I am trying to work on the adapter to map the cdk class hierarchy to the Jmol view of the world. Some of us discussed this briefly the other day on #cdk irc. However, I have now spent some time on it and I am (once again :) confused and frustrated. The Jmol picture of the world is pretty simple. A clientFile contains one or more frames A frame contains one or more atoms/bonds/vectors/crystal cells Someone needs to help me map this over to the cdk world. There are simply too many layers for me to figure it out. This class hierarchy seems very complicated to me. I only want to ask a few (seemingly simple) questions: - How many frames are in your file? For each frame: - How many atoms do you have? (the client can answer '0' if it doesn't want to figure it out) - Iterate over all the atoms - Iterate over all the bonds (if you have any) - Iterate over all the vectors (if you have any) - Iterate over all the lines which make up your crystal cell (if you have any) I assume that a jmol.clientFile is a cdk.ChemFile. However, this may not be correct. Please confirm. Does a ChemSequence correspond to a single "frame" of an animation? If so, then a ChemSequence would map to a single 'frame' in the Jmol world. That is, the atoms which get rendered to the screen at one time are: - all the Atoms -- in all the Molecules --- in the SetOfMolecules ---- in all the ChemModels ----- contained in the specified ChemSequence ------ contained in the ChemFile Now a Crystal is not a Molecule. Therefore, it cannot be contained in a SetOfMolecules. Therefore, it must be handled differently. But it seems that there is only one Crystal in a ChemModel, so I suppose that simplifies things somewhat down the crystal branch.
However, a crystal is in theory infinite in space. When we want to show it on the screen we (the user) chose to represent only a part of the crystal. In a sens, the part of the crystal can be considered as a molecule. In Jmol a CrystalFile extends a ChemFile because it was easier for me to access the ChemFile fields afterwards. A better implementation would be (maybe) to have CrystalFile not extending ChemFile but being at the same level. Then, an instance (in the sens of a limited part) of the crystal would become an instance of a ChemFile. This was a rapid though....
Fabian
Please advise. Miguel ------------------------------------------------------- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
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-- Fabian Dortu <[EMAIL PROTECTED]> |
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