[MMTK] energy minimizing a small molecule

Robert Jorissen robjorissen at yahoo.com.au
Sat Sep 27 21:59:09 UTC 2008


Hi Guido

Thanks for your quick reply. I am using the latest Windows distribution of MMTK which does not contain an Examples directory. However, it is in the "regular" distribution MMTK which I downloaded recently to get some updated (i.e. bug-fixed) code. And lo and behold, there is the molecule_factory.py. This is not the only difference between the distribution I am using (the Windows distribution of MMTK-2.5.22) and the latest release, MMTK-2.5.24. (Having said that, I wish to note that very grateful that there is a reasonably up-to-date Windows version of MMTK.)

Rob


--- On Sat, 27/9/08, Guido Wagner <wagner at chemie.uni-frankfurt.de> wrote:

> From: Guido Wagner <wagner at chemie.uni-frankfurt.de>
> Subject: Re: [MMTK] energy minimizing a small molecule
> To: robjorissen at yahoo.com.au, mmtk at starship.python.net
> Received: Saturday, 27 September, 2008, 10:36 AM
> Hi Robert,
> 
> the examples are in the Examples/Miscellaneous directory:
> 
> molecule_factory.py and read_xml.py
> 
> The XML-molecule factory class is in MMTK/XML.py
> 
> I have MMTK 2.5.18
> 
> There is no support for the attribute
> "amber_atomtype" yet, so you will 
> have to add this yourself. This is only a few lines of
> extra code: Just 
> stick to the lines that handel "elementType".
> 
> On the homepage of the cElementTree Module 
> (http://effbot.org/zone/celementtree.htm) they have good
> tutorials on 
> how to use it to read an manipulate XML files.
> 
> Regards,
> 
> Guido
> 
> Robert Jorissen schrieb:
> > Thank you to Guido and Konrad for your replies.
> >
> > With Konrad's two extra lines of code, I able to
> read in and minimize my heme molecule. Likewise, I could
> read in and minimize a benzene molecule (I had created an
> appropriate database entry.)
> >
> > I would like to know more about the MMTK
> XML-molecule-factory. I am unable to find an appropriate
> example. It seems that there used to be one, but I am unable
> to find one.
> >
> > Rob Jorissen
> > Ludwig Institute for Cancer Research, Melbourne branch
> >
> >


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