Peter and Henry,
I have been looking at the CIFReader in cdk, with an eye towards sharing it with Jmol.
I started looking at it because I thought it would be easier to do than CML,
Possibly
and I am hoping that Egon can help me with CML.
And hopefully we can as well!
Searching the web seems to reveal that the you spent a lot of your pre-CML days working on CIF/mmCIF.
Yes.
The 'CIFReader' in CDK is only a partial reader. Egon put in comments saying that it is ad hoc and only extracts some fields. It looks to me like it extracts: 1. cell data 2. atom coordinates 3. _symmetry_space_group_name_H-M
Q: In the context of Jmol, would it be useful to have a reader that only supports these items?
Several new things:
- Billy (smt) has been updating my previous CIF reader
- The CIF reader uses a DOM-like structure (although this is very flat) and can read any CIF file, including mmCIF into memory
- Billy has extensible Tools that can extract CIF1 concepts. CIF is designed to be dictionary driven and we can validate against the CIF dictionary.
- the Southampton group now publishes its results online (ePrints) and is now setting up CMLRSS feed. The idea is that Simon Coles and Billy jointly work on CIF2CML. SimonC has installed Jmol and I think is very pleased with it. I suggested he contact you directly about new functionality. All of us are concentrating on small molecules structures at present.
SimonC, Miguel/Jmol has done a lot of scripting work - I think this gives an excellent way to package the display of crystal structures. I think if packing can be scripted then this is an excellent way to take things forward.
P.
The PDB offically supports/promotes mmCIF. The .pdb reader in Jmol now extracts quite a bit of information from .pdb files.
We don't support mmCIF semantics. I am sure that our architecture is a good way to do it. I looked at it at Brookhaven ca 1994. It is a lot of work to do it properly. As always it is easier to write something that read it. But if Jmol read mmCIF I think it would create considerable interest.
In addition to the data listed above, Jmol would like to have the mmCIF entries that define secondary structure (the HELIX/SHEET/TURN equivalents)
It seems to me that there are a few more, but not too many.
Q: Do you think it would be worthwhile for Jmol to support mmCIF files?
Yes
Q: It seems to me that this is a serious amount of work, but not intractable. Any comments?
See above. It is best to write a generic mmCIF reader - which needs an internal structures capable of resolving relational links.
Q: Do you have any old code laying around that might be of value?
Possibly.
Q: Would you be available to answer questions?
Of course - except I fly to US tomorrow and am in Edinburgh the week after
Q: Any other comments/suggestions?
Miguel
Best
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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