[ghemical-devel] Reg. build_amino routine

[Shameer Khadar]

Dear Professor,

Thanks for your detailed reply about the procedure to develop a stand-alone
program using libghemical.
But I am afraid, I am not able to identify the "examples" subdirectory in
the CVS page at Bioinformatics.org
or the current download page at libghemical website. May be am missing the
important link.

URLs I tried : http://www.uku.fi/~thassine/projects/download/
http://bioinformatics.org/cgi-bin/cvsweb.cgi/libghemical/

Can you please direct me to the URL from which I can get the libghemical
source tree with examples subdirectory ?

Thanks,
K. Shameer


On Sat, Nov 15, 2008 at 10:34 PM, Tommi Hassinen <Tommi.Hassinen at uku.fi>wrote:

> Hello,
>
> please see the "examples" subdirectory under the libghemical source tree.
> There are some similar example command line programs, which do something
> similar but not exactly what you need. Take one of them as a template and
> do the
> modifications needed. What you will need in your program, is this:
>
> 1) first get the input data somewhere : the sequence to be generated and
> the output file name ; perhaps from command line parameters?
>
> 2) you have to create a new "model" object (using libghemical code) ; it
> will contain an empty model (with no atoms or bonds).
>
> 3) then use a "sequencebuilder" object to build the sequence you need ;
> perhaps you can copy/paste most of the code
> from the ghemical application's implementation of the "build_amino"
> command/routine (look for "build_amino" in ghemical sources,
> it's probably somewhere in the project.cpp source file).
>
> 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
> ghemical application source tree. After this the program can end because
> the task is completed.
>
> I hope you can get started with these instructions ; if you have problems
> please then contact again.
> This program sounds like a useful new example program, so I hope we could
> eventually add it to the example set!
>
> With best regards,
> Tommi
>
> ________________________________________
> From: ghemical-devel-bounces at bioinformatics.org [
> ghemical-devel-bounces at bioinformatics.org] On Behalf Of Shameer Khadar [
> skhadar at gmail.com]
> Sent: Friday, November 14, 2008 7:32 PM
> To: ghemical-devel at bioinformatics.org
> Subject: [ghemical-devel] Reg. build_amino routine
>
> Dear Ghemical Team,
>
> 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.
>
> Many thanks in advance,
>
> --
> K. Shameer
> ------------------------------------------------------------
> Computational Biology Lab, NCBS - TIFR
> Molecular Biophysics Unit, IISc
>
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