pdb_format.py

#!/usr/bin/env python

"""
Validates each ATOM/HETATM line against the 'official' PDB format specs.

usage: python pdb_format.py <pdb file>
example: python pdb_format.py 1CTF.pdb

Author: {0} ({1})

This program is part of the PDB tools distributed with HADDOCK
or with the HADDOCK tutorial. The utilities in this package
can be used to quickly manipulate PDB files, with the benefit
of 'piping' several different commands. This is a rewrite of old
FORTRAN77 code that was taking too much effort to compile. RIP.
"""

from __future__ import print_function

import os
import re
import sys

__author__ = "Joao Rodrigues"
__email__ = "j.p.g.l.m.rodrigues@gmail.com"

USAGE = __doc__.format(__author__, __email__)


def check_input(args):
    """
    Checks whether to read from stdin/file and validates user input/options.
    """

    if not len(args):
        # Read from pipe
        if not sys.stdin.isatty():
            pdbfh = sys.stdin
        else:
            sys.stderr.write(USAGE)
            sys.exit(1)
    elif len(args) == 1:
        # File
        if not os.path.isfile(args[0]):
            sys.stderr.write('File not found: ' + args[0] + '\n')
            sys.stderr.write(USAGE)
            sys.exit(1)
        pdbfh = open(args[0], 'r')
    else:
        sys.stderr.write(USAGE)
        sys.exit(1)

    return pdbfh


def _check_pdb_format(fhandle):
    """
    Compares each ATOM/HETATM line with the format defined on the official
    PDB website.

    http://deposit.rcsb.org/adit/docs/pdb_atom_format.html
    """

    has_error = False
    _fmt_check = (
            ('Atm. Num.', (slice(6, 11), re.compile('[\d\s]+'))),
            ('Alt. Loc.', (slice(11, 12), re.compile('\s'))),
            ('Atm. Nam.', (slice(12, 16), re.compile('\s*[A-Z0-9]+\s*'))),
            ('Spacer #1', (slice(16, 17), re.compile('[A-Z0-9 ]{1}'))),
            ('Res. Nam.', (slice(17, 20), re.compile('\s*[A-Z0-9]+\s*'))),
            ('Spacer #2', (slice(20, 21), re.compile('\s'))),
            ('Chain Id.', (slice(21, 22), re.compile('[A-Za-z0-9 ]{1}'))),
            ('Res. Num.', (slice(22, 26), re.compile('\s*[\d]+\s*'))),
            ('Ins. Code', (slice(26, 27), re.compile('[A-Z0-9 ]{1}'))),
            ('Spacer #3', (slice(27, 30), re.compile('\s+'))),
            ('Coordn. X', (slice(30, 38), re.compile('\s*[\d\.\-]+\s*'))),
            ('Coordn. Y', (slice(38, 46), re.compile('\s*[\d\.\-]+\s*'))),
            ('Coordn. Z', (slice(46, 54), re.compile('\s*[\d\.\-]+\s*'))),
            ('Occupancy', (slice(54, 60), re.compile('\s*[\d\.\-]+\s*'))),
            ('Tmp. Fac.', (slice(60, 66), re.compile('\s*[\d\.\-]+\s*'))),
            ('Spacer #4', (slice(66, 72), re.compile('\s+'))),
            ('Segm. Id.', (slice(72, 76), re.compile('[\sA-Z0-9\-\+]+'))),
            ('At. Elemt', (slice(76, 78), re.compile('[\sA-Z0-9\-\+]+'))),
            ('At. Charg', (slice(78, 80), re.compile('[\sA-Z0-9\-\+]+'))),
    )

    def _make_pointer(column):
        col_bg, col_en = column.start, column.stop
        pt = ['^' if c in range(col_bg+1, 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:
                print('[!] Line {0} is short: {1} < 80'.format(iline, linelen))
                has_error = True

            elif linelen > 80:
                print('[!] Line {0} is long: {1} > 80'.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}'
                    print(emsg.format(fname, iline))

                    print('{0!r}'.format(line))
                    print('{0}'.format(pointer))

                    has_error = True
                    break
        else:
            # Do basic line length check
            linelen = len(line)
            if linelen < 80:
                print('[!] Line {0} is short: {1} < 80'.format(iline, linelen))
                has_error = True
            elif linelen > 80:
                print('[!] Line {0} is long: {1} > 80'.format(iline, linelen))
                has_error = True

    if has_error:
        print('\nTo understand your errors, read the format specification:')
        print('  http://deposit.rcsb.org/adit/docs/pdb_atom_format.html')
    else:
        print('It *seems* everything is OK.')


if __name__ == '__main__':

    # Check Input
    pdbfh = check_input(sys.argv[1:])

    # Do the job

    _check_pdb_format(pdbfh)

    # last line of the script
    # We can close it even if it is sys.stdin
    pdbfh.close()
    sys.exit(0)