Pidibble is a Python package for parsing standard Protein Data Bank (PDB) files. It conforms to the most recent standard (v.3.3 Atomic Coordinate Entry Format, ca. 2011).
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.pdbparser module.
>>> 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=list(sorted(list(p.parsed.keys())))
>>> print(keys)
['ANISOU', 'ATOM', 'AUTHOR', 'CISPEP', 'COMPND', 'CONECT', 'CRYST1', 'DBREF', 'END', 'EXPDTA', 'FORMUL', 'HEADER', 'HELIX', 'HET', 'HETATM', 'HETNAM', 'JRNL.AUTH', 'JRNL.DOI', 'JRNL.PMID', 'JRNL.REF', 'JRNL.REFN', 'JRNL.TITL', 'KEYWDS', 'LINK', 'MASTER', 'ORIGX1', 'ORIGX2', 'ORIGX3', 'REMARK.100', 'REMARK.2', 'REMARK.200', 'REMARK.280', 'REMARK.290', 'REMARK.290.CRYSTSYMMTRANS', 'REMARK.3', 'REMARK.300', 'REMARK.350', 'REMARK.350.BIOMOLECULE.1', 'REMARK.4', 'REMARK.465', 'REMARK.500', 'REVDAT', 'SCALE1', 'SCALE2', 'SCALE3', 'SEQADV', 'SEQRES', 'SHEET', 'SOURCE', 'SSBOND', 'TER', 'TITLE']
>>> 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:
>>> from pidibble.pdbparse import PDBParser
>>> p=PDBParser(alphafold='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:
- 1.1.2
- Added ability to retrieve pdbs from AlphaFold database
- 1.1.1
- version detection
- 1.0.9.1
- added limited functionality to parse mmCIF files, in particular to generate any ATOM, HETATM, SSBOND, LINK, SEQADV, REMARK 350, and REMARK 465 records
- 1.0.8
- bug fix: handle variations in how symmetry operation matrices are represented
- 1.0.7.7
- cleaned up logging
- 1.0.7.6
- bug fix: leading whitespace in resname field of Residue10 record sometimes ignored
- 1.0.7.5
- support for four-letter residue names
- 1.0.7.4
- added logging functionality
- 1.0.7.3
- improved parsing of BIOMT transforms
- 1.0.7.2
- added documentation stub at readthedocs
- 1.0.7.1
- support for split BIOMT tables and REMARKS 280, 375, 650, and 700
- 1.0.7
- pretty-print enabled
- 1.0
- Initial version
