Dear Professor, <br><br>I hope I got the files :) from this link <a href="http://bioinformatics.org/cgi-bin/cvsweb.cgi/libghemical/src/simple_test/">http://bioinformatics.org/cgi-bin/cvsweb.cgi/libghemical/src/simple_test/</a><br>
I will try it as you suggested and get back to you soon. <br><br>Thanks, <br>Shameer <br><br><div class="gmail_quote">On Sat, Nov 15, 2008 at 10:45 PM, Shameer Khadar <span dir="ltr"><<a href="mailto:skhadar@gmail.com">skhadar@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear Professor, <br><br>Thanks for your detailed reply about the procedure to develop a stand-alone program using libghemical. <br>
But I am afraid, I am not able to identify the "examples" subdirectory in the CVS page at Bioinformatics.org <br>
or the current download page at libghemical website. May be am missing the important link. <br><br>URLs I tried : <a href="http://www.uku.fi/%7Ethassine/projects/download/" target="_blank">http://www.uku.fi/~thassine/projects/download/</a> <br>
<a href="http://bioinformatics.org/cgi-bin/cvsweb.cgi/libghemical/" target="_blank">http://bioinformatics.org/cgi-bin/cvsweb.cgi/libghemical/</a> <br><br>Can you please direct me to the URL from which I can get the libghemical source tree with examples subdirectory ? <br>
<br>Thanks, <br>K. Shameer <br><div><div></div><div class="Wj3C7c"><br><br><div class="gmail_quote">On Sat, Nov 15, 2008 at 10:34 PM, Tommi Hassinen <span dir="ltr"><<a href="mailto:Tommi.Hassinen@uku.fi" target="_blank">Tommi.Hassinen@uku.fi</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
please see the "examples" subdirectory under the libghemical source tree.<br>
There are some similar example command line programs, which do something<br>
similar but not exactly what you need. Take one of them as a template and do the<br>
modifications needed. What you will need in your program, is this:<br>
<br>
1) first get the input data somewhere : the sequence to be generated and the output file name ; perhaps from command line parameters?<br>
<br>
2) you have to create a new "model" object (using libghemical code) ; it will contain an empty model (with no atoms or bonds).<br>
<br>
3) then use a "sequencebuilder" object to build the sequence you need ; perhaps you can copy/paste most of the code<br>
from the ghemical application's implementation of the "build_amino" command/routine (look for "build_amino" in ghemical sources,<br>
it's probably somewhere in the project.cpp source file).<br>
<br>
4) finally save the newly built molecule in a .gpr file ; the code for this can be taken from fileio.cpp source file from the<br>
ghemical application source tree. After this the program can end because the task is completed.<br>
<br>
I hope you can get started with these instructions ; if you have problems please then contact again.<br>
This program sounds like a useful new example program, so I hope we could eventually add it to the example set!<br>
<br>
With best regards,<br>
<font color="#888888">Tommi<br>
</font><div><br>
________________________________________<br>
From: <a href="mailto:ghemical-devel-bounces@bioinformatics.org" target="_blank">ghemical-devel-bounces@bioinformatics.org</a> [<a href="mailto:ghemical-devel-bounces@bioinformatics.org" target="_blank">ghemical-devel-bounces@bioinformatics.org</a>] On Behalf Of Shameer Khadar [<a href="mailto:skhadar@gmail.com" target="_blank">skhadar@gmail.com</a>]<br>
Sent: Friday, November 14, 2008 7:32 PM<br>
To: <a href="mailto:ghemical-devel@bioinformatics.org" target="_blank">ghemical-devel@bioinformatics.org</a><br>
Subject: [ghemical-devel] Reg. build_amino routine<br>
<br>
</div><div><div></div><div>Dear Ghemical Team,<br>
<br>
I need to generate rough x-y-z co-ordinates of amino acid sequences for a set of random sequences. I was looking for an open source solution to generate this in an automated way. I find the buid_amino routine in Ghemical is exactly doing what I wanted. I would like to know if I can get a command line version of build_amino routine in Ghemical as a stand alone program or is there a way that I can access Ghemical with out x-windows as a command line tool.<br>
<br>
Many thanks in advance,<br>
<br>
--<br>
K. Shameer<br>
------------------------------------------------------------<br>
Computational Biology Lab, NCBS - TIFR<br>
Molecular Biophysics Unit, IISc<br>
</div></div></blockquote></div><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>K. Shameer<br>------------------------------------------------------------<br>Computational Biology Lab, NCBS - TIFR <br>Molecular Biophysics Unit, IISc <br>