Science Score: 36.0%
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
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○Academic publication links
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✓Committers with academic emails
2 of 15 committers (13.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.3%) to scientific vocabulary
Keywords
Repository
A Python API for the RCSB Protein Data Bank (PDB)
Basic Info
- Host: GitHub
- Owner: williamgilpin
- License: mit
- Language: Python
- Default Branch: master
- Size: 601 KB
Statistics
- Stars: 328
- Watchers: 19
- Forks: 77
- Open Issues: 7
- Releases: 0
Topics
Metadata Files
README.md
PyPDB
A Python 3 toolkit for performing searches with the RCSB Protein Data Bank (PDB). This can be used to perform advanced searches for PDB IDs matching various criteria, as well as to look up information associated with specific PDB IDs. This tool allows standard operations that can be perfomed from within the PDB website (BLAST, PFAM lookup, etc.) to be performed from within Python scripts.
If you use this module for any published work, please consider citing the accompanying paper
Gilpin, W. "PyPDB: A Python API for the Protein Data Bank."
Bioinformatics, Oxford Journals, 2016.
Installation
Install using pip:
$ pip install pypdb
To install the development version, which contains the latest features and fixes, install directly from GitHub using
$ pip install git+https://github.com/williamgilpin/pypdb
If you need to install directly from setup.py,
$ python setup.py install
Test the installation, and check that the code successfully connects to the PDB, navigate to the root directory and run
$ pytest
This code has been designed and tested for Python 3.
Usage
PDB Text Search
This package can be used to get lists of PDB IDs associated with specific search terms, experiment types, structures, and other common criteria. To use the simple API, see the examples in demos/demos.ipynb. For advanced search and query logic, see the examples in search/EXAMPLES.md.
PDB Data Fetch
Given a list of PDBs, this package can be used to fetch data associated with those PDBs, including their dates of deposition, lists of authors and associated publications, their sequences or structures, their top BLAST matches, and other query-specific attributes like lists of a ligands or chemical structure. To use the simple API, see the examples in demos/demos.ipynb. For advanced search and query logic, see the examples in data/EXAMPLES.md.
Issues and Feature Requests
If you run into an issue, or if you find a workaround for an existing issue, please post your question or code as a GitHub issue.
If posting a feature request, please check that your request is possible using the current GUI on current RCSB website. If so, please perform your search, and then click the link that says JSON in the upper right hand corner of the Advanced Search box. Please post that JSON code with your feature request.
Owner
- Name: William Gilpin
- Login: williamgilpin
- Kind: user
- Location: United States
- Company: The University of Texas at Austin
- Website: http://www.wgilpin.com
- Twitter: wgilpin0
- Repositories: 23
- Profile: https://github.com/williamgilpin
Director of the @GilpinLab at UT Austin.
GitHub Events
Total
- Watch event: 17
- Issue comment event: 1
- Push event: 3
- Fork event: 2
- Create event: 1
Last Year
- Watch event: 17
- Issue comment event: 1
- Push event: 3
- Fork event: 2
- Create event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| williamgilpin | w****n | 40 |
| lacoperon | e****s@g****m | 34 |
| williamgilpin | w****n@g****m | 33 |
| william | w****m@D****t | 10 |
| sodiumnitrate | i****n@g****m | 6 |
| jthornton-0 | p****8@p****m | 3 |
| jonwells90 | j****0@g****m | 1 |
| Diego Prada | p****a@g****m | 1 |
| eac709 | e****4@g****m | 1 |
| Owen O'Connor | t****3@g****m | 1 |
| rlangefe | l****8@w****u | 1 |
| samuelstanton | s****5@c****u | 1 |
| Katja Linnemann | k****4@w****e | 1 |
| davidoskky | d****y@y****t | 1 |
| Antje Relitz | r****z@i****e | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 36
- Total pull requests: 31
- Average time to close issues: 3 months
- Average time to close pull requests: 9 days
- Total issue authors: 31
- Total pull request authors: 15
- Average comments per issue: 3.14
- Average comments per pull request: 1.29
- Merged pull requests: 28
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- williamgilpin (3)
- lacoperon (2)
- inthesomeday000 (2)
- ynskoroglu (2)
- tux2603 (1)
- erfantoloue (1)
- Chokerino (1)
- jhxu003 (1)
- perllaghu (1)
- Talianash (1)
- GMC1997 (1)
- mirix (1)
- Shkev (1)
- noahharrison64 (1)
- chuliangcui (1)
Pull Request Authors
- lacoperon (14)
- jbenjoseph (3)
- ajm13 (2)
- jthornton-0 (2)
- sodiumnitrate (2)
- amorehead (1)
- rlangefe (1)
- tux2603 (1)
- kalinni (1)
- davidoskky (1)
- jonathan-wells (1)
- samuelstanton (1)
- dataroo (1)
- dprada (1)
- echen1214 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 7,207 last-month
- Total docker downloads: 292
-
Total dependent packages: 7
(may contain duplicates) -
Total dependent repositories: 23
(may contain duplicates) - Total versions: 25
- Total maintainers: 1
pypi.org: pypdb
A Python wrapper for the RCSB Protein Data Bank (PDB) API
- Homepage: https://github.com/williamgilpin/pypdb
- Documentation: https://pypdb.readthedocs.io/
- License: mit
-
Latest release: 2.4
published almost 2 years ago
Rankings
Maintainers (1)
conda-forge.org: pypdb
- Homepage: http://www.wgilpin.com/pypdb_docs/html/
- License: MIT
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Latest release: 2.2
published over 3 years ago