Camelia, the Perl 6 bug

IRC log for #cdk, 2012-04-05

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All times shown according to UTC.

Time Nick Message
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12:58 mgerlich Hi, I've got a question related to CDK's conversion of implicit to explicit hydrogens
13:00 mgerlich when I use the function AtomContainerHandler.addExplicitHydrogens() from CDK 1.3.6, write an SD file with these modified structures
13:01 mgerlich and load this SD file into Bioclipse 2.4, I see that the added hydrogens are floating on position (0,0) which gives a weird look at the structure
13:03 mgerlich it is easy to fix with Bioclipse's "Clean Up" context menu action, but I'd rather like to have a correct solution for the CDK
13:04 mgerlich are there some fixes for this in the latest CDK, or are there additional steps necessary to add explicit hydrogens to AtomContainers or SD files, respectively?
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13:57 sneumann_ mgerlich: I couldn't find an open ticket for this in the cdksf.net tracker.
13:57 sneumann What could be the solution ?
13:57 sneumann 1) Reset 2D coordinates upon adding hydrogens
13:58 sneumann or 2) call generate2D on the newly added atoms ?
14:00 mgerlich there's another way to add explicit hydrogens, i.e. convert implicit to explicit ones
14:00 mgerlich I'm going to try this and have a look at the SDF
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