'''
Elliot Williams
August 29th, 2018
5' PO4 3- Removal Script
This Python file exists to allow us to remove the 5' phosphate groups from
nucleotide chains within PDB files we are attempting to import into TLEAP .
We do this because tleap won't accept any input nucleotide chain in which there
is a 5' phosphate group.
This script was originally intended to work 'in place', but I realize that
doing so prevents assurances that it was run in the first place. So, new files
will be created.
'''
import sys
def remove_phosphates(input_file, output_file):
lines = open(input_file).readlines()
output_lines = []
after_ter = True
after_resid = None
i = 0
while i < len(lines):
line = lines[i]
resid = line[21:26]
atom_name = line[13:16]
# print(atom_name)
if after_ter:
after_resid = resid
after_ter = False
if "TER" in line:
after_ter = True
print("TER HIT")
if after_resid == resid and atom_name.strip() in ["P","OP1","OP2","OP3"]:
print("Deleting {} at {}".format(atom_name, resid))
else:
output_lines.append(line)
i += 1
out_content = "".join(output_lines)
out_writer = open(output_file, "w")
out_writer.write(out_content)
out_writer.close()
if __name__ == "__main__":
assert len(sys.argv) >= 2
input_files = sys.argv[1:]
output_files = [x.split(".")[0] + "_pfilt.pdb" for x in input_files]
for i in range(len(input_files)):
remove_phosphates(input_files[i], output_files[i])
