https://github.com/choderalab/pymbar
Python implementation of the multistate Bennett acceptance ratio (MBAR)
https://github.com/choderalab/pymbar
Keywords
bennett-acceptance-ratio equilibrium extended-bridge-sampling free-energies mbar molecular-dynamics-simulations multistate-bennett-acceptance-ratio pymbar python research single-molecule-pulling thermodynamic-states
Keywords from Contributors
conda chemistry computational-chemistry package-management quantum-chemistry standards molecular-dynamics openmm optimizing-compiler trajectory-analysis
Last synced: 11 months ago
JSON representation
Acceptance Criteria
- Revelant topics? true
- External users? true
- Open source license? true
- Active? true
- Fork? false
Repository metadata
Python implementation of the multistate Bennett acceptance ratio (MBAR)
- Host: GitHub
- URL: https://github.com/choderalab/pymbar
- Owner: choderalab
- License: mit
- Created: 2013-05-10T22:45:44.000Z (almost 12 years ago)
- Default Branch: master
- Last Pushed: 2024-04-02T13:37:20.000Z (about 1 year ago)
- Last Synced: 2024-05-13T12:46:17.699Z (12 months ago)
- Topics: bennett-acceptance-ratio, equilibrium, extended-bridge-sampling, free-energies, mbar, molecular-dynamics-simulations, multistate-bennett-acceptance-ratio, pymbar, python, research, single-molecule-pulling, thermodynamic-states
- Language: Python
- Homepage: http://pymbar.readthedocs.io
- Size: 29 MB
- Stars: 219
- Watchers: 26
- Forks: 89
- Open Issues: 115
- Releases: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Owner metadata
- Name: Chodera lab // Memorial Sloan Kettering Cancer Center
- Login: choderalab
- Email: [email protected]
- Kind: organization
- Description:
- Website: http://choderalab.org
- Location: Memorial Sloan-Kettering Cancer Center, Manhattan, NY
- Twitter:
- Company:
- Icon url: https://avatars.githubusercontent.com/u/4217481?v=4
- Repositories: 269
- Last ynced at: 2024-04-15T13:43:38.830Z
- Profile URL: https://github.com/choderalab
Committers metadata
Last synced: over 1 year ago
Total Commits: 806
Total Committers: 25
Avg Commits per committer: 32.24
Development Distribution Score (DDS): 0.748
Commits in past year: 16
Committers in past year: 6
Avg Commits per committer in past year: 2.667
Development Distribution Score (DDS) in past year: 0.375
| Name | Commits | |
|---|---|---|
| Michael Shirts | m****s@g****m | 203 |
| kyleabeauchamp | k****p@g****m | 184 |
| Michael Shirts | m****s@c****u | 85 |
| John Chodera (MSKCC) | c****j@m****g | 83 |
| Levi Naden | l****n@v****u | 72 |
| Jaime RGP | j****e@g****m | 58 |
| Michael Shirts | m****s@v****u | 35 |
| Levi Naden | l****n@c****g | 32 |
| Levi Naden | l****c@v****u | 17 |
| Stefano Martiniani | s****i@g****m | 8 |
| ChayaSt | c****n@c****g | 5 |
| Mike Henry | 1****y | 5 |
| Jaime RodrĂguez-Guerra | j****p | 3 |
| Richard Gowers | r****s@g****m | 2 |
| John Chodera | j****a@c****g | 2 |
| Robert McGibbon | r****o@g****m | 2 |
| Josh Fass | j****s@r****m | 2 |
| Tucker Burgin | t****n@u****u | 1 |
| Matt Thompson | m****n@o****g | 1 |
| Forrest York | b****a | 1 |
| Bradley Dice | b****e@b****m | 1 |
| James Barnett | j****4@t****u | 1 |
| David Dotson | d****l@g****m | 1 |
| Iván Pulido | 2****s | 1 |
| Chris | c****4@u****u | 1 |
Committer domains:
- choderalab.org: 3
- virginia.edu: 2
- u.boisestate.edu: 1
