grab_atom_radius

protein-science - Scripts and Tools

Grab Atom Radius

Sebastian Raschka, 09/01/2014
** Version 1.0**

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The grab_atom_radius.py script extracts atoms within a radius from a PDB file.

Requirements:

• Python 2.7.x or Python 3.x

Usage:

run python grab_atom_radius.py --help for the usage information:

usage: grab_atom_radius.py [-h] [-r int/float] [-c X,Y,Z] [-i coordinate-ID]
                           [-o out.fasta]
                           PDBfile

Extracts atoms within a radius from a PDB file.
By default, all atoms in the PDB file are included in the calculation.

positional arguments:
  PDBfile

optional arguments:
  -h, --help            show this help message and exit
  -r int/float, --radius int/float
                        radius in Angstrom for atoms to extract (default 10.0)
  -c X,Y,Z, --coordinates X,Y,Z
                        center for extracting atoms (default "0,0,0")
  -i coordinate-ID, --include coordinate-ID
                        Coordinate lines to include (default: "ATOM,HETATM")
  -o out.fasta, --out out.fasta
                        writes atoms to an output file instead of printing it to the screen

Example

command:

python grab_atom_radius.py 3B7V.pdb -c 13.863,26.129,19.407 -r 7.0 -o 3B7V_rad7.pdb