#!/usr/bin/env python
'''
Changes "randomly" atom occupancies to a particular value.

If e.g. divisor = 10 and part = 3, then it changes the occupancy of 
3 successive atoms and let the original occupancy of 7 successive atoms.
And round and round... If cyclus_start=0, the FIRST 3 atoms are modified, 
it is possible to shift the divisor-fold cycling by this parameter.

Usage: python change_some_occupancies.py structure.pdb

Then the output file is structure.pdb_occ.pdb.
'''
__author__ = "Martin Maly"
__license__ = "Creative Commons Attribution 4.0 International License"
__email__ = "malymar9@fjfi.cvut.cz"
import sys


# # # Setting # # #
divisor = 10
part = 3
set_occupancy_to = "0.10"
cyclus_start = 0

# # # Script # # #
filename_in = sys.argv[1]
filename_out = sys.argv[1] + "_occ.pdb"
with open(filename_in, "r") as file:
    lines = file.readlines()
counter = cyclus_start - 1
for i in range(len(lines)):
    if lines[i][0:6] == "ATOM  " or lines[i][0:6] == "HETATM":
        counter += 1
        for j in range(part):
            if counter % divisor == j:
                lines[i] = lines[i][:56] + set_occupancy_to + lines[i][60:]
with open(filename_out, "w") as file:
	file.writelines(lines)