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80a72c3 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 | #!/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.
"""
Renumbers the residues of the PDB file starting from a given number (default 1).
Usage:
python pdb_reres.py -<number> <pdb file>
Example:
python pdb_reres.py -10 1CTF.pdb # renumbers from 10
python pdb_reres.py --1 1CTF.pdb # renumbers from -1
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
import logging
LOG = logging.getLogger(__name__)
__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 = 1
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
try:
option = int(option)
except ValueError:
emsg = 'ERROR!! You provided an invalid residue number: \'{}\''
sys.stderr.write(emsg.format(option))
sys.exit(1)
return (fh, option)
def pad_line(line):
"""Helper function to pad line to 80 characters in case it is shorter"""
size_of_line = len(line)
if size_of_line < 80:
padding = 80 - size_of_line + 1
line = line.strip('\n') + ' ' * padding + '\n'
return line[:81] # 80 + newline character
def run(fhandle, starting_resid):
"""
Reset the residue number column to start from a specific number.
This function is a generator.
Parameters
----------
fhandle : a line-by-line iterator of the original PDB file.
starting_resid : int
The starting residue number.
Yields
------
str (line-by-line)
The modified (or not) PDB line.
"""
_pad_line = pad_line
prev_resid = None # tracks chain and resid
resid = starting_resid - 1 # account for first residue
records = ('ATOM', 'HETATM', 'TER', 'ANISOU')
for line in fhandle:
line = _pad_line(line)
if line.startswith('MODEL'):
resid = starting_resid - 1 # account for first residue
prev_resid = None # tracks chain and resid
yield line
elif line.startswith(records):
line_resuid = line[17:27]
if line_resuid != prev_resid:
prev_resid = line_resuid
resid += 1
if resid > 9999:
emsg = 'Cannot set residue number above 9999.\n'
sys.stderr.write(emsg)
sys.exit(1)
yield line[:22] + str(resid).rjust(4) + line[26:]
else:
yield line
renumber_residues = run
def main():
# Check Input
pdbfh, starting_resid = check_input(sys.argv[1:])
# Do the job
new_pdb = run(pdbfh, starting_resid)
# Output results
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
# Close file handle even if it is sys.stdin, no problem here.
pdbfh.close()
sys.exit(0)
if __name__ == '__main__':
main()
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