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. This needs the optional mmCIF reader: pip install 'pidibble[mmcif]'.

>>> 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.