problems using Group, ZMatrix

Konrad Hinsen
Thu, 12 Mar 1998 14:09:32 +0100

> I've been playing around with mmtk1.1b1, trying to start a component
> library that might be usefull for contructing complex artificial molecules.

Sounds interesting...

>  I first tried to read a Group file from a .py file like this:
> from mmtk import *
> block1 = Group('lego1')
> view(block1)
> but got the message
> "Warning: Some atoms are missing in the output file because their
>          positions are undefined."
>  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.

>  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')

The definition of chloroform is in the MMTK database as an example,
and it uses a ZMatrix notation for the input configuration without
importing anything. If that works, then your example should work
as wel...

>  When I got the system to understand some of ZMatrix instances, I found that
> class ZMatrix was pretty buggy. The final angle in the example above had to

I have tested it on a grand total of two molecules, for which it worked,
but I am not surprised to hear about problems. Thanks for your patch!

Konrad Hinsen                          | E-Mail:
Laboratoire de Dynamique Moleculaire   | Tel.: +33-
Institut de Biologie Structurale       | Fax:  +33-
41, av. des Martyrs                    | Deutsch/Esperanto/English/
38027 Grenoble Cedex 1, France         | Nederlands/Francais