Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 6 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.3%) to scientific vocabulary
Keywords
Repository
Open source library to work with molecular systems
Basic Info
- Host: GitHub
- Owner: uibcdf
- License: other
- Language: Python
- Default Branch: main
- Homepage: https://www.uibcdf.org/molsysmt/
- Size: 376 MB
Statistics
- Stars: 13
- Watchers: 3
- Forks: 3
- Open Issues: 22
- Releases: 32
Topics
Metadata Files
README.md
MolSysMT
Installation | Documentation | License | Credits | Team
Molecular Systems MultiToolkit
This library was thought as a humble frontend to make the life of a computational molecular biology lab, the UIBCDF, easier. MolSysMT is design to cover specific needs, or to speed up workflows, when you are working with tools such as:
- MDTraj
- MDAnalysis
- PDBFix
- OpenMM
- Yank
- HTMD
- PyEmma
- ParmEd
- NGLview
- pdbtools?
Although MolSysMT was not concived to do what other tools do better, this toolkit can be used alone to do few simple tasks.
All credit should be given to the developers and mantainers of these former packages and the libraries they depend on.
Molecular Systems: - Aqui deberia de ir todo el tema de la creacion del sistema molecular junto con parametros y topologia - Deberia tambien estar esto preparado para trabajar con moleculas como ligandos.
poner ParmEd y OpenBabel: parmed.github.io http://openbabel.org/wiki/Main_Page
pdbfixer
Molecular Dynamics:
Installation
Dependencies
-Fortran Compiler (gfortran or intel fortran compiler) -Lapack ('conda install lapack' would work?)
Other python packages as those mentioned here(link to section) and included in this list(file).
Conda
Updating
GitHub
bash
git clone git@github.com:UIBCDF/MolSysMT.git
cd MolSysMT
python setup.py develop
bash
pip uninstall molsysmt
Updating
To be written
Documentation
http://www.uibcdf.org/MolSysMT/
Contributions
Want to contribute? Check out our contributing guide!
License
Credits
All credit should be given to the developers and mantainers of the following tools and dependencies:
...
Team
Responsables
Diego Prada Gracia
Liliana M. Moreno Vargas
Contributors
...
Citation
Last version DOI:
Cite the last version with the following DOI provided by Zenodo:
Cite all versions?
You can cite all versions by using the following DOI.
This DOI represents all versions, and will always resolve to the latest one:
Acknowledgments and Copyright
Copyright
Copyright (c) 2021, UIBCDF
Acknowledgements
Project based on the Computational Molecular Science Python Cookiecutter version 1.5.
Owner
- Name: Unit of Research on Computational Biology and Drug Design. Mexico Children's Hospital Federico Gómez.
- Login: uibcdf
- Kind: organization
- Email: uibcdf@gmail.com
- Location: Mexico Children's Hospital Federico Gómez
- Website: www.uibcdf.org
- Repositories: 120
- Profile: https://github.com/uibcdf
Unidad de Investigación en Biología Computacional y Diseño de Fármacos, Hospital Infantil de México Federico Gómez. Ciudad de México, México.
GitHub Events
Total
- Create event: 6
- Issues event: 4
- Release event: 4
- Watch event: 3
- Delete event: 5
- Issue comment event: 1
- Push event: 148
- Pull request event: 4
Last Year
- Create event: 6
- Issues event: 4
- Release event: 4
- Watch event: 3
- Delete event: 5
- Issue comment event: 1
- Push event: 148
- Pull request event: 4
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Diego Prada | p****a@g****m | 1,581 |
| Daniel-Ibarrola | d****1@g****m | 70 |
| Liliana M. Moreno Vargas | l****s@g****m | 14 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 52
- Total pull requests: 54
- Average time to close issues: 4 months
- Average time to close pull requests: about 6 hours
- Total issue authors: 3
- Total pull request authors: 3
- Average comments per issue: 0.88
- Average comments per pull request: 0.3
- Merged pull requests: 52
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- dprada (49)
- LMMV (2)
- AngelRuizMoreno (1)
Pull Request Authors
- dprada (45)
- Daniel-Ibarrola (8)
- LMMV (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v2 composite
- codecov/codecov-action v1 composite
- conda-incubator/setup-miniconda v2 composite
- actions/checkout v2 composite
- codecov/codecov-action v1 composite
- conda-incubator/setup-miniconda v2 composite
- actions/checkout v2 composite
- conda-incubator/setup-miniconda v2 composite
- uibcdf/action-build-and-upload-conda-packages v1.1.0 composite
- actions/checkout v1 composite
- conda-incubator/setup-miniconda v2 composite
- actions/checkout v2 composite
- conda-incubator/setup-miniconda v2 composite
- uibcdf/action-sphinx-docs-to-gh-pages v1.0.0 composite
- actions/checkout v2 composite
- conda-incubator/setup-miniconda v2 composite
- uibcdf/action-build-and-upload-conda-packages v1.2.0 composite
- actions/checkout v2 composite
- uibcdf/action-html-dir-to-gh-pages v1.0.0 composite
- actions/checkout v2 composite
- conda-incubator/setup-miniconda v2 composite
- uibcdf/action-sphinx-docs-to-gh-pages v1.1.0-beta composite