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: 

Release History

• 1.5.2
  • added capability to download from OPM and split out DUM resi's into a "dum" pdb
• 1.4.2
  • updated alphafold interface
• 1.4.1
  • Fixed parsing bug in PDBRecordList
• 1.4.0
  • Introduced PDBRecordList and PDBRecordDict classes
• 1.3.3
  • fixed bugs regarding assuming missing records actually present in mmcif parsing
• 1.3.2
  • implemented filepath parameter in PDBParser() to make reading local files more transparent
• 1.3.0
  • streamline class attribute usage; full API documentation
• 1.2.3:
  • bugfix: negative resids allowed
• 1.2.1:
  • bugfix: hex issues AGAIN
• 1.2.0
  • bugfix: hex issues again
• 1.1.9
  • gently handles any nan values or '*' fillers
• 1.1.8
  • Allow unstructured REMARK records (thanks a lot, packmol) to be parsed as REMARK.-1
• 1.1.6
  • bugfix: detection of hex when no abcdef present based on a trip
• 1.1.5
  • bugfix: allow for ONLY atom serial numbers to be hex-or-int
• 1.1.4
  • Added ability to read hexadecimal atom indices for files with > 99999 atoms
• 1.1.3
  • Added ability to group into models for multiple-model entries
• 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