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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.
"""
Validates the PDB file ATOM/HETATM lines according to the format specifications.
Does not catch all the errors though... people are creative!
Usage:
python pdb_validate.py <pdb file>
Example:
python pdb_validate.py 1CTF.pdb
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 re
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
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:
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')
else: # Whatever ...
emsg = 'ERROR!! Script takes 1 argument, not \'{}\'\n'
sys.stderr.write(emsg.format(len(args)))
sys.stderr.write(__doc__)
sys.exit(1)
return fh
def run(fhandle):
"""
Compare each ATOM/HETATM line with the format defined on the
official PDB website.
http://deposit.rcsb.org/adit/docs/pdb_atom_format.html
Parameters
----------
fhandle : a line-by-line iterator of the original PDB file.
Returns
-------
int
1 if error was found. 0 if no errors were found.
"""
has_error = False
_fmt_check = (
('Atm. Num.', (slice(6, 11), re.compile(r'[\d\s]+'))),
('Alt. Loc.', (slice(11, 12), re.compile(r'\s'))),
('Atm. Nam.', (slice(12, 16), re.compile(r'\s*[A-Z0-9]+\s*'))),
('Spacer #1', (slice(16, 17), re.compile(r'[A-Z0-9 ]{1}'))),
('Res. Nam.', (slice(17, 20), re.compile(r'\s*[A-Z0-9]+\s*'))),
('Spacer #2', (slice(20, 21), re.compile(r'\s'))),
('Chain Id.', (slice(21, 22), re.compile(r'[A-Za-z0-9 ]{1}'))),
('Res. Num.', (slice(22, 26), re.compile(r'\s*[\d\-]+\s*'))),
('Ins. Code', (slice(26, 27), re.compile(r'[A-Z0-9 ]{1}'))),
('Spacer #3', (slice(27, 30), re.compile(r'\s+'))),
('Coordn. X', (slice(30, 38), re.compile(r'\s*[\d\.\-]+\s*'))),
('Coordn. Y', (slice(38, 46), re.compile(r'\s*[\d\.\-]+\s*'))),
('Coordn. Z', (slice(46, 54), re.compile(r'\s*[\d\.\-]+\s*'))),
('Occupancy', (slice(54, 60), re.compile(r'\s*[\d\.\-]+\s*'))),
('Tmp. Fac.', (slice(60, 66), re.compile(r'\s*[\d\.\-]+\s*'))),
('Spacer #4', (slice(66, 72), re.compile(r'\s+'))),
('Segm. Id.', (slice(72, 76), re.compile(r'[\sA-Z0-9\-\+]+'))),
('At. Elemt', (slice(76, 78), re.compile(r'[\sA-Z0-9\-\+]+'))),
('At. Charg', (slice(78, 80), re.compile(r'[\sA-Z0-9\-\+]+'))),
)
def _make_pointer(column):
col_bg, col_en = column.start, column.stop
pt = ['^' if c in range(col_bg, col_en) else ' ' for c in range(80)]
return ''.join(pt)
for iline, line in enumerate(fhandle, start=1):
line = line.rstrip('\n').rstrip('\r') # CR/LF
if not line:
continue
# Type check for ATOM/HETATM lines
if line[0:6] in ('ATOM ', 'HETATM'):
linelen = len(line)
if linelen < 80:
emsg = '[!] Line {0} is short: {1} < 80\n'
sys.stdout.write(emsg.format(iline, linelen))
has_error = True
elif linelen > 80:
emsg = '[!] Line {0} is long: {1} > 80\n'
sys.stdout.write(emsg.format(iline, linelen))
has_error = True
for fname, (fcol, fcheck) in _fmt_check:
field = line[fcol]
if not fcheck.match(field):
pointer = _make_pointer(fcol)
emsg = '[!] Offending field ({0}) at line {1}\n'
sys.stdout.write(emsg.format(fname, iline))
sys.stdout.write(repr(line) + '\n')
sys.stdout.write(pointer + '\n')
has_error = True
break
else:
# Do basic line length check
linelen = len(line)
if linelen < 80:
emsg = '[!] Line {0} is short: {1} < 80\n'
sys.stdout.write(emsg.format(iline, linelen))
has_error = True
elif linelen > 80:
emsg = '[!] Line {0} is long: {1} > 80\n'
sys.stdout.write(emsg.format(iline, linelen))
has_error = True
if has_error:
msg = '\nTo understand your errors, read the format specification:\n'
msg += ' http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM\n'
sys.stdout.write(msg)
return 1
else:
msg = 'It *seems* everything is OK.'
sys.stdout.write(msg)
return 0
check_pdb_format = run
def main():
# Check Input
pdbfh = check_input(sys.argv[1:])
# Do the job
retcode = run(pdbfh)
# last line of the script
# We can close it even if it is sys.stdin
pdbfh.close()
sys.exit(retcode)
if __name__ == '__main__':
main()
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