Metadata-Version: 2.1
Name: pidibble
Version: 1.0.7
Summary: A complete Protein Data Bank (PDB) file parser
Project-URL: Homepage, https://github.com/cameronabrams/pidibble
Project-URL: Bug Tracker, https://github.com/cameronabrams/pidibble/issues
Author-email: Cameron F Abrams <cfa22@drexel.edu>
License-File: LICENSE
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.7
Requires-Dist: numpy>=1.24
Requires-Dist: pyyaml>=6
Description-Content-Type: text/markdown

# 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](https://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html) (v.3.3 Atomic Coordinate Entry Format, ca. 2010).

Unlike parsers like that found in packages like [BioPython](https://biopython.org/wiki/PDBParser), `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
    * pretty-print enabled
* 1.0
    * Initial version


