[PRE REVIEW]: MD-SAPT: Python Based Toolkit for Running Symmetry Adapted Perturbation Theory Calculations on Molecular Dynamics Trajectories

[editorialbot]

Submitting author: !--author-handle-->@armcdona<!--end-author-handle-- (Ashley Ringer McDonald) Repository: https://github.com/calpolyccg/MDSAPT Branch with paper.md (empty if default branch): JOSS_Pub Version: v2.0 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: @wiederm, @CarvFS Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/baf524e08bec6dcbd6f57a0e9b6236b9"><img src="https://joss.theoj.org/papers/baf524e08bec6dcbd6f57a0e9b6236b9/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/baf524e08bec6dcbd6f57a0e9b6236b9/status.svg)](https://joss.theoj.org/papers/baf524e08bec6dcbd6f57a0e9b6236b9)

Author instructions

Thanks for submitting your paper to JOSS @armcdona. Currently, there isn't a JOSS editor assigned to your paper.

@armcdona if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

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

For a list of things I can do to help you, just type:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (667.9 files/s, 74431.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          21            876           1707           2433
XML                              1              0              0            463
YAML                            14             59            120            380
Markdown                        10             99              1            297
TeX                              1             13              0            201
reStructuredText                 8             57             75             57
Bourne Shell                     3              8             10             43
JSON                             2              5              0             42
DOS Batch                        1              8              1             27
make                             1              4              6             10
Dockerfile                       1              4             12              3
-------------------------------------------------------------------------------
SUM:                            63           1133           1932           3956
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1255

[editorialbot]

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

OK DOIs

- 10.1021/acs.jcim.8b00989 is OK
- 10.1093/bioinformatics/btx789 is OK
- 10.1063/5.0006002 is OK
- 10.1002/jcc.21787 is OK
- 10.25080/Majora-629e541a-00e is OK
- 10.1002/jcc.23753 is OK
- 10.1002/wcms.1452 is OK
- 10.6084/M9.FIGSHARE.17156018.V1 is OK
- 10.1002/wcms.84 is OK
- 10.1021/bk-2007-0958 is OK
- 10.1002/9780470399545.ch1 is OK
- 10.1016/j.bpj.2015.08.015 is OK
- 10.6084/m9.figshare.20520726.v1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[armcdona]

Possible reviewers: tluchko, FoleyLab, cadalyjr

[Kevin-Mattheus-Moerman]

@editorialbot invite @jarvist as editor

[editorialbot]

Invitation to edit this submission sent!

[jarvist]

@editorialbot assign @jarvist as editor

Perfect fit to my area! Thank you for the reviewer suggestions @armcdona Ashley.

[editorialbot]

Assigned! @jarvist is now the editor

[Kevin-Mattheus-Moerman]

@jarvist hope you are doing well. Thanks for editing this one. Are you able to recruit reviewers here? Let me know if you need help.

[jarvist]

Suggestions of reviewers would be very well received! There's relatively few people in SAPT, and your code seems quite a particular application to MD.

On Thu, 23 Mar 2023 at 09:42, Kevin Mattheus Moerman < @.***> wrote:

@jarvist https://github.com/jarvist hope you are doing well. Thanks for editing this one. Are you able to recruit reviewers here? Let me know if you need help.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5141#issuecomment-1480879779, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAUHJFNVGNGT2TFBDSW6CDW5QLKFANCNFSM6AAAAAAUXDD5H4 . You are receiving this because you were mentioned.Message ID: @.***>

[Kevin-Mattheus-Moerman]

@armcdona see the request from the editor ☝️ @jarvist. Do you think you can help suggest some potential reviewers? If you have some in mind, please mention them here but leave out the @ symbol, so they are not tagged. Thanks!

[Kevin-Mattheus-Moerman]

@jarvist any luck finding reviewers yourself?

[Kevin-Mattheus-Moerman]

@jarvist :wave:

[arfon]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

Five most similar historical JOSS papers:

pyscal: A python module for structural analysis of atomic environments Submitting author: @srmnitc Handling editor: @melissawm (Active) Reviewers: @lucydot, @bocklund Similarity score: 0.8347

BioSimSpace: An interoperable Python framework for biomolecular simulation Submitting author: @lohedges Handling editor: @will-rowe (Retired) Reviewers: @amritagos, @richardjgowers Similarity score: 0.8315

polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories Submitting author: @symmy596 Handling editor: @richardjgowers (Active) Reviewers: @hmacdope, @lscalfi Similarity score: 0.8312

pyCADMium: Chemical Atoms in Diatomic Molecules. A prolate spheroidal Python module for embedding calculations Submitting author: @VHchavez Handling editor: @lucydot (Active) Reviewers: @raghurama123, @srmnitc Similarity score: 0.8293

Sapsan: Framework for Supernovae Turbulence Modeling with Machine Learning Submitting author: @pikarpov-lanl Handling editor: @dfm (Active) Reviewers: @kburns, @milescranmer Similarity score: 0.8275

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before before considering asking the reviewers of these papers to review again for JOSS.

