[PRE REVIEW]: PiLAH: Command-line tool for protein and ligand extraction, bond order correction, and protonation

[editorialbot]

Submitting author: @radifar (Muhammad Radifar)
Repository: https://github.com/radifar/pilah
Branch with paper.md (empty if default branch):
Version: 0.1.0b2
Editor: @fboehm
Reviewers: @moritzobenauer, @dominiquesydow
Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/bb44f24915c6d2d066baa20343e92df1"><img src="https://joss.theoj.org/papers/bb44f24915c6d2d066baa20343e92df1/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/bb44f24915c6d2d066baa20343e92df1/status.svg)](https://joss.theoj.org/papers/bb44f24915c6d2d066baa20343e92df1)

Author instructions

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

@radifar if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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 1.90  T=0.07 s (797.2 files/s, 114168.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30            788            508           3681
JSON                             3             20              0           1915
Markdown                        17            334              0            920
TeX                              1              7              0             71
TOML                             1              7              0             45
Jupyter Notebook                 1              0             16             29
YAML                             2              4              4             29
DOS Batch                        1              8              1             27
Bourne Shell                     2              1              0             15
make                             1              4              5             10
-------------------------------------------------------------------------------
SUM:                            59           1173            534           6742
-------------------------------------------------------------------------------

Commit count by author:

    49	Muhammad Radifar

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1561

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[editorialbot]

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

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: RDKit
- No DOI given, and none found for title: Meeko: interface for AutoDock
- No DOI given, and none found for title: PyInstaller: Freeze (package) Python programs into...

❌ MISSING DOIs

- 10.1007/s10822-010-9385-x may be a valid DOI for title: pK a based protonation states and microspecies for...
- 10.1186/s13321-019-0336-9 may be a valid DOI for title: Dimorphite-DL: an open-source program for enumerat...
- 10.1021/acs.jctc.2c00308.s001 may be a valid DOI for title: A fast and interpretable deep learning approach fo...
- 10.1093/bioinformatics/btp163 may be a valid DOI for title: Biopython: freely available Python tools for compu...
- 10.1186/1758-2946-3-33 may be a valid DOI for title: Open Babel: An open chemical toolbox

❌ INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

Five most similar historical JOSS papers:

Project RACCOON: Automated construction of PDB files for polymers and polymer peptide conjugates
Submitting author: @moritzobenauer
Handling editor: @jromanowska (Active)
Reviewers: @taoliu032, @lorenzo-rovigatti
Similarity score: 0.6735

buildH: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters
Submitting author: @patrickfuchs
Handling editor: @richardjgowers (Retired)
Reviewers: @lilyminium, @ojeda-e, @blakeaw
Similarity score: 0.6722

MolPainter: A Tool for Painting and Solvating Layered Molecular Systems
Submitting author: @gpantel
Handling editor: @jgostick (Active)
Reviewers: @HubLot, @arkajitmandal
Similarity score: 0.6652

HylleraasMD: Massively parallel hybrid particle-field molecular dynamics in Python
Submitting author: @mortele
Handling editor: @rkurchin (Active)
Reviewers: @blakeaw, @yhtang, @abb58
Similarity score: 0.6606

OpenCADD-KLIFS: A Python package to fetch kinase data from the KLIFS database
Submitting author: @dominiquesydow
Handling editor: @richardjgowers (Retired)
Reviewers: @ojeda-e, @andrewtarzia, @mcs07
Similarity score: 0.6601

⚠️ 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 considering asking the reviewers of these papers to review again for JOSS.

[Kevin-Mattheus-Moerman]

@radifar Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

• Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.

[radifar]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1007/s10822-010-9385-x is OK
- 10.1186/s13321-019-0336-9 is OK
- 10.1021/acs.jctc.2c00308 is OK
- 10.1093/bioinformatics/btp163 is OK
- 10.1186/1758-2946-3-33 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: RDKit
- No DOI given, and none found for title: Meeko: interface for AutoDock
- No DOI given, and none found for title: PyInstaller: Freeze (package) Python programs into...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[radifar]

@Kevin-Mattheus-Moerman Dear editor, I have added the required DOIs and the reference check seems OK.

[Kevin-Mattheus-Moerman]

@editorialbot invite @fboehm as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@radifar Apologies for the delays encountered to date. Unfortunately we have a bit of a backlog of submissions and many editors are preoccupied with other submissions. I've just waitlisted this submission as a consequence. However I have issued an invite to @fboehm just now to see if they can help.

For the moment, @radifar I noticed one minor issue, I see you are using the Apache 2.0 license, however Github and our systems do not recognise it as such. I think this is because the license text was altered/shortened a bit. We would recommend that you adopt the full standard text (see also: https://opensource.org/license/apache-2-0).

[radifar]

Thank you, we appreciate that. As for, the license, we already replace it with the full standard text as requested.

[Kevin-Mattheus-Moerman]

@fboehm can you handle this one?

[fboehm]

@editorialbot assign me as editor

[editorialbot]

Assigned! @fboehm is now the editor

[fboehm]

@moritzobenauer @patrickfuchs @gpantel @mortele @dominiquesydow - would you be willing to review this submission for JOSS? My name is Fred, and I'm the editor for this submission. It seems to overlap with your expertise. Please let me know if you have any questions.

[moritzobenauer]

Hey @fboehm , dear authors,
I would be happy to review this submission!

[dominiquesydow]

Hi @fboehm, happy to review this submission as well!

…

On Thu 23. Jan 2025 at 16:02, Moritz Obenauer ***@***.***> wrote: Hey @fboehm <https://github.com/fboehm> , dear authors, I would be happy to review this submission! — Reply to this email directly, view it on GitHub <#7511 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABW7RNLBMAT7ZK2HDTLY5WL2MEHBHAVCNFSM6AAAAABSEHMZGCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMJQGIYTIOJVGY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[fboehm]

@editorialbot assign @moritzobenauer as reviewer

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[fboehm]

@editorialbot add @moritzobenauer as reviewer

[editorialbot]

@moritzobenauer added to the reviewers list!

[fboehm]

@editorialbot add @dominiquesydow as reviewer

[editorialbot]

@dominiquesydow added to the reviewers list!

[fboehm]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7720.