- tulane.edu: 1
- bradleydice.com: 1
- openforcefield.org: 1
- umich.edu: 1
- relaytx.com: 1
- vt.edu: 1
- mskcc.org: 1
- colorado.edu: 1
Issue and Pull Request metadata
Last synced: 12 months ago
Total issues: 63
Total pull requests: 66
Average time to close issues: 11 months
Average time to close pull requests: about 2 months
Total issue authors: 29
Total pull request authors: 15
Average comments per issue: 3.79
Average comments per pull request: 5.24
Merged pull request: 49
Bot issues: 0
Bot pull requests: 0
Past year issues: 13
Past year pull requests: 16
Past year average time to close issues: about 2 months
Past year average time to close pull requests: 13 days
Past year issue authors: 10
Past year pull request authors: 8
Past year average comments per issue: 3.08
Past year average comments per pull request: 2.06
Past year merged pull request: 10
Past year bot issues: 0
Past year bot pull requests: 0
Top Issue Authors
- mrshirts (21)
- xiki-tempula (6)
- jaimergp (4)
- Lnaden (3)
- mattwthompson (2)
- jchodera (2)
- shawnhsueh (2)
- hannahbaumann (2)
- maxentile (1)
- mikemhenry (1)
- PhilippHoellmer (1)
- proteneer (1)
- svandenhaute (1)
- udlich (1)
- Vinvin-Zhang (1)
Top Pull Request Authors
- mrshirts (23)
- Lnaden (11)
- mikemhenry (9)
- jaimergp (8)
- zhang-ivy (3)
- mattwthompson (3)
- rosadche (1)
- shawnhsueh (1)
- bdice (1)
- nielskm (1)
- ijpulidos (1)
- schuhmc (1)
- maxentile (1)
- badisa (1)
- jchodera (1)
Top Issue Labels
- pymbar 4 (7)
- enhancement (5)
- bug (3)
- question (3)
- documentation (2)
- pymbar-3-lts (1)
- tests (1)
- pymbar 5 (1)
Top Pull Request Labels
- pymbar 4 (5)
- pymbar-3-lts (2)
- bug (1)
- high priority (1)
Package metadata
- Total packages: 2
-
Total downloads:
- pypi: 5,279 last-month
- Total docker downloads: 101
- Total dependent packages: 21 (may contain duplicates)
- Total dependent repositories: 45 (may contain duplicates)
- Total versions: 23
- Total maintainers: 2
pypi.org: pymbar
Python implementation of the multistate Bennett acceptance ratio (MBAR) method
- Homepage: http://github.com/choderalab/pymbar
- Documentation: https://pymbar.readthedocs.io/
- Licenses: MIT
- Latest release: 4.0.3 (published about 1 year ago)
- Last Synced: 2024-05-13T12:42:29.839Z (12 months ago)
- Versions: 14
- Dependent Packages: 6
- Dependent Repositories: 28
- Downloads: 5,279 Last month
- Docker Downloads: 101
-
Rankings:
- Dependent packages count: 1.398%
- Dependent repos count: 2.742%
- Docker downloads count: 3.297%
- Average: 3.699%
- Stargazers count: 4.846%
- Forks count: 4.858%
- Downloads: 5.052%
- Maintainers (2)
conda-forge.org: pymbar
- Homepage: http://github.com/choderalab/pymbar
- Licenses: MIT
- Latest release: 4.0.1 (published almost 3 years ago)
- Last Synced: 2024-05-13T06:01:20.656Z (12 months ago)
- Versions: 9
- Dependent Packages: 15
- Dependent Repositories: 17
-
Rankings:
- Dependent packages count: 4.202%
- Dependent repos count: 8.618%
- Average: 15.199%
- Forks count: 20.47%
- Stargazers count: 27.506%
Dependencies
- numpy *
- numpydoc *
- pytest *
- scipy *
- sphinxcontrib-bibtex *
- actions/checkout v3 composite
- actions/checkout v1 composite
- codecov/codecov-action v1 composite
- mamba-org/provision-with-micromamba main composite
- jax *
- jaxlib *
- numexpr *
- numpy >=1.12
- scipy *
Score: 17.633571174909182