[arfon]

@armcdona – my apologies it has taken so long to get this submission moving. Can you confirm you're still interested in pursuing this submission with JOSS?

[armcdona]

Yes, we would like to continue with the submission. My suggested reviewers were provided above in the message from 10 February 2023.

[arfon]

Thanks for confirming. I'll take this one on @Kevin-Mattheus-Moerman @jarvist.

[arfon]

@editorialbot assign me as editor

[editorialbot]

Assigned! @arfon is now the editor

[arfon]

@tluchko, @FoleyLab,@cadalyjr @lohedges @symmy596 @hmacdope @lscalfi – :wave: would any of you be willing to review this submission for JOSS? The submission under consideration isMD-SAPT: Python Based Toolkit for Running Symmetry Adapted Perturbation Theory Calculations on Molecular Dynamics Trajectories – https://github.com/calpolyccg/MDSAPT

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks Arfon

[hmacdope]

@arfon I will have to excuse myself on the basis of a COI, as I am an MDAnalysis core-developer (creators of the MDAKit ecosystem, which this package is a member of :smile: ), and have worked with Alia (the first author) in an open source capacity as a member of our dev community a few times. I believe this falls under the COI policy but you can correct me if I am wrong. :+1:

[arfon]

Got it. Thanks @hmacdope – I think it's best to avoid that conflict if we can yes. If you have any other folks you would recommend as potential reviewers, please let me know!

[hmacdope]

@wiederm expressed some interest :+1: He may need to sign up to be a reviewer before I can ping him. I can't spell.

[arfon]

:wave: @wiederm – would you be willing to review this submission for JOSS? The submission under consideration isMD-SAPT: Python Based Toolkit for Running Symmetry Adapted Perturbation Theory Calculations on Molecular Dynamics Trajectories – https://github.com/calpolyccg/MDSAPT

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks Arfon

[wiederm]

Hi @arfon and @hmacdope , happy to review this manuscript!

[arfon]

Amazing, thanks @wiederm! I'll wait for a second reviewer to accept before opening the main review issue. Hopefully this won't take more than a couple of days.

[tluchko]

@afron, I'm sorry but I can't. I'm over committed right now and wouldn't be able to complete the review in a timely manner.

[lohedges]

I also don't have the bandwidth right now, I'm afraid. Thanks for the consideration.

[arfon]

@tluchko @lohedges – are there any people you could recommend that might be able to contribute a review?

[tluchko]

@CarvFS would be a good choice. He is a postdoc in my group, if that matters.

[arfon]

👋 @CarvFS – would you be willing to review this submission for JOSS? The submission under consideration ishttps://github.com/openjournals/joss-reviews/issues/5141 – https://github.com/calpolyccg/MDSAPT

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks Arfon

[CarvFS]

Hello Arfon!

I would be delighted to review this submission! I will take a look at the submission and guidelines to review it!

Thank you very much! Felipe Silva Carvalho

---

From: Arfon Smith @.> Sent: Sunday, October 8, 2023 12:25 AM To: openjournals/joss-reviews @.> Cc: Felipe_SC @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: MD-SAPT: Python Based Toolkit for Running Symmetry Adapted Perturbation Theory Calculations on Molecular Dynamics Trajectories (Issue #5141)

👋 @CarvFShttps://github.com/CarvFS – would you be willing to review this submission for JOSS? The submission under consideration ishttps://github.com//issues/5141https://github.com/openjournals/joss-reviews/issues/5141 – https://github.com/calpolyccg/MDSAPT

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks Arfon

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/5141#issuecomment-1751947089, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AX6EO3YA4WFMHZ6AYT2HM7TX6JIOVAVCNFSM6AAAAAAUXDD5H6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJRHE2DOMBYHE. You are receiving this because you were mentioned.Message ID: @.***>

[arfon]

@editorialbot add @wiederm as reviewer

[editorialbot]

@wiederm added to the reviewers list!

[arfon]

@editorialbot add @CarvFS as reviewer

[editorialbot]

@CarvFS added to the reviewers list!

[arfon]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5931.

[arfon]

@wiederm, @CarvFS, @armcdona – see you over in #5931 where the actual review will take place.