pidibble 1.5.3

A complete Protein Data Bank (PDB) file parser

Pidibble

a complete PDB-file parser

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.

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=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: 

Example downloading from AlphaFold

>>> 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: 

Changelog

See CHANGELOG.md for the full release history.