[ghemical-devel] Reg. build_amino routine

[Tommi Hassinen]

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