[PRE REVIEW]: Project RACCOON: Automated construction of PDB files for polymers and polymer peptide conjugates

[editorialbot]

Submitting author: !--author-handle-->@moritzobenauer<!--end-author-handle-- (Moritz Obenauer) Repository: https://github.com/moritzobenauer/ProjectRaccoon Branch with paper.md (empty if default branch): Version: v1.0.1 Editor: !--editor-->@jromanowska<!--end-editor-- Reviewers: @taoliu032, @lorenzo-rovigatti Managing EiC: Kevin M. Moerman

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (682.3 files/s, 95886.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             1              0              0           1683
Python                          21            468            325           1465
YAML                             5             22             12            147
Markdown                         4             52              0            126
TeX                              1              9              0            116
Bourne Shell                     1             11              7             41
Jupyter Notebook                 1              0            267             27
-------------------------------------------------------------------------------
SUM:                            34            562            611           3605
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 805

[editorialbot]

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

OK DOIs

- 10.1038/s41467-021-27627-4 is OK
- 10.1021/acs.jctc.9b00054 is OK
- 10.1080/08927022.2010.507247 is OK
- 10.1002/marc.201800459 is OK
- 10.1146/annurev-chembioeng-092319-083243 is OK

MISSING DOIs

- 10.1186/1758-2946-4-17 may be a valid DOI for title: Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

INVALID DOIs

- https://doi.org/10.1002/jcc.20945 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.54677/MNMH8546 is INVALID because of 'https://doi.org/' prefix

[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:

E2EDNA 2.0: Python Pipeline for Simulating DNA Aptamers with Ligands Submitting author: @taoliu032 Handling editor: @csoneson (Active) Reviewers: @JoaoRodrigues, @rvhonorato Similarity score: 0.8082

oxDNA: coarse-grained simulations of nucleic acids made simple Submitting author: @lorenzo-rovigatti Handling editor: @ppxasjsm (Active) Reviewers: @ptmerz, @degiacom Similarity score: 0.8068

Cocktail Shaker: An open source drug expansion and enumeration library for peptides Submitting author: @Sulstice Handling editor: @csoneson (Active) Reviewers: @olivertomic, @richardjgowers Similarity score: 0.8052

polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories Submitting author: @symmy596 Handling editor: @richardjgowers (Active) Reviewers: @hmacdope, @lscalfi Similarity score: 0.7999

ELECTRIC: Electric fields Leveraged from multipole Expansion Calculations in Tinker Rapid Interface Code Submitting author: @valeriewelborn Handling editor: @richardjgowers (Active) Reviewers: @amandadumi, @govarguz Similarity score: 0.7976

⚠️ 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.

[moritzobenauer]

Hello everybody,

in the following is a list of potential reviewers I find suitable for the project: Xujian Wang Benjamin Riesrichardjgowers Yuxuan Zhuang Matt Thompson

(Invalid DOIs pointed out by the editorialbot have been fixed 01/12/23)

If I can be of any further help, please let me know. Looking forward to the reviewing process. Best, Moritz

[Kevin-Mattheus-Moerman]

@moritzobenauer thanks for this submission. I am the AEiC on this track and here to help with initial steps. I have just flagged this work for a scope review. This is because I need some help from the domain specialists in the editorial board to judge if this submission is in scope for JOSS. This scope review should take about two weeks.

[Kevin-Mattheus-Moerman]

@moritzobenauer I am happy to inform you that the editorial board has determined that this submission may be in scope for JOSS. I have removed the query-scope label and will now be looking to assign a handling editor.

[Kevin-Mattheus-Moerman]

@editorialbot invite @jromanowska as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

:wave: @jromanowska would you be able to edit this one? Thanks!

[jromanowska]

@editorialbot assign me as editor

[editorialbot]

Assigned! @jromanowska is now the editor

[jromanowska]

Hi, @moritzobenauer , I will be serving as an editor on your submission. I'll try to find suitable reviewers asap. In the meantime, let me know if any changes occur.

[jromanowska]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/s41467-021-27627-4 is OK
- 10.1021/acs.jctc.9b00054 is OK
- 10.1080/08927022.2010.507247 is OK
- 10.1002/marc.201800459 is OK
- 10.1146/annurev-chembioeng-092319-083243 is OK
- 10.1002/jcc.20945 is OK
- 10.54677/MNMH8546 is OK

MISSING DOIs

- 10.1186/1758-2946-4-17 may be a valid DOI for title: Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

INVALID DOIs

- None

[jromanowska]

@moritzobenauer - could you add a correct DOI to the reference, as shown above?

[moritzobenauer]

Hey, @jromanowska, the missing DOI was added. Sorry for the oversight!

[jromanowska]

@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:

E2EDNA 2.0: Python Pipeline for Simulating DNA Aptamers with Ligands Submitting author: @taoliu032 Handling editor: @csoneson (Active) Reviewers: @JoaoRodrigues, @rvhonorato Similarity score: 0.8130

oxDNA: coarse-grained simulations of nucleic acids made simple Submitting author: @lorenzo-rovigatti Handling editor: @ppxasjsm (Active) Reviewers: @ptmerz, @degiacom Similarity score: 0.8127

Cocktail Shaker: An open source drug expansion and enumeration library for peptides Submitting author: @Sulstice Handling editor: @csoneson (Active) Reviewers: @olivertomic, @richardjgowers Similarity score: 0.8119

polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories Submitting author: @symmy596 Handling editor: @richardjgowers (Active) Reviewers: @hmacdope, @lscalfi Similarity score: 0.8079

ELECTRIC: Electric fields Leveraged from multipole Expansion Calculations in Tinker Rapid Interface Code Submitting author: @valeriewelborn Handling editor: @richardjgowers (Active) Reviewers: @amandadumi, @govarguz Similarity score: 0.8050

⚠️ 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.

[jromanowska]

@editorialbot add @taoliu032 as reviewer

[editorialbot]

@taoliu032 added to the reviewers list!

[jromanowska]

@editorialbot add @lorenzo-rovigatti as reviewer

[editorialbot]

@lorenzo-rovigatti added to the reviewers list!

[jromanowska]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6293.