problems using Group, ZMatrix

Peter C. McCluskey
Fri, 13 Mar 1998 11:05:50 -0800 (Konrad Hinsen) writes:
>>  I found I could view the component by moving the lego1 file to Molecules
>> and reading it via "block1 = Molecule('lego1')". Why aren't group files
>> useable by themselves?
>By definition, groups represent incomplete parts of molecules
>that do not exist by themselves. They are supposed to be
>building blocks for molecules, and some properties (such as the
>configurations) are defined only at the molecule level. So you
>can create an isolated group (as you did), but this operation is
>of limited use.
>BTW, I don't claim that this interpretation of groups is the only
>reasonable one; it just turned out to be useful for my work. I am
>always open for suggestions for improvements.

 What I want is a quick and dirty way of deducing from the bond info
enough configuration info to display the topology of a group, plus a
general purpose way of putting groups together to form a molecule.
Do you think it would be reasonable to have the quick and dirty method
add the configuration info to the group object, or would it be better
to create an incomplete molecule object? Do you have any thoughts
about what it would take to convert your apparently protein specific
way of putting groups together into something that would work with
arbitrary chemical parts?

>>  The next problem I found was the need to put an "import ZMatrix"
>> statement in my molecule file in order to use the ZMatrix (is there a
>> better way to do this? I'm just starting to learn Python.):
>That's weird, it shouldn't be necessary to import anything in
>molecule definitions. Could you try the following:
>  from mmtk import *
>  m = Molecule('chloroform')

 Oops, I see now that it looked necessary when I was trying to get it
to work as a group definition, but wasn't needed after I switched to a
molecule definition.
 Also, the only entry that came with the Molecules directory was water.
A larger set of sample molecules would certainly be nice.
 Also, the README mentions a COPYRIGHT file, but I can't find any
file named COPYRIGHT.
Peter McCluskey  |  | Has anyone used           | to comment on your web pages?