Bob Hanson wrote:
> I have just committed an upgrade of Jmol that will allow indication and
> selection of isotopes. Since this is a fairly complex upgrade, I thought
> I would describe what I have done. For my own sake and for others, here
> is a rundown of how it works. If you see a flaw, do let me know.
>
Nice addition :)
> Q: Should the smiles matcher get "H" or "D" for deuterium -- or
> something completely different -- 2H?
>
You're talking about org.jmol.viewer.PatternMatcher ?
The SmilesParser already parses correctly atomic mass (that's the
isotope number, isn't it ?) restrictions in Smiles strings.
The only thing that needs to be added in PatternMatcher is to restrict
matches when the atomic mass has been given in the Smiles string.
The method to modify is searchMatch(BitSet bs, SmilesMolecule pattern,
SmilesAtom patternAtom, int atomNum, int i).
There's only a comment ("Check atomic mass : NO because Jmol doesn't
know about atomic mass") that needs to be replaced by an actual test.
You want to do the modification ?
I am working on marking translated pages on the website as outdated.
Nico
>
> Well, that's more than anyone wants to know. Is there more to implement
> on this?
>
>
>
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