https://github.com/samuellimce/pdbx
A PDBx/mmCIF-format parser and extractor.
https://github.com/samuellimce/pdbx
bioinformatics cheminformatics computational-biology computational-chemistry hacktoberfest mmcif pdb pdbx structural-biology
Last synced: 4 months ago
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A PDBx/mmCIF-format parser and extractor.
- Host: GitHub
- URL: https://github.com/samuellimce/pdbx
- Owner: samuellimce
- Created: 2021-10-05T20:50:22.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2021-11-01T04:44:18.000Z (about 4 years ago)
- Last Synced: 2025-01-16T06:12:46.758Z (11 months ago)
- Topics: bioinformatics, cheminformatics, computational-biology, computational-chemistry, hacktoberfest, mmcif, pdb, pdbx, structural-biology
- Homepage:
- Size: 1.95 KB
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 1
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Metadata Files:
- Readme: README.md
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README
# PDBX
`pdbx` is a current rewrite of an internal PDBx/mmCIF toolkit for use with other lab projects. The new tools seek to be compatible with current local data and usable with the V4.0 and V5.0 editions [with official specification changes provided by wwPDB](https://mmcif.wwpdb.org/). The preferred format of the live PDB, to current knowledge, is V3.30 where possible and PDBx/mmCIF otherwise ([see wwPDB FAQ](https://mmcif.wwpdb.org/docs/faqs/pdbx-mmcif-faq-general.html)). Additionally, related structure pipelines in the wild (incl. the [AMBER molecular dynamics suite](http://ambermd.org/)) may produce PDB files that do not strictly adhere to any specific version, so it is necessary to consider flexibility in the format specification.
General syntax examples of the format can be found [here](https://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html). [wwPDB](https://www.wwpdb.org/) provides the legacy PDB specification [here](https://www.wwpdb.org/documentation/file-format). A comparative source of implementation can be found on the OpenStructure documentation [here](https://openstructure.org/docs/dev/io/structure_formats/).
## Contributing
Project documentation is provided in English. Please contact the author(s) if you have any questions.