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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2018 João Pedro Rodrigues
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
Fixes insertion codes in a PDB file.
Works by deleting an insertion code and shifting the residue numbering of
downstream residues. Allows for picking specific residues to delete insertion
codes for.
Usage:
python pdb_fixinsert.py [-<option>] <pdb file>
Example:
python pdb_fixinsert.py 1CTF.pdb # delete ALL insertion codes
python pdb_fixinsert.py -A9,B12 1CTF.pdb # deletes ins. codes for res
# 9 of chain A and 12 of chain B.
This program is part of the `pdb-tools` suite of utilities and should not be
distributed isolatedly. The `pdb-tools` were created to quickly manipulate PDB
files using the terminal, and can be used sequentially, with one tool streaming
data to another. They are based on old FORTRAN77 code that was taking too much
effort to maintain and compile. RIP.
"""
import os
import sys
__author__ = "Joao Rodrigues"
__email__ = "j.p.g.l.m.rodrigues@gmail.com"
def check_input(args):
"""Checks whether to read from stdin/file and validates user input/options.
"""
# Defaults
option = ''
fh = sys.stdin # file handle
if not len(args):
# Reading from pipe with default option
if sys.stdin.isatty():
sys.stderr.write(__doc__)
sys.exit(1)
elif len(args) == 1:
# One of two options: option & Pipe OR file & default option
if args[0].startswith('-'):
option = args[0][1:]
if sys.stdin.isatty(): # ensure the PDB data is streamed in
emsg = 'ERROR!! No data to process!\n'
sys.stderr.write(emsg)
sys.stderr.write(__doc__)
sys.exit(1)
else:
if not os.path.isfile(args[0]):
emsg = 'ERROR!! File not found or not readable: \'{}\'\n'
sys.stderr.write(emsg.format(args[0]))
sys.stderr.write(__doc__)
sys.exit(1)
fh = open(args[0], 'r')
elif len(args) == 2:
# Two options: option & File
if not args[0].startswith('-'):
emsg = 'ERROR! First argument is not an option: \'{}\'\n'
sys.stderr.write(emsg.format(args[0]))
sys.stderr.write(__doc__)
sys.exit(1)
if not os.path.isfile(args[1]):
emsg = 'ERROR!! File not found or not readable: \'{}\'\n'
sys.stderr.write(emsg.format(args[1]))
sys.stderr.write(__doc__)
sys.exit(1)
option = args[0][1:]
fh = open(args[1], 'r')
else: # Whatever ...
sys.stderr.write(__doc__)
sys.exit(1)
# Validate option
option_list = [o for o in option.split(',') if o.strip()]
if option_list:
for o in option_list:
if len(o) < 2 or not o[1:].isdigit():
emsg = 'ERROR!! Option invalid: \'{}\''
sys.stderr.write(emsg.format(o))
fh.close()
sys.exit(1)
return (fh, option_list)
def run(fhandle, option_list):
"""
Delete insertion codes (at specific residues).
By default, removes ALL insertion codes on ALL residues. Also bumps
the residue numbering of residues downstream of each insertion.
This function is a generator.
Parameters
----------
fhandle : a line-by-line iterator of the original PDB file.
option_list : list
List of insertion options to act on.
Example ["A9", "B12"]. An empty list performs the default
action.
Yields
------
str (line-by-line)
The modified (or not) PDB line.
"""
option_set = set(option_list) # empty if option_list is empty
# Keep track of residue numbering
# Keep track of residues read (chain, resname, resid)
offset = 0
prev_resi = None
seen_ids = set()
clean_icode = False
records = ('ATOM', 'HETATM', 'ANISOU', 'TER')
for line in fhandle:
if line.startswith(records):
res_uid = line[17:27] # resname, chain, resid, icode
id_res = line[21] + line[22:26].strip() # A99, B12
has_icode = line[26].strip() # ignore ' ' here
# unfortunately, this is messy but not all PDB files follow a nice
# order of ' ', 'A', 'B', ... when it comes to insertion codes..
if prev_resi != res_uid: # new residue
# Does it have an insertion code
# OR have we seen this chain + resid combination before?
# #2 to catch insertions WITHOUT icode ('A' ... ' ' ... 'B')
if (has_icode or id_res in seen_ids):
# Do something about it
# if the user provided options and this residue is in them
# OR if the user did not provide options
if (not option_set) or (id_res in option_set):
clean_icode = True
else:
clean_icode = False
else:
clean_icode = False
prev_resi = res_uid
if id_res in seen_ids: # offset only if we have seen this res.
offset += 1
if clean_icode: # remove icode
line = line[:26] + ' ' + line[27:]
# Modify resid if necessary
resid = int(line[22:26]) + offset
line = line[:22] + str(resid).rjust(4) + line[26:]
seen_ids.add(id_res)
# Reset offset on TER
if line.startswith('TER'):
offset = 0
yield line
fix_insertions = run
def main():
# Check Input
pdbfh, option_list = check_input(sys.argv[1:])
# Do the job
new_pdb = run(pdbfh, option_list)
try:
_buffer = []
_buffer_size = 5000 # write N lines at a time
for lineno, line in enumerate(new_pdb):
if not (lineno % _buffer_size):
sys.stdout.write(''.join(_buffer))
_buffer = []
_buffer.append(line)
sys.stdout.write(''.join(_buffer))
sys.stdout.flush()
except IOError:
# This is here to catch Broken Pipes
# for example to use 'head' or 'tail' without
# the error message showing up
pass
# last line of the script
# We can close it even if it is sys.stdin
pdbfh.close()
sys.exit(0)
if __name__ == '__main__':
main()
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