pdb2fasta.py

#!/usr/bin/env python3
# -*- coding: UTF8 -*-

# Author: Guillaume Bouvier -- guillaume.bouvier@pasteur.fr
# https://research.pasteur.fr/en/member/guillaume-bouvier/
# 2018-11-19 16:26:10 (UTC+0100)

from pymol import cmd
import sys

try:
    PDBFILENAME = sys.argv[1]
    SELECTION = sys.argv[2]
except IndexError:
    print("Help:")
    print("    pdb2fasta input.pdb 'selection string'")
    sys.exit()

cmd.load(PDBFILENAME)
seq = cmd.get_fastastr(SELECTION)
print(seq)