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

[editorialbot]

Submitting author: !--author-handle-->@radifar<!--end-author-handle-- (Muhammad Radifar) Repository: https://github.com/radifar/pilah Branch with paper.md (empty if default branch): Version: 0.1.0b2 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

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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]

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

[editorialbot]

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[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:

• [x] Please study the above reference check :point_up: 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.