Camelia, the Perl 6 bug

IRC log for #cdk, 2011-05-24

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All times shown according to UTC.

Time Nick Message
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09:12 CIA-117 cdk: Egon Willighagen cdk-1.4.x * r310cd0c / (2 files in 2 dirs):
09:12 CIA-117 cdk: Added unit tests to calculate tautomers from a handcrafted IAtomContainer
09:12 CIA-117 cdk: Signed-off-by: mrynbeek <markr@ebi.ac.uk> - http://bit.ly/lwkwSW
09:12 CIA-117 cdk: Egon Willighagen cdk-1.4.x * r54d5ff9 / src/main/org/openscience/cdk/taut​omers/InChITautomerGenerator.java :
09:12 CIA-117 cdk: Added note about required atom type perception
09:12 CIA-117 cdk: Signed-off-by: mrynbeek <markr@ebi.ac.uk> - http://bit.ly/kD8JPz
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10:52 andy hello?
10:52 egonw hi andy
10:52 andy oh thank god
10:53 andy someone
10:53 egonw :)
10:53 andy anyways
10:53 andy umm you think you can tell me what this chemical formula means? LiSO4
10:53 egonw lithium sulphate, I guess
10:53 andy awesome
10:54 andy also this is for a chem assignment so i need a reference from ya
10:55 andy just your name would do
10:55 egonw have you tried google?
10:55 andy yes
10:56 andy my problem is that im getting confused if it was the same as Li2SO4
10:56 egonw well, which of the two is wrong?
10:56 andy i dont think its either
10:57 egonw explain
10:57 andy but to be honest i dont know alot about chem
10:57 egonw that's the point of assignments, I guess
10:57 andy yep
10:58 andy so do you think you could give me a name cause no offence but egonw doesnt look very good for a reference
10:58 egonw I'm not going to do your homework
10:58 andy i wouldnt ask if i didnt have to but this is a very stupid assignment
10:59 egonw most certainly not your 'stupid' homework
10:59 andy compared to some others
10:59 egonw well, why not write that to the teacher?
10:59 andy the intext referencing get over dramatic due to little amount of resources other than the internet
11:00 andy no point in arguing
11:00 egonw make sure to add a paragraph on Open Access publishing
11:00 andy k thanks
11:00 andy cya
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12:26 CIA-117 cdk: jonalv master * rdfb3e86 / (2 files in 2 dirs): (log message trimmed)
12:26 CIA-117 cdk: fix bug #3305550 - moved SMARTSQuery to where used
12:26 CIA-117 cdk: It was initialised staticly for the outer class. However since the
12:26 CIA-117 cdk: SMARTSQueryTool has state it can not be shared among multiple FingerPrinters.
12:26 CIA-117 cdk: Now every CountSubstructures instance will have it's own which should make it
12:26 CIA-117 cdk: possible to run multiple PubchemFingerprinters in parallel.
12:26 CIA-117 cdk: Also, made the SMARTSQueryTool throw an IllegelargumentException instead of a checked CDKException if something is wrong with the SMARTS string.
12:27 egonw_ peer review yields better code :)
12:27 egonw_ it's good to see it in action :)
12:27 egonw_ jonalv++
12:27 egonw_ is now known as egonw
12:27 jonalv mm karma
12:29 jonalv egonw: which rpo is that?
12:29 jonalv |repo
12:30 * jonalv is still confused by all clones...
12:31 egonw github.com/cdk/cdk
12:31 egonw master branch
12:31 egonw I'd say this should have gone into cdk-1.4.x
12:31 egonw can you please ask that
12:31 egonw or maybe it's not so important
12:33 jonalv well it's not so important I guess, how many versions are you supporting?
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12:40 egonw jonalv: https://github.com/cdk/cdk/commit/dfb3e8624323f0​15628cdbe7202530510d458056#commitcomment-396777
12:40 jonalv egonw: hm that pattern always confused me
12:41 egonw why?
12:41 egonw that is, why do you find it confusing?
12:41 egonw ummm
12:41 egonw what do you find confusing about it?
12:41 egonw umm
12:41 egonw what confusion does it give you?
12:41 jonalv egonw: I mean you are attaching the causing exception to the new Exception. It will show up in the stacktrace, why keep concatenating the messges as well? The message sring can get very long in that way...
12:42 egonw true
12:42 egonw I see your point
12:42 egonw I guess the thing is, that at GUI level, people normally just see the top most message
12:43 jonalv hm, at a gui level people writing the gui should do something smart about the exceptions...
12:44 jonalv but yea I am not sure a concatenation of 5 levels of exceptions (which actually is not unreasonable in JAva) is much better...
12:44 egonw ack
12:45 jonalv having said that I guess it might make sense to actually add the actual SMARTS String to that exception message String. Once again I aimed at changing as little as possible in that patch...
14:02 CIA-117 cdk: Rajarshi Guha master * r1ef89fb / src/main/org/openscience/cdk/smil​es/smarts/parser/SMARTSParser.jjt : Updated SMARTS parser JJT file, to drop the use of CDKException when a invalid SMARTS is provided. - http://bit.ly/ifw2qm
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