/dpocket_extractor

Runs dpocket to get pocket descriptors for a given set of atoms or residues

Primary LanguagePython

dpocket Extractor

Given a PDB file and a list of atoms or residues, sets up an input file for and runs dpocket to determine pocket descriptors for those atoms/residues.

Requirements

  • Python 2.7+ or Python 3.x
  • pip install -r requirements.txt
  • dpocket from http://fpocket.sourceforge.net/ (version 2.0 dev)
    • Change DPOCKET_EXEC in config.py to point to dpocket on your system

Usage

$ python extractor.py -h
usage: extractor.py [-h] pdb entities [entities ...]

positional arguments:
  pdb         PDB file to extract descriptors from
  entities    One or more atoms or residues in the format of
              {model}/{chain}/{resnum}/{inscode}/[{atomname}]

optional arguments:
  -h, --help  show this help message and exit