Pidibble
a complete parser for PDB and PDBx/mmCIF files
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.
1 maintainer
Metadata
1 maintainer
Release files for pidibble 1.11.1
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Source distribution (sdist)
| File | Size | Uploaded | |
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| pidibble-1.11.1.tar.gz | 3.3 MB | Details |
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| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pidibble-1.11.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 3.3 MB
Release files / pidibble-1.11.1.tar.gz
| Download URL | pidibble-1.11.1.tar.gz |
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| Size | 3.3 MB |
| Tags | Source |
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| Uploaded via |
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