Camelia, the Perl 6 bug

IRC log for #cdk, 2009-11-10

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All times shown according to UTC.

Time Nick Message
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09:21 LillePedro I give up. After running UniversalIsomorphismTester.getOverlaps(..) I end up with 3 molecules, but there is no way for me to match atom X1 in molecule Y1 with atom X2 in molecule Y2, using an equality operator.
09:23 LillePedro When reactants and products are read from file, the very crucial ID (field 'identifier' in ChemObject class, I believe) are sometimes missing, hence making an id comparison impossible.
09:24 LillePedro Thinking of rewriting method getOverlaps (or its called methods), but I cannot wrap my brains around this challenge.
09:25 LillePedro Any pointers?
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09:38 egonw hi LillePedro
09:38 egonw what file format are you using that the IDs are not read...?
09:38 egonw that's sounds like something we can fix
09:39 egonw what are the three molecules?
09:39 egonw == does indeed not work, as that compares object instances
09:39 egonw that's what getoverlaps is for...
09:39 egonw last week I wrote code to do the mapping, for the kabsch alignment in Bioclipse
09:39 egonw you could have a look at that code
09:44 LillePedro Well, the IDs are read, but sometimes they end up being zeroes, meaning they don't even get set in the atom instance.
09:46 egonw if you like, send offline email with file and I'll check
09:46 egonw confidentially, if you indicate
09:47 LillePedro I am using MDLRXNReader.readReaction(..)
09:47 LillePedro sending you the small file by mail.
09:47 egonw ok, great
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