[chimera-dev] writing atom information using the mol2 atom order.

[Jean Didier Pie Marechal]

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 at uab.es

----- Missatge original -----
De: chimera-dev-request at cgl.ucsf.edu
Data: Dilluns, Octubre 26, 2009 8:00 pm
Assumpte: Chimera-dev Digest, Vol 69, Issue 1

> Send Chimera-dev mailing list submissions to
> 	chimera-dev at cgl.ucsf.edu
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
> or, via email, send a message with subject or body 'help' to
> 	chimera-dev-request at cgl.ucsf.edu
> 
> You can reach the person managing the list at
> 	chimera-dev-owner at cgl.ucsf.edu
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Chimera-dev digest..."
> 
> 
> Today's Topics:
> 
>   1. thank you so much (Corey Fugate)
>   2. Re: thank you so much (Eric Pettersen)
> 
> 
> --------------------------------------------------------------------
> --
> 
> Message: 1
> Date: Fri, 23 Oct 2009 16:57:11 -1000
> From: Corey Fugate <fugate at hawaii.edu>
> To: chimera-dev at cgl.ucsf.edu
> Subject: [chimera-dev] thank you so much
> Message-ID: <D445EAAC-78D8-4394-85E0-997DBED43CD8 at 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 at cgl.ucsf.edu>
> To: Corey Fugate <fugate at hawaii.edu>
> Cc: chimera-dev at cgl.ucsf.edu
> Subject: Re: [chimera-dev] thank you so much
> Message-ID: <26F83250-86D7-4E19-8B17-304418C8169D at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"; Format="flowed";
> 	DelSp="yes"
> 
> 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.
> > _______________________________________________
> > Chimera-dev mailing list
> > Chimera-dev at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
> 
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://www.cgl.ucsf.edu/pipermail/chimera-
> dev/attachments/20091026/6fa67784/attachment-0001.html>
> 
> ------------------------------
> 
> _______________________________________________
> Chimera-dev mailing list
> Chimera-dev at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
> 
> 
> End of Chimera-dev Digest, Vol 69, Issue 1
> ******************************************
>