The "abstract classes" are the code...
On Tue, Jun 9, 2009 at 10:57 PM, Jonathan Gutow <[email protected]> wrote:
>
> On Jun 9, 2009, at 10:16 PM, Robert Hanson wrote:
>
> > 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.
> I am using eclipse and that matches with what I found. The problem I
> was running into was that eclipse kept linking me back to the
> abstract classes and not the actual code. What is unclear to me
> trying to follow the code is when the atoms for a frame are read in
> and when the MOs are read in. It looks to me as if they might be
> done on separate passes.
single pass, but coordinates come first.
> If that is true that could explain why all
> the MOs are being associated with the first and last frame of a multi-
> frame GAMESS file and not with the frame to which they belong.
how do you know which ones they belong in?
send file?
>
> >
> > 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.
> I think ModelLoader is the set of routines I haven't yet looked at.
> Thanks. I'll take a look at that.
>
> Jonathan
> >
> > Bob
> >
> >
> >
> > On Tue, Jun 9, 2009 at 2:10 PM, Jonathan Gutow <[email protected]>
> > 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 [email protected]
> > UW-Oshkosh Office:
> > 920-424-1326
> > 800 Algoma Boulevard FAX:920-424-2042
> > Oshkosh, WI 54901
> > http://www.uwosh.edu/faculty_staff/gutow/
> >
> >
> >
> >
> >
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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
> > ----------------------------------------------------------------------
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> > Crystal Reports - New Free Runtime and 30 Day Trial
> > Check out the new simplified licensing option that enables unlimited
> > royalty-free distribution of the report engine for externally facing
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> > _______________________________________________
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>
> Dr. Jonathan H. Gutow
> Chemistry Department [email protected]
> UW-Oshkosh Office:920-424-1326
> 800 Algoma Boulevard FAX:920-424-2042
> Oshkosh, WI 54901
> http://www.uwosh.edu/faculty_staff/gutow/
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Crystal Reports - New Free Runtime and 30 Day Trial
> Check out the new simplified licensing option that enables unlimited
> royalty-free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> Jmol-developers mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
--
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
------------------------------------------------------------------------------
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables unlimited
royalty-free distribution of the report engine for externally facing
server and web deployment.
http://p.sf.net/sfu/businessobjects
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