#!/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.

"""
Merges several PDB files into one multi-model (ensemble) file. Strips all
HEADER information and adds REMARK statements with the provenance of each
conformer.

Usage:
    python pdb_mkensemble.py <pdb file> <pdb file>

Example:
    python pdb_mkensemble.py 1ABC.pdb 1XYZ.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 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.
    """

    if len(args) >= 1:
        for fn in args:
            if not os.path.isfile(fn):
                emsg = 'ERROR!! File not found or not readable: \'{}\'\n'
                sys.stderr.write(emsg.format(fn))
                sys.stderr.write(__doc__)
                sys.exit(1)

    else:  # Whatever ...
        sys.stderr.write(__doc__)
        sys.exit(1)

    return args


def make_ensemble(f_name_list):
    """
    Combines several PDB files into a multi-model ensemble file.
    """

    # REMARK     THIS ENTRY
    fmt_REMARK = "REMARK     {:<67s}\n"

    # MODEL        1
    fmt_MODEL = "MODEL {:>5d}\n"

    for fileno, file_name in enumerate(f_name_list, start=1):
        fpath = os.path.basename(file_name)
        yield fmt_REMARK.format("MODEL {} FROM {}".format(fileno, fpath))

    conect = []
    records = ('ATOM', 'HETATM', 'TER')
    for fileno, file_name in enumerate(f_name_list, start=1):

        yield fmt_MODEL.format(fileno)

        with open(file_name, 'r') as fhandle:

            for line in fhandle:
                if line.startswith(records):
                    yield line

                # only store CONECT for first model
                elif fileno == 1 and line.startswith('CONECT'):
                    conect.append(line)

        yield 'ENDMDL\n'

    # Write CONECT
    for line in conect:
        yield line

    yield 'END\n'


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

    # Do the job
    new_pdb = make_ensemble(pdbfile_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

    sys.exit(0)


if __name__ == '__main__':
    main()

@@ -1857,16 +1857,312 @@
  args%0A%0A%0A
+def pad_line(line):%0A    %22%22%22Helper function to pad line to 80 characters in case it is shorter%22%22%22%0A    size_of_line = len(line)%0A    if size_of_line %3C 80:%0A        padding = 80 - size_of_line + 1%0A        line = line.strip('%5Cn') + ' ' * padding + '%5Cn'%0A    return line%5B:81%5D  # 80 + newline character%0A%0A%0A
 def make
@@ -2185,16 +2185,16 @@
 _list):%0A
-
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@@ -2263,24 +2263,50 @@
 e.%0A    %22%22%22%0A%0A
+    _pad_line = pad_line%0A%0A
     # REMARK
@@ -2904,28 +2904,39 @@
       yield 
-line
+_pad_line(line)
 %0A%0A          
@@ -3165,20 +3165,31 @@
   yield 
-line
+_pad_line(line)
 %0A%0A    yi

Add pad_line