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[PRE REVIEW]: MoSDeF-dihedral-fit: A lightweight software for fitting dihedrals within MoSDeF
Submitting author: @jpotoff (Jeffrey Potoff) Repository: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/ Branch with paper.md (empty if default branch): Version: 0.0.3 Editor: @phibeck Reviewers: @naik-aakash Managing EiC: Kyle Niemeyer
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HTML: <a href="https://joss.theoj.org/papers/2d6869aa8dce990c7dec7267815a8efc"><img src="https://joss.theoj.org/papers/2d6869aa8dce990c7dec7267815a8efc/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/2d6869aa8dce990c7dec7267815a8efc)
Author instructions
Thanks for submitting your paper to JOSS @jpotoff. Currently, there isn't a JOSS editor assigned to your paper.
@jpotoff 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.
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Checking the BibTeX entries failed with the following error:
Failed to parse BibTeX on value "pages" (NAME) ["@", #<BibTeX::Entry >, {:author=>["Mayne, C.G. Mayne and Saam, J, and Schulten, K. and Tajkhorshid, E. and Gumbart, J.C."], :journal=>["J. Comp. Chem."], :volume=>["34"], :issue=>["32"]}]
Software report:
github.com/AlDanial/cloc v 1.90 T=0.11 s (395.7 files/s, 148136.3 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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Python 11 1081 1961 10109
XML 4 2 10 597
TeX 3 44 33 426
reStructuredText 13 272 278 392
DOS Batch 1 29 1 212
YAML 6 23 3 182
Markdown 2 59 0 147
make 1 28 6 143
Dockerfile 1 15 2 33
Bourne Shell 1 2 0 9
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SUM: 43 1555 2294 12250
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Commit count by author:
185 bc118
50 pre-commit-ci[bot]
37 Brad Crawford
28 CalCraven
28 Co Quach
5 GOMC
3 Jeffrey Potoff
Paper file info:
📄 Wordcount for paper.md is 1360
✅ The paper includes a Statement of need section
Hello @jpotoff, this pre-review issue is where we will sort out any issues, assign an editor, and find reviewers.
First, I noticed the unusual LICENSE in the software repo: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/blob/main/LICENSE.rst. Why are you including the license information for vmd-python and VMD, when these do not appear to be distributed in this software?
Second, the paper compilation issue appears to stem from a missing comma at the end of line 6 of paper.bib.
@editorialbot invite @phibeck as editor
Hi @phibeck, could you edit this submission?
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1002/jcc.23422 is OK
- 10.1007/s00894-008-0305-0 is OK
- 10.1021/jp972543 is OK
- 10.1098/rspa.1938.0173 is OK
- 10.1063/1.1740026 is OK
- 10.1021/ja00315a051 is OK
- 10.1002/jcc.540070216 is OK
- 10.1002/jcc.20035 is OK
- 10.1002/jcc.21287 is OK
- 10.1021/acs.jctc.5b00935 is OK
- 10.1063/1.1674022 is OK
- 10.1021/acs.jctc.9b01183 is OK
- 10.1021/acs.jcim.2c01498 is OK
- 10.1016/j.softx.2018.11.005 is OK
- 10.1016/j.softx.2020.100627 is OK
- 10.1021/jp990988n is OK
- 10.1021/jp9072137 is OK
- 10.1021/acs.jpcb.5b01354 is OK
MISSING DOIs
- 10.1021/ja9621760 may be a valid DOI for title: Development and Testing of the OPLS All-Atom Force...
- No DOI given, and none found for title:
- No DOI given, and none found for title: Sur le mélange des gaz
- 10.1002/andp.18812480110 may be a valid DOI for title: Ueber die Anwendung des Satzes vom Virial in der k...
- No DOI given, and none found for title: Gaussian 16 Revision C.01
- No DOI given, and none found for title: GMSO: General Molecular Simulation Object
- No DOI given, and none found for title: forcefield-utilities
- No DOI given, and none found for title: Open-Source Molecular Modeling Software in Chemica...
- No DOI given, and none found for title: MoSDeF-dihedral-fit: A simple software package to ...
- 10.1021/acs.jcim.2c01498.s001 may be a valid DOI for title: MoSDeF-GOMC: Python software for the creation of s...
- 10.1016/0263-7855(96)00018-5 may be a valid DOI for title: VMD – Visual Molecular Dynamics
- No DOI given, and none found for title: A System for Interactive Molecular Dynamics Simula...
- No DOI given, and none found for title: Multiple Alignment of protein structures and seque...
- No DOI given, and none found for title: \em An Efficient Library for Parallel Ray Tracing ...
- No DOI given, and none found for title: Knowledge-based secondary structure assignment
- No DOI given, and none found for title: Linearly Scalable Computation of Smooth Molecular ...
- 10.1145/220279.220324 may be a valid DOI for title: Fast and Robust Computation of Molecular Surfaces
- No DOI given, and none found for title: Speech/Gesture Interface to a Visual-Computing Env...
- No DOI given, and none found for title: vmd-python
INVALID DOIs
- None
Hi @jpotoff, thanks for your submission. I'll be looking for reviewers next. A few things you can do to speed up the review process in addition to what was pointed out above by @kyleniemeyer:
- it would be helpful if you could identify a few potential reviewers from this list https://reviewers.joss.theoj.org/reviewers (without tagging them with an @)
- there are some missing DOIs, please add them and regenerate the pdf using
@editorialbot generate pdf
Hi @jpotoff could you please have a look and address these issues? I will wait with inviting reviewers until we have a working manuscript link.
What is the preferred method of referring to software that does not have an associated DOI?
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1002/jcc.23422 is OK
- 10.1007/s00894-008-0305-0 is OK
- 10.1021/jp972543 is OK
- 10.1098/rspa.1938.0173 is OK
- 10.1063/1.1740026 is OK
- 10.1021/ja00315a051 is OK
- 10.1002/jcc.540070216 is OK
- 10.1002/jcc.20035 is OK
- 10.1021/ja9621760 is OK
- 10.1002/andp.19033160802 is OK
- 10.1002/jcc.21287 is OK
- 10.1021/acs.jctc.5b00935 is OK
- 10.1063/1.1674022 is OK
- 10.1002/andp.18812480110 is OK
- 10.1002/aic.17206 is OK
- 10.1021/acs.jctc.9b01183 is OK
- 10.1021/acs.jcim.2c01498 is OK
- 10.1016/j.softx.2018.11.005 is OK
- 10.1016/j.softx.2020.100627 is OK
- 10.1021/jp990988n is OK
- 10.1021/jp9072137 is OK
- 10.1021/acs.jpcb.5b01354 is OK
- 10.1016/0263-7855(96)00018-5 is OK
- 10.1145/364338.364398 is OK
MISSING DOIs
- No DOI given, and none found for title: Sur le mélange des gaz
- No DOI given, and none found for title: Gaussian 16 Revision C.01
- No DOI given, and none found for title: GMSO: General Molecular Simulation Object
- No DOI given, and none found for title: forcefield-utilities
- No DOI given, and none found for title: MoSDeF-dihedral-fit: A simple software package to ...
- 10.1021/acs.jcim.2c01498.s001 may be a valid DOI for title: MoSDeF-GOMC: Python software for the creation of s...
- No DOI given, and none found for title: vmd-python
INVALID DOIs
- None
What is the preferred method of referring to software that does not have an associated DOI?
If the software is on GitHub, referencing by URL and with project name makes sense. Seems like this is what you did already.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left: