -- thanks!

On Sun, Nov 22, 2020 at 6:30 PM Irfan Alibay [email protected] wrote:

@sobolevnrm https://github.com/sobolevnrm apologies for the confusion, my proposal here is to do two things:

1. Document I/O in detail as a new entry in the main docs.
2. Add extra docstring details (probably through notes) to protein_precheck / set_properties / anything related (also maybe looking to add type hints, f-strings if/where appropriate).

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