I'm onto it. Why is:
boolean canMatch = true;
Atom atom = frame.getAtomAt(i);
// Check symbol
if ((patternAtom.getSymbol() != "*") &&
(patternAtom.getSymbol() != atom.getElementSymbol())) {
canMatch = false;
}
// Check charge
if (patternAtom.getCharge() != atom.getFormalCharge()) {
canMatch = false;
}
not just:
// Check symbol
if ((patternAtom.getSymbol() != "*") &&
(patternAtom.getSymbol() != atom.getElementSymbol())) {
return;
}
// Check charge
if (patternAtom.getCharge() != atom.getFormalCharge())
return;
? I don't see any reason to continue checking if any of these fail. Right?
Bob
Nicolas Vervelle wrote:
>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I am working on marking translated pages on the website as outdated.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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