pdb_reres.py

#!/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

__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 (option, fh)


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 renumber_residues(fhandle, starting_resid):
    """Resets the residue number column to start from a specific number.
    """
    _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(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


def main():
    # Check Input
    starting_resid, pdbfh = check_input(sys.argv[1:])

    # Do the job
    new_pdb = renumber_residues(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()