[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
Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/bb44f24915c6d2d066baa20343e92df1/status.svg)](https://joss.theoj.org/papers/bb44f24915c6d2d066baa20343e92df1)

Reviewers and authors:

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Reviewer instructions & questions

@moritzobenauer & @dominiquesydow, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @fboehm know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @moritzobenauer

[editorialbot]

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[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

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.06 s (1273.9 files/s, 160825.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30            875            508           4882
JSON                             3             20              0           1915
Markdown                        17            334              1            919
Text                            23             77              0            486
TOML                             1             11              0             88
TeX                              1              7              0             76
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:                            82           1341            535           8476
-------------------------------------------------------------------------------

Commit count by author:

    55	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: Apache License 2.0 (Valid open source OSI approved license)

[editorialbot]

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

[moritzobenauer]

Review checklist for @moritzobenauer

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/radifar/pilah?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@radifar) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1. Contribute to the software 2. Report issues or problems with the software 3. Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[moritzobenauer]

Dear authors,

Thank you for submitting this repository to JOSS. The following comments are categorized as Minor Revisions needed and Major Revisions needed following the JOSS guidelines.

Major Revisions:

Quality of writing. This manuscript suffers from major grammatical and ellipsis errors. This makes the manuscript hard to read and understand, and, therefore, detrimental to reaching a larger audience. The software has scientific merit and it would be a shame if the quality of the manuscript prevented new users from using it.

Installation instructions: You describe the installation of the binary file. Please add a step-by-step installation guide to set up the correct virtual environment and download the repo so that you can run the software without downloading the binary executable. This would allow Windows and Mac users to run the software and pilah would reach a broader audience.

Automated tests: Please include detailed instructions for running the included Python tests along with the installation instructions mentioned above. Even a novice user without experience should be able to follow these steps and be able to verify the functionality of the software. According to the JOSS guidelines, a Github actions integration of these tests would be perfect, but is not necessary, however.

A statement of need: Please add a statement of need to your readme file. You can use a shortened version of the one from your manuscript.

Minor Revisions:

Contribution and authorship: According to the repo's commit history only M. Radifar committed to this repo. What was the role of the article's second author E. P. Istyastono? Please note that according to JOSS policy, purely financial contributions are not considered sufficient for co-authorships.

Comments on the Manuscript:

1. It is best practice to cite all of the software used and mentioned in the main text of the manuscript instead of the acknowledgments. Also, Figure 1 needs a proper caption describing the workflow.

2. Is it planned to include a command line interface to pilah so that users can input options via flags instead of a text file? Looking at your parser structure this should be straight forward and would allow for high-throughput analysis in the future.

3. You mention that competing software suffers from bad accuracy of the bond order assignment. How does pilah compare to SPORES regarding this?

4. Please elaborate further on the deleting of residues with missing atoms or wrong bond lengths. Is this common practice in competing software? I would suspect that deleting individual residues might alter the resulting protein significantly, hence influencing the chemical/physical properties.

A few minor things/tips:

Since your docs are more detailed than your readme file you could link the docs a bit more prominently in your readme file.

If you want to make the software more accessible to people with no coding background, you should try to catch common parser errors (e.g. entering a string instead of a float for pH, wrong SMILES code, etc.) instead of outputting the Python error messages. This might be helpful to people with no substantial background knowledge.

Thank you for contributing this software to the community.

Best,
Moritz

[fboehm]

@dominiquesydow - just wanted to see if you have any questions about getting started with the review. Please feel free to issue the command to produce a review checklist. thanks again!

[dominiquesydow]

Thanks a lot, still blocked by a sick baby but hope to have time to review this weekend!

…

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