On Feb 23, 2005, at 3:25 AM, Peter Murray-Rust wrote:
At 09:13 22/02/2005 -0500, Ren� Kanters wrote:Hi Peter,
Yes. I was simply saying let's start with the most popular/tractable one to give us experience rather than trying to do all.
Does anybody have an idea which file format is most used? Is it xyz, pdb, or some computational chemistry log file?
I am not sure whether I would be able to implement this, though.
If I were the one that needs to do this (and again, that may not be the best person for the task), I would probably try to get JUMBOMarker to run properly
yes
I got it to run, but the test_mopac.xml output file is different from mopac.xml, so either it is not working as it should, or the template used to generate the shipped xml file is different.
and see whether I can develop a template.xml for some of the Jmol supported filed formats,
yes
I tried to follow what is going on with the mopac file from looking at the template for it. I am a bit discouraged by the fact that I see 20 entity files and 7 xml files used for this, while gamess needs 16 entity files and 2 xml files... It all looks very complicated to me, and I am starting to wonder whether I should have brought this up to begin with :-(...
do the conversion and see how well Jmol's CML reader is able to handle it.
yes
I assume that that will give a me a sense as to how feasible it is for me to come up with those templates.
Seems fine. I think the main questions will be:
- what info other than molecules does Jmol wish to process
- what should Jmol do with multiple molecules (e.g. optimsation and dynamics).
Maybe life is not as complicated for Jmol since/if the amount of information we are trying to capture is limited.
Currently most readers only read atomic positions, and possibly charges and vibration data. In the NWChem reader I added just a tiny bit more (to test out the AtomSetProperty part) and I started using a PATH property that the AtomSetChooser uses to logically group AtomSets for flip-book type animation purposes.
All molecules are read as a separate AtomSet which are put in an AtomSetCollection. Each AtomSet is then associated with a 'frame' or 'model' on the display side.
Before going to far into this, I would really like to know what other people think about this. I am starting to get the feeling that it may make things overly complicated.
Ren�
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