openpathsampling
An open source Python framework for transition interface and path sampling calculations.
Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
3 of 16 committers (18.8%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (5.3%) to scientific vocabulary
Keywords
biomolecular-simulation
molecular-dynamics
molecular-dynamics-simulation
molecular-modeling
monte-carlo
path-sampling
Last synced: 6 months ago
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JSON representation
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Repository
An open source Python framework for transition interface and path sampling calculations.
Basic Info
- Host: GitHub
- Owner: openpathsampling
- License: mit
- Language: Python
- Default Branch: master
- Homepage: http://openpathsampling.org
- Size: 268 MB
Statistics
- Stars: 112
- Watchers: 12
- Forks: 49
- Open Issues: 104
- Releases: 20
Topics
biomolecular-simulation
molecular-dynamics
molecular-dynamics-simulation
molecular-modeling
monte-carlo
path-sampling
Created over 12 years ago
· Last pushed 9 months ago
Metadata Files
Readme
License
Citation
Support
README.md
OpenPathSampling
An open source Python framework for transition interface and path sampling calculations.
See documentation here:
http://openpathsampling.org
Owner
- Name: OpenPathSampling
- Login: openpathsampling
- Kind: organization
- Website: http://openpathsampling.org
- Twitter: pathsampling
- Repositories: 5
- Profile: https://github.com/openpathsampling
An open source Python framework for path sampling simulations
Citation (CITATIONS.md)
OpenPathSampling was described in a pair of papers published in JCTC: 1. David W.H. Swenson, Jan-Hendrik Prinz, Frank Noé, John D. Chodera, and Peter G. Bolhuis. "OpenPathSampling: A flexible, open framework for path sampling simulations. 1. Basics." J. Chem. Theory Comput. **15**, 813 (2019). https://doi.org/10.1021/acs.jctc.8b00626 2. David W.H. Swenson, Jan-Hendrik Prinz, Frank Noé, John D. Chodera, and Peter G. Bolhuis. "OpenPathSampling: A flexible, open framework for path sampling simulations. 2. Building and Customizing Path Ensembles and Sample Schemes." J. Chem. Theory Comput. **15**, 837 (2019). https://doi.org/10.1021/acs.jctc.8b00627 Both citations: [openpathsampling.bib](https://raw.githubusercontent.com/openpathsampling/openpathsampling/master/docs/openpathsampling.bib) (citation keys ``ops1`` and ``ops2``).
GitHub Events
Total
- Issues event: 3
- Watch event: 7
- Issue comment event: 26
- Push event: 8
- Pull request review comment event: 4
- Pull request review event: 9
- Pull request event: 22
- Fork event: 2
Last Year
- Issues event: 3
- Watch event: 7
- Issue comment event: 26
- Push event: 8
- Pull request review comment event: 4
- Pull request review event: 9
- Pull request event: 22
- Fork event: 2
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| David W.H. Swenson | d****s@h****t | 3,005 |
| Jan-Hendrik Prinz | j****z@g****e | 1,999 |
| Jan-Hendrik Prinz | j****z@c****g | 183 |
| sroet | s****t@h****m | 146 |
| hejung | h****g@g****m | 18 |
| John Chodera (MSKCC) | c****j@m****g | 13 |
| Bradley Dice | b****e@b****m | 8 |
| bolhuis | p****s@u****l | 8 |
| hejung | h****g@b****e | 7 |
| Andreas Singraber | a****r@g****t | 6 |
| oliverdutton | 4****n@u****m | 4 |
| Silveira | a****a@h****m | 3 |
| Alberto | a****o@g****m | 2 |
| Jan-Hendrik Prinz | j****z@S****x | 2 |
| Peter Bolhuis | b****s@M****l | 1 |
| Peter Bolhuis | b****s@w****l | 1 |
Committer Domains (Top 20 + Academic)
wcw-staff-145-18-169-134.wireless.uva.nl: 1
stevie.fritz.box: 1
gmx.at: 1
biophys.mpg.de: 1
uva.nl: 1
bradleydice.com: 1
mskcc.org: 1
choderalab.org: 1
gmx.de: 1
hyperblazer.net: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 39
- Total pull requests: 107
- Average time to close issues: 11 months
- Average time to close pull requests: 2 months
- Total issue authors: 15
- Total pull request authors: 5
- Average comments per issue: 3.21
- Average comments per pull request: 2.69
- Merged pull requests: 88
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 16
- Average time to close issues: 1 day
- Average time to close pull requests: 9 days
- Issue authors: 3
- Pull request authors: 1
- Average comments per issue: 3.0
- Average comments per pull request: 2.63
- Merged pull requests: 13
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- dwhswenson (11)
- sroet (6)
- gyorgy-hantal (5)
- bdice (2)
- Bernadette-Mohr (2)
- SesswireD (2)
- smlee99 (2)
- hejung (2)
- jjfsteuer (1)
- gianmarcolazzeri (1)
- skhabib388 (1)
- jhprinz (1)
- samarjeet (1)
- ShenWenHuibit (1)
- KeweiZhao (1)
Pull Request Authors
- dwhswenson (100)
- sroet (24)
- bdice (3)
- hejung (2)
- Jhp1983 (2)
- singraber (1)
Top Labels
Issue Labels
2.0 (3)
bug report (1)
discussion (1)
question (1)
Pull Request Labels
misc PR (57)
enhancement (21)
experimental (15)
bugfix (14)
upstream changed (9)
2.0 (7)
ci (7)
docs (6)
feature (5)
Deprecations (2)
refactor (2)
API Break (1)
Packages
- Total packages: 2
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Total downloads:
- pypi 3,619 last-month
-
Total dependent packages: 1
(may contain duplicates) -
Total dependent repositories: 3
(may contain duplicates) - Total versions: 21
- Total maintainers: 1
pypi.org: openpathsampling
A Python package for path sampling simulations
- Homepage: https://github.com/openpathsampling/openpathsampling
- Documentation: https://openpathsampling.readthedocs.io/
- License: MIT
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Latest release: 1.7.0
published over 1 year ago
Rankings
Forks count: 5.8%
Dependent packages count: 7.4%
Stargazers count: 7.4%
Average: 13.4%
Dependent repos count: 22.2%
Downloads: 24.1%
Maintainers (1)
Last synced:
6 months ago
conda-forge.org: openpathsampling
OpenPathSampling is a library for trajectory-based rare events simulations, including transition path sampling, transition interface sampling, and committor simulations. Note that for real-world usage, you must also install one of the powerful molecular dynamics engines that OPS interfaces with, such as OpenMM or Gromacs. If you install those seprately, OPS will automatically support your installation of them.
- Homepage: https://github.com/openpathsampling/openpathsampling
- License: MIT
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Latest release: 1.5.2
published over 4 years ago
Rankings
Dependent repos count: 20.0%
Forks count: 25.5%
Average: 27.2%
Dependent packages count: 28.9%
Stargazers count: 34.4%
Last synced:
7 months ago
Dependencies
docs/requirements.txt
pypi
- jinja2 *
- jupyter *
- matplotlib *
- nbconvert >=5
- nbsphinx *
- netcdf4 *
- openmm *
- packaging *
- pytables *
- scikit-learn *
- sphinx *
- sphinx_rtd_theme *
.github/workflows/autorelease-deploy.yml
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setup.py
pypi