Hi Peter,
I had an off-line discussion with Miguel about JUMBO and JUMBOMarker. Based on that he thought it might be a good idea for me to get in touch with you and see what you think/are willing to do.
When I was working on the NWChemReader in JMol it occurred to me that it was tedious to have to write 'parsers' for each type of input file for JMol (i.e., output file from a computational package) and wondered about trying to come up with a regular expression based approach. It turns out that the old VMs don't have libraries for that, so if we go that way, we'd have to add a library for that to JMol, but Miguel thinks that that would be fine.
When I saw your email about JUMBO and in following up saw in you pdf file of the paper what you do with JUMBOMarker, I realized that you had done just that.
What I was wondering about: Do you think it would be useful to create a new 'ModelAdapter' that basically works like JUMBOMarker in that it can take a template xml file for a file format and parse it based on that. Internally that could either go to a CML stream that is then interpreted by a CML parser, or it could go directly into mapping the result in JMol's internals.
The advantage could be that is JMol uses this, more template files may be developed for the translation, and the two communities could share them...
Also having JMol with this mechanism allows for direct visualization of the resulting file, making development of the templates (fine-tuning) a bit easier.
Finally if the JMol application then also allows one to save the file, we'd basically deliver a nice, visual checkable CML converter, and one that keeps the proper hierarchy (based on the template).
Miguel suggested that I play around with it and see whether that would work, but I am pretty busy with other stuff too (my job gets in the way of having fun some times). Also I am not familiar with the details of JUMBO and you are :-). On the other hand it may be a lot easier if some of the JUMBOMarker code could be used. Is it maybe even available as a nice package?
There was one major thing that did cross my mind that this approach may not be able to do: In some cases it is necessary to calculate one value based on something else. For example: NWChem does not report the atomic charge in a calculation, but the total number of electrons for that atom, so that the charge is really the atomic number - total number of electrons. In this case the same line has both values in it. So the question becomes: can the template describe that kind of operations to be performed? If not, going to direct java code for the interpretation of comp-chem output files may still be needed....
Ren�
-------- Ren� P.F Kanters, Ph.D. Director of Computer Assisted Science Education Department of Chemistry University of Richmond, Virginia 23173 Phone: (804) 287-6873 Fax: (804) 287-1897 Email: [EMAIL PROTECTED] Web: http://www.richmond.edu/~rkanters
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