writing atom information using the mol2 atom order.

3 Nov 2009

      Dear all,
I have a mol2 file and I would like to generate an input for an external program using chimera. For a great ease in practicability, I would like the mol2 order to be kept.
I used the following artefact to get to what I want:
def input(molecule):
    ##for compatibility with mol2 atom ordering I use the doble loop as follow
    ##makes the writing substantially slower, but yet the compatibility with mol2 format seems absolute. 
    for i in range(len(molecule.atoms)):
        for atoms in molecule.atoms:
            if atoms.serialNumber == i:
                text=str(atoms.element)+"-"+str(atoms.gaffType)+"-"+str(atoms.charge)+"    "+str(atoms.flex)+"    "+str(atoms.coord()) +"\n"
                filename.write(text)
        i=i+1
I think I could order directly the writing in function of the serialNumber (which is preserved regarding the mol2) file. But how could I do this?
Best,
JD
Dr. Jean-Didier Maréchal
Lecturer
Computational Biotechnological Chemistry @ Transmet
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
Edifici C.n.
08193 Cerdanyola (Barcelona)
Tel: +34.935814936
e-mail: JeanDidier.Marechal@uab.es
----- Missatge original -----
De: chimera-dev-request@cgl.ucsf.edu
Data: Dilluns, Octubre 26, 2009 8:00 pm
Assumpte: Chimera-dev Digest, Vol 69, Issue 1
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Today's Topics:

thank you so much (Corey Fugate)
Re: thank you so much (Eric Pettersen)

--
Message: 1
Date: Fri, 23 Oct 2009 16:57:11 -1000
From: Corey Fugate fugate@hawaii.edu
To: chimera-dev@cgl.ucsf.edu
Subject: [chimera-dev] thank you so much
Message-ID: D445EAAC-78D8-4394-85E0-997DBED43CD8@hawaii.edu
Content-Type: text/plain; charset=US-ASCII; format=flowed
I started using Chimera a few weeks ago.  It is wonderful, I love it.

Message: 2
Date: Mon, 26 Oct 2009 11:03:55 -0700
From: Eric Pettersen pett@cgl.ucsf.edu
To: Corey Fugate fugate@hawaii.edu
Cc: chimera-dev@cgl.ucsf.edu
Subject: Re: [chimera-dev] thank you so much
Message-ID: 26F83250-86D7-4E19-8B17-304418C8169D@cgl.ucsf.edu
Content-Type: text/plain; charset="us-ascii"; Format="flowed";
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So glad you like it.  And always struggling to make it better.   
Thanks! :-)
--Eric
                    Eric Pettersen
                    UCSF Computer Graphics Lab
                    http://www.cgl.ucsf.edu

On Oct 23, 2009, at 7:57 PM, Corey Fugate wrote:
...
I started using Chimera a few weeks ago.  It is wonderful, I
love it.
...

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Jean Didier Pie Marechal

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