Pidibble

a complete parser for PDB and PDBx/mmCIF files

PyPI version Python versions License Tests Documentation Status PyPI Downloads

Pidibble is a Python package for parsing Protein Data Bank structures in both the legacy PDB format (v.3.3 Atomic Coordinate Entry Format, ca. 2011) and the modern PDBx/mmCIF format that is now standard at the RCSB.

Unlike parsers like that found in packages like BioPython, pidibble provides meaningfully parsed objects from all standard PDB record types, not just ATOMs and CONECTs.

Once installed, the user has access to the PDBParser class in the pidibble.pdbparse module. Full documentation is at pidibble.readthedocs.io.

Example interactive usage

>>> from pidibble.pdbparse import PDBParser
>>> p=PDBParser(PDBcode='4zmj').parse()
>>> print (p.parsed['HEADER'].classification)
VIRAL PROTEIN
>>> print (p.parsed['HEADER'].depDate)
04-MAY-15
>>> print (p.parsed['HEADER'].idCode)
4ZMJ
>>> keys=sorted(p.parsed.keys())
>>> len(keys)
60
>>> keys[:8]
['ANISOU', 'ATOM', 'AUTHOR', 'CISPEP', 'COMPND', 'CONECT', 'CRYST1', 'DBREF']
>>> header=p.parsed['HEADER']
>>> print(header.pstr())
HEADER
      classification: VIRAL PROTEIN
             depDate: 04-MAY-15
              idCode: 4ZMJ
>>> atoms=p.parsed['ATOM']
>>> len(atoms)
4518
>>> print(atoms[0].pstr())
ATOM
              serial: 1
                name: N
              altLoc: 
             residue: resName: LEU; chainID: G; seqNum: 34; iCode: 
                   x: -0.092
                   y: 99.33
                   z: 57.967
           occupancy: 1.0
          tempFactor: 137.71
             element: N
              charge:

Example downloading from AlphaFold

>>> from pidibble.pdbparse import PDBParser
>>> p=PDBParser(source_db='alphafold', source_id='O46077').parse()
>>> p.parsed['TITLE'].title
'ALPHAFOLD MONOMER V2.0 PREDICTION FOR ODORANT RECEPTOR 2A (O46077)'
>>> print(p.parsed['ATOM'][0].pstr())
ATOM
              serial: 1
                name: N
              altLoc: 
             residue: resName: MET; chainID: A; seqNum: 1; iCode: 
                   x: -0.553
                   y: 26.513
                   z: 23.174
           occupancy: 1.0
          tempFactor: 39.74
             element: N
              charge:

Example reading a PDBx/mmCIF file

Many recent RCSB entries have no legacy PDB file at all. Pass input_format='mmCIF' and pidibble parses the mmCIF/PDBx file into the same record objects (using author numbering), so downstream code stays the same:

>>> from pidibble.pdbparse import PDBParser
>>> p=PDBParser(source_db='rcsb', source_id='4tvp', input_format='mmCIF').parse()
>>> p.parsed['HEADER'].idCode
'4TVP'
>>> p.parsed['HEADER'].classification
'VIRAL PROTEIN/IMMUNE SYSTEM'
>>> len(p.parsed['ATOM'])
11344

See the mmCIF guide for the full coverage and the small, deliberate differences from the PDB parse.

Changelog

See CHANGELOG.md for the full release history.

Project links

Data verified by PyPI on Jul 21, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (1.11.0)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for cameronabrams from gravatar.com cameronabrams

Credits

PyPI data
Data sourced directly from PyPI's database.

Author: Cameron F Abrams

GitHub Statistics

Data verified by PyPI on Jul 21, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

MIT License

Requires

Python >=3.7

Provides Extra

test

Classifiers

Report project as malware

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pidibble-1.7.2.tar.gz (3.0 MB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

pidibble-1.7.2-py3-none-any.whl (35.0 kB view details)

Uploaded Python 3

File details

Details for the file pidibble-1.7.2.tar.gz.

File metadata

  • Download URL: pidibble-1.7.2.tar.gz
  • Upload date:
  • Size: 3.0 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.14

File hashes

Hashes for pidibble-1.7.2.tar.gz
Algorithm Hash digest
SHA256 afc0e0bf33661ba74a1d3d140ea10cd5687e199423e57e9d69497e424ee5b2b4
MD5 7c63483b79fbfdeb9154f4fc2c397666
BLAKE2b-256 e2bc8900b2856d8f5787fea0ddbf62ae13f9fc3aeb39be640c389ec1b4787b19

See more details on using hashes here.

Provenance

The following attestation bundles were made for pidibble-1.7.2.tar.gz:

Publisher: release.yaml on cameronabrams/pidibble

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

File details

Details for the file pidibble-1.7.2-py3-none-any.whl.

File metadata

  • Download URL: pidibble-1.7.2-py3-none-any.whl
  • Upload date:
  • Size: 35.0 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.14

File hashes

Hashes for pidibble-1.7.2-py3-none-any.whl
Algorithm Hash digest
SHA256 c20192c95cb47fb5948f07863562f4eb59fdbe1a1235facd5197a3a63571ba54
MD5 18dbe4597a8f7c1b4a734e56489d0817
BLAKE2b-256 942bf6efdabecb7d510f5e6405691e42494bbfbd835bb4b4d658c207b0ffc8c2

See more details on using hashes here.

Provenance

The following attestation bundles were made for pidibble-1.7.2-py3-none-any.whl:

Publisher: release.yaml on cameronabrams/pidibble

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Release history Release notifications | RSS feed

1.11.0

2 files

1.10.0

2 files

1.9.0

2 files

1.8.0

2 files

This release

1.7.2 This release

2 files

1.7.1

2 files

1.7.0

2 files

1.6.0

2 files

1.5.4

2 files

1.5.3

2 files

1.5.2

2 files

1.5.1

2 files

1.5.0

2 files

1.4.2

2 files

1.4.1

2 files

1.4.0

2 files

1.3.3

2 files

1.3.2

2 files

1.3.1

2 files

1.3.0

2 files

1.2.3

2 files

1.2.2

2 files

1.2.1

2 files

1.2.0

2 files

1.1.9

2 files

1.1.8

2 files

Yanked

1.1.7

2 files

1.1.6

2 files

1.1.5

2 files

1.1.4

2 files

1.1.3

2 files

1.1.2

2 files

1.1.1

2 files

1.1.0

2 files

1.0.9.1

2 files

1.0.9

2 files

1.0.8

2 files

1.0.7.7

2 files

1.0.7.6

2 files

1.0.7.5

2 files

1.0.7.4

2 files

1.0.7.3

2 files

1.0.7.2

2 files

1.0.7.1

2 files

1.0.7

2 files

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Sentry Error logging StatusPage Status page