[PRE REVIEW]: PyMut: A rotamer based mutation library implemented in Python

[whedon]

Submitting author: @gerdos (Erdős Gábor) Repository: https://github.com/gerdos/pyMUT Version: 1.0 Editor: Pending Reviewer: Pending Managing EiC: Kevin M. Moerman

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[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.08 s (47.4 files/s, 10518.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           2             55             62            634
Markdown                         1             22              0             71
TeX                              1              3              0             40
-------------------------------------------------------------------------------
SUM:                             4             80             62            745
-------------------------------------------------------------------------------

Statistical information for the repository '991b75d21f72a307e20b21bc' was
gathered on 2021/03/25.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Erdos Gabor                      4           905            155           97.70
gerdos                           2            11             14            2.30

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
gerdos                      751         6827.3          0.3                4.79

[whedon]

PDF failed to compile for issue #3134 with the following error:

ORCID looks to be the wrong length /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:155:in block in check_orcids': Problem with ORCID (000-0001-6218-5192) for Erdős Gábor^[Corresponding author] (RuntimeError) from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:153:ineach' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:153:in check_orcids' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:90:ininitialize' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in new' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:inset_paper' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:58:in prepare' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:131:in<top (required)>' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in

'

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1016/j.str.2011.03.019 may be a valid DOI for title: A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@whedon query scope

[whedon]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@gerdos thanks for this submission. I've flagged this submission for additional scope review by our editorial board. This is default for submissions of this size (see our "substantial scholarly effort" requirements) and should take about a week to complete. Thanks for your patience.

[Kevin-Mattheus-Moerman]

Note to editorial board, it looks like this is the core code contribution which appears to be about ~350 lines of code followed by mostly hardcoded (e.g. angle) definitions: https://github.com/gerdos/pyMUT/blob/master/pymut.py

@gerdos if you disagree with this finding :point_up: or want to elaborate on the extent of scholarly work contained in your submission please do let us know. Thanks.

@gerdos a side note, I noticed RESIDUE_STRUCTUES in the code which perhaps should read RESIDUE_STRUCTURES?

[gerdos]

Dear @Kevin-Mattheus-Moerman!

Thanks a lot for reviewing my work! Indeed, the length of the code does not reach the suggested 1000 lines, but reaches the minimum in the submission rules. I usually try to code in a more compact manner while keeping my code in line with the current standards. I also though a lot about the aforementioned hardcoded angles, to supply them in a data file, however at the end, I put all the things inside the code that were calculated by me, and only supplied external data in separated file, like the rotamer library itself.

I hope the shortage of the code will not hider the possibility of the publication.

Thanks you for the notice as well, it is indeed a typo, I will correct it now!

Earlier yesterday I was also contacted by the good people behind Biopython, and they offered me to intergrate PyMut inside Biopython. I hope this will not cause problems with JOSS!

Thanks a lot, again!

[kthyng]

Hi @gerdos and thanks for your submission. Unfortunately the editorial board has determined that your submission does not pass the substantial scholarly effort bar. It sounds excellent to join with Biopython, and perhaps the larger combined package could even be submitted to JOSS sometime.

[kthyng]

@whedon reject

[whedon]

Paper rejected.