Camelia, the Perl 6 bug

IRC log for #cdk, 2009-01-26

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All times shown according to UTC.

Time Nick Message
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12:40 CIA-62 cdk: gilleain * r13974 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/g​enerators/HighlightGenerator.java: Stray semicolon.
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16:28 sneumann hi there
16:28 sneumann I am currently trying to draw a number of molecules with jchempaint 2.4.0
16:29 sneumann and it keep putting all sorts of CH2, CH3 and even CH4 into aromatic rings.
16:30 sneumann I also tried editing the file saved by jchempaint 2.4.0 in 2.5.3
16:30 sneumann but while loading the file I get
16:31 sneumann org.openscience.cdk.exception.CDKException: Found well-formedness error in line 1
16:31 sneumann Are these known problems ?
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16:33 maclean_ sneumann : hi, what do you mean by "putting into aromatic rings"?
16:36 sneumann I took naringenin http://www.ebi.ac.uk/chebi/sea​rchId.do?chebiId=CHEBI%3A50202
16:36 zarah sneumann's link is also http://tinyurl.com/b9n265
16:36 sneumann and cut&pasted fragments as new molecules
16:36 maclean_ ok
16:37 sneumann during the cut&paste some bits seem to have duplicated,
16:38 sneumann trying a screenshot
16:38 maclean_ ahh, okay. that sounds bad. shk3?
16:39 shk3 reading
16:39 shk3 mom
16:40 sneumann http://msbi.ipb-halle.de/~sneumann/S​creenshot-naringenfragments4.cml.png
16:40 zarah sneumann's link is also http://tinyurl.com/cawksz
16:40 sneumann So currently I am trying to cleanup the error in the two fragments at the bottom
16:42 shk3 these extra atoms seem to be put in when converting to reaction
16:43 shk3 copy & paste seems to be ok
16:44 shk3 save & open in 2.5.3 (this is development) not working is not much of a surprise
16:44 shk3 I will file a bug report for it
16:44 shk3 but don't expect too much from 2.5 right now
16:45 sneumann ack
16:45 maclean_ ack?
16:46 maclean_ er, as in, you need 2.5 to be working?
16:46 sneumann no
16:46 sneumann 2.5.3 was a try whether it gets things right
16:46 sneumann i'll stick with 2.4
16:46 shk3 I am keen on getting 2.5 (or 3.0) out myself
16:46 shk3 but might take a while
16:46 shk3 still
16:47 shk3 I think in 2.4 you have to delete these extra atoms manually
16:47 shk3 don
16:47 shk3 't think
16:47 shk3 we should fix stuff in there
16:47 shk3 what do you think?
16:48 sneumann I could come over ...
16:49 shk3 well, what does maclean_ think?
16:49 shk3 bug fixes in old jcp yes or no?
16:49 maclean_ probably not, unless they are major, I would have thought.
16:50 maclean_ or easy.
16:50 sneumann shk3: did you mean deleting atoms manually in jchempaint
16:51 sneumann or in emacs ?
16:51 shk3 in jcp
16:56 sneumann deleted the extra H2C which broke the aromatic ring, added the ring, I get duplicate bond bxx when trying to save.
16:57 sneumann sorry, "bond not unique"
16:57 shk3 mom
17:01 shk3 hm, when I delete the extra atoms it's fine
17:03 CIA-62 cdk: shk3 * r13975 /jchempaint/trunk/po/ (fr.po nl.po pl.po pt_BR.po): added headers
17:03 sneumann anyway,
17:04 sneumann created my reaction with emacs ;-)
17:04 sneumann things are fine (at least for me)
17:05 shk3 will double check for these problems in jcp 2.5
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18:05 shk3 sneumann: any plans for this evening?
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