pdb2pqr
PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
Science Score: 23.0%
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
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○DOI references
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○Academic publication links
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✓Committers with academic emails
14 of 44 committers (31.8%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (4.7%) to scientific vocabulary
Keywords
bioinformatics
biophysics
chemistry
hacktoberfest
help-wanted
Keywords from Contributors
transformation
Last synced: 9 months ago
·
JSON representation
Repository
PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
Basic Info
- Host: GitHub
- Owner: Electrostatics
- License: other
- Language: Python
- Default Branch: master
- Homepage: http://www.poissonboltzmann.org/
- Size: 39.6 MB
Statistics
- Stars: 151
- Watchers: 16
- Forks: 39
- Open Issues: 61
- Releases: 19
Topics
bioinformatics
biophysics
chemistry
hacktoberfest
help-wanted
Created almost 6 years ago
· Last pushed over 1 year ago
Metadata Files
Readme
Contributing
License
Code of conduct
README.md
PDB2PQR
This package contains the PDB2PQR software. For more information, please see
- Home page: http://www.poissonboltzmann.org/
- Documentation: http://pdb2pqr.readthedocs.io
Owner
- Name: APBS, PDB2PQR, and related software
- Login: Electrostatics
- Kind: organization
- Website: http://www.poissonboltzmann.org
- Repositories: 34
- Profile: https://github.com/Electrostatics
GitHub Events
Total
- Create event: 7
- Release event: 1
- Issues event: 38
- Watch event: 23
- Delete event: 7
- Member event: 4
- Issue comment event: 111
- Push event: 18
- Pull request review comment event: 72
- Pull request review event: 72
- Pull request event: 32
- Fork event: 5
Last Year
- Create event: 7
- Release event: 1
- Issues event: 38
- Watch event: 23
- Delete event: 7
- Member event: 4
- Issue comment event: 111
- Push event: 18
- Pull request review comment event: 72
- Pull request review event: 72
- Pull request event: 32
- Fork event: 5
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| yhuang01 | y****1@a****b | 433 |
| Nathan Baker | n****r@g****m | 392 |
| pdb2pqr | p****r@a****b | 215 |
| Kyle Monson | k****n@p****v | 206 |
| todd_dolinsky | t****y@a****b | 180 |
| kmonson | k****n@a****b | 83 |
| sobolevnrm | s****m@a****b | 81 |
| Karina Liles | l****r@e****u | 74 |
| jens_nielsen | j****n@a****b | 62 |
| kmonson | m****e@g****m | 55 |
| intendo | i****3@g****m | 53 |
| srunni | s****i@a****b | 45 |
| lizutah | l****z@s****u | 37 |
| Stefan Doerr | s****r@g****m | 35 |
| bran780 | j****o@p****v | 27 |
| Peter | p****i@p****v | 26 |
| kukaq | k****q@a****b | 18 |
| Darren Curtis | D****s@p****v | 16 |
| mabaran | m****n@a****b | 16 |
| Nathan Baker | n****r@o****m | 15 |
| Nathan Baker | n****r@m****m | 14 |
| Minju Chun | m****n@p****v | 14 |
| Curtis, Darren S | 12 | |
| Toni G | t****o@g****m | 8 |
| czodro | c****o@a****b | 8 |
| Thomas Holder | t****r@s****m | 7 |
| Elvis Offor | e****1@g****m | 7 |
| Mark Jensen | m****n@p****v | 6 |
| Keith T. Star | k****h@p****v | 4 |
| kozlac | j****i@p****v | 4 |
| and 14 more... | ||
Committer Domains (Top 20 + Academic)
pnnl.gov: 9
sphuber.net: 1
we37482.pnl.gov: 1
smu.edu: 1
we28402.pnl.gov: 1
we25369.pnl.gov: 1
we39447.pnl.gov: 1
constance01.pnl.gov: 1
stanford.edu: 1
schrodinger.com: 1
microsoft.com: 1
sci.utah.edu: 1
email.sc.edu: 1
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 123
- Total pull requests: 60
- Average time to close issues: 8 months
- Average time to close pull requests: about 1 month
- Total issue authors: 71
- Total pull request authors: 11
- Average comments per issue: 2.16
- Average comments per pull request: 2.92
- Merged pull requests: 47
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 23
- Pull requests: 20
- Average time to close issues: 4 days
- Average time to close pull requests: 13 days
- Issue authors: 15
- Pull request authors: 3
- Average comments per issue: 1.13
- Average comments per pull request: 4.5
- Merged pull requests: 13
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- sobolevnrm (41)
- stefdoerr (5)
- kiyoon (3)
- ljmartin (2)
- khelmy55 (2)
- dargen3 (2)
- lizutah (2)
- jacob-r-anderson (2)
- dadaix (1)
- HeheHahaHoHoHo (1)
- Tonylac77 (1)
- sunghh44 (1)
- amarkrishna47 (1)
- pineappleXmen (1)
- quockerwodger (1)
Pull Request Authors
- sobolevnrm (36)
- kiyoon (14)
- stefdoerr (9)
- sastrys1 (8)
- SSchott (4)
- nimijkrap (2)
- sphuber (1)
- intendo (1)
- danny305 (1)
- mimminou (1)
- rkretsch (1)
Top Labels
Issue Labels
help wanted (2)
wontfix (1)
NPP (1)
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 131,884 last-month
- Total docker downloads: 452
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Total dependent packages: 4
(may contain duplicates) -
Total dependent repositories: 11
(may contain duplicates) - Total versions: 24
- Total maintainers: 3
pypi.org: pdb2pqr
Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation.
- Homepage: https://www.poissonboltzmann.org
- Documentation: https://pdb2pqr.readthedocs.io/
- License: Copyright (c) 2002-2024, Jens Erik Nielsen; Nathan A. Baker; Battelle Memorial Institute, Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy.; Paul Czodrowski & Gerhard Klebe, University of Marburg. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the names of University College Dublin, Battelle Memorial Institute, Pacific Northwest National Laboratory, US Department of Energy, or University of Marburg nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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Latest release: 3.7.1
published over 1 year ago
Rankings
Docker downloads count: 2.6%
Dependent packages count: 3.2%
Downloads: 4.7%
Average: 5.0%
Dependent repos count: 5.2%
Stargazers count: 7.2%
Forks count: 7.3%
Maintainers (3)
Funding
- https://bit.ly/apbs-funding
Last synced:
10 months ago
conda-forge.org: pdb2pqr
- Homepage: http://www.poissonboltzmann.org
- License: BSD-3-Clause
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Latest release: 3.4.1
published over 4 years ago
Rankings
Dependent repos count: 18.1%
Dependent packages count: 29.0%
Average: 30.3%
Forks count: 36.0%
Stargazers count: 38.0%
Last synced:
10 months ago