pidibble 1.0.7.5

A complete Protein Data Bank (PDB) file parser

Pidibble - a complete PDB 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: 
>>> b=p.parsed['REMARK.350.BIOMOLECULE.1']
>>> print(b.pstr())
REMARK.350.BIOMOLECULE.1
             rowName: ['BIOMT2', 'BIOMT3', 'BIOMT1', 'BIOMT2', 'BIOMT3', 'BIOMT1', 'BIOMT2', 'BIOMT3']
             replNum: [1, 1, 2, 2, 2, 3, 3, 3]
                  m1: [0.0, 0.0, -0.5, 0.866025, 0.0, -0.5, -0.866025, 0.0]
                  m2: [1.0, 0.0, -0.866025, -0.5, 0.0, 0.866025, -0.5, 0.0]
                  m3: [0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0]
                   t: [0.0, 0.0, 107.18, 185.64121, 0.0, -107.18, 185.64121, 0.0]

>>> from pidibble.pdbparse import get_symm_ops
>>> Mlist,Tlist=get_symm_ops(b)
>>> for m in Mlist:
...     print(str(m))
... 
[[1. 0. 0.]
 [0. 1. 0.]
 [0. 0. 1.]]
[[-0.5      -0.866025  0.      ]
 [ 0.866025 -0.5       0.      ]
 [ 0.        0.        1.      ]]
[[-0.5       0.866025  0.      ]
 [-0.866025 -0.5       0.      ]
 [ 0.        0.        1.      ]]

Release History

• 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