[ghemical-devel] Reg. build_amino routine

[Shameer Khadar]

Dear Professor,

I hope I got the files :) from this link
http://bioinformatics.org/cgi-bin/cvsweb.cgi/libghemical/src/simple_test/
I will try it as you suggested and get back to you soon.

Thanks,
Shameer

On Sat, Nov 15, 2008 at 10:45 PM, Shameer Khadar <skhadar at gmail.com> wrote:

> 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://www.uku.fi/%7Ethassine/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
>>
>
>


-- 
K. Shameer
------------------------------------------------------------
Computational Biology Lab, NCBS - TIFR
Molecular Biophysics Unit, IISc
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