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                      babel_convert
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An OpenBabel wrapper for the conversion of CIF files to a single SDFile.

The advantage is that all your cpu cores will be utilized and typical OpenBabel
problems of CIF conversion (like endless loops and unexpected segmentation 
faults) are handled automatically.


License:
--------
    Copyright (C) 2015  Hans-Philipp Brachvogel

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.


What it does:
-------------
Converts the individual CIF-files of a COD checkout into a single SDFile 
containing all molecules WITHOUT hydrogens and NO properties 
or metadata. Every resulting molecule entry will contain only one
connected molecule (OpenBabels --separate flag is used).
    * converts many CIFs to a single SDFile
    * hydrogens are removed
    * properties and metadata are deleted
    * connected components are separated into individual molecule entries


Installation/Dependencies:
--------------------------
Have OpenBabel (version 2.3.2) and Python (version 2.7.x) installed and make
sure that they are on your 'PATH' i.e.: you can start the programs by typing 
'babel' or 'python' in your commandline in any directory.

Use the tool with any POSIX compatible operating system (MacOS, Linux) but
'babel_convert' probably won't work on windows.


How to use:
-----------
Change directory to ..somewhere../COD_converter_tool/ and call

    ./babel_convert <path to cifs>

Where <path to cifs> is the root directory containing all cifs in some 
subdirectory. The resulting SDFfile will appear in the directory and is named
"conversion_out.sdf". 
During conversion individual SDFiles will be written into a temporary directroy
within COD_converter_tool. Do NOT touch them they will be cleaned up at the end.
To convert the whole COD I need about 70 minutes on a hexa core i7-3930.

Example for the cif directory:
The SNV COD-checkout directory is initially called 
"<where you called svn co>/cod/" and all cifs can be found under 
"<where you called svn co>/cod/cif". This would be the necessary path to 
specify.

You can make a test run with the directory "test_cifs" that conatins 3 cif files
2 of them producing errors and one being actually converted.


Where do I get the COD data?
----------------------------
Download the COD via commandline using SVN (subversion):

    svn co svn://www.crystallography.net/cod

and the following commands to update it:

    cd cod

    svn update


What is in "individual_steps"
-----------------------------
It contains some python and bash scripts that do parts of the main tool 
'babel_convert'. Only the tool 'single_convert.py' is necessary for the main 
tool to work. Theo ther ones are additional for you to play with.

"find_cif_pathes" lists all absolute pathes to the cif files. It shows you
how to use UNIX 'find' to locate those files