model/comp_surface/prepare_target/input_output/protonate.py

"""
protonate.py: Wrapper method for the reduce program: protonate (i.e., add hydrogens) a pdb using reduce 
                and save to an output file.
Pablo Gainza - LPDI STI EPFL 2019
Released under an Apache License 2.0
"""

from subprocess import Popen, PIPE
from IPython.core.debugger import set_trace
import os


def protonate(in_pdb_file, out_pdb_file):
    # protonate (i.e., add hydrogens) a pdb using reduce and save to an output file.
    # in_pdb_file: file to protonate.
    # out_pdb_file: output file where to save the protonated pdb file. 
    
    # Remove protons first, in case the structure is already protonated
    args = ["reduce", "-Trim", in_pdb_file]
    p2 = Popen(args, stdout=PIPE, stderr=PIPE)
    stdout, stderr = p2.communicate()
    outfile = open(out_pdb_file, "w")
    outfile.write(stdout.decode('utf-8').rstrip())
    outfile.close()
    # Now add them again.
    args = ["reduce", "-HIS", out_pdb_file]
    p2 = Popen(args, stdout=PIPE, stderr=PIPE)
    stdout, stderr = p2.communicate()
    outfile = open(out_pdb_file, "w")
    outfile.write(stdout.decode('utf-8'))
    outfile.close()