Re: [Jmol-developers] I'm trying to find the problem with the GAMESS MO reader, but need some help...

[Robert H. <ha...@st...>]

Johathan, I'm guessing you are not using Eclipse. I recommend it -- then you
just start clicking on names to find anything you want. Ah, let's see. The
Gamess reader is an abstract class - GamessUK and GamessUS being the
instantiated ones. They are subclasses of AtomSetCollectionReader.
(org.jmol.adapters.smarter.AtomSetCollectionReader.java) In fact, the Gamess
reader itself is a subclass of MOReader, another abstract class.

MOs certainly could be associated with any model. They start out in a
Hashtable that is stored in the AuxilliaryInfo Hashtable. There's no general
way set up to move these around, but it wouldn't be difficult. It's just a
Vector of MOs and associated wave function basis information. When they get
loaded by ModelLoader.java, they get associated with the models as they are
read.

Bob



On Tue, Jun 9, 2009 at 2:10 PM, Jonathan Gutow <gu...@uw...> wrote:

> Bob et al.
>        I need some help figuring out what is going on with the file
> readers.  I don't seem to be able to find where the actual version of
> readAtomSetCollection(BufferedReader reader) that reads more than MOs
> is located.  I must be missing it.  I've looked at the
> AtomSetCollection...java files and all the GAMESSReader files.  Is
> the generic reader in one of the other speciality reader files?  I'm
> sure I've just missed it, but need to figure out the logic for
> associating MOs with a frame.  Am I even looking in the right place?
> Are the frames built later?
>
> Jonathan
>
>                          Dr. Jonathan H. Gutow
> Chemistry Department                                 gu...@uw...
> UW-Oshkosh                                           Office:920-424-1326
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>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900