Camelia, the Perl 6 bug

IRC log for #cdk, 2012-05-16

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All times shown according to UTC.

Time Nick Message
04:09 egonw joined #cdk
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07:35 jonalv egonw: do you have a minut or two?
07:39 egonw yes
07:39 jonalv I am wondering about org.openscience.cdk.io.iterator.IteratingMDLReader
07:40 jonalv I am having some trouble with it when reading a large sd file with a molecule containing query bonds
07:40 jonalv if molecule 5 contains strange bond orders it refuses to move on to molecule number 6
07:41 jonalv I am wondering if we could change the behavior so that it is possible to go trhough a file even if some entries contain chemistry that CDK does not yet handle
07:41 egonw the iterating reader does that
07:42 egonw you can also tell it to accept 4 bond orders...
07:42 egonw cehcking how...
07:42 jonalv this was bond order 8 or something like that
07:42 jonalv it all started with this bug: http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3197
07:43 jonalv I realise that it is diffciult when slurping the enitre file but it would be nice to get it working when iterating
07:44 jonalv egonw: however line 180 in org.openscience.cdk.io.iterator.IteratingMDLReader indicates that it does not. (+ the fact that I can't get ti to work....)
07:44 egonw 180?
07:44 egonw that's for me:     @TestMethod("testGetFormat")
07:45 jonalv catch (Exception exception) {
07:45 jonalv logger.error("Error while reading next molecule: " +
07:45 jonalv exception.getMessage());
07:45 jonalv logger.debug(exception);
07:45 jonalv hasNext = false;
07:45 jonalv hm sry for long paste
07:45 jonalv line 180 is hasNext=false
07:46 egonw mmm... we recently had a patch around this...
07:46 egonw maybe that went into master...
07:46 jonalv okey, I am looking at the CDK version used from Bioclipse. I never remember which one that is...
07:49 egonw commit ca8f142daa01000e8b21140ded1ca4ab65d95b0f
07:49 egonw https://github.com/egonw/cdk/commit/ca​8f142daa01000e8b21140ded1ca4ab65d95b0f
07:50 egonw OK, should be part of 1.4.8
07:50 jonalv egonw: that looks promising
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11:49 s9asad Hello
11:49 zarah saluton s9asad
13:29 s9asad joined #cdk
14:06 egonw hi s9asad
14:18 s9asad hi egonw
14:24 s9asad I was wonder if I could generate a patch for the CDKFingerprinter from https://github.com/asad/CDKHashFingerPrint/blob/​master/src/fingerprints/HashedFingerprinter.java
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