Camelia, the Perl 6 bug

IRC log for #bioclipse, 2011-08-31

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All times shown according to UTC.

Time Nick Message
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09:40 jonalv hm who is the king of molecular properties on Bioclipse molcules?
09:40 jonalv How can I see what properties a molecule has?
09:42 jonalv olass, egonw: does one of you know?
09:42 egonw Gpox is
09:42 egonw olass: that reminds me... roman wanted to know about molprop viz in table form too...
09:43 egonw in particular, if sorting was possible...
09:43 egonw olass: I said I would ask you if there was any recent work in that area
09:43 egonw currently you cannot sort on prop columns, correct?
09:43 olass nope, no sorting yet
09:43 egonw well, Roman has a use case for that .)
09:43 olass hehe, good
09:44 olass it's really important to work out but 2.6 comes first
09:44 jonalv there are plans to bend StructureDB into doing the sorting for us
09:44 jonalv but it seems a bit further into the future, no?
09:45 egonw future, now... that's just a matter of priorities, itches, and paper opportunities
09:46 jonalv but olass, in regards to that bug, how do I test for the properties if I can't list all properties of a molecule
09:46 jonalv I am beginning to think there is something fundementally wrong with the way we treat properties
09:46 jonalv egonw: yea, and right now I see neither an easy paper nor a big enough itch regarding that. Maybe I donät see the whole picture?
09:47 egonw that's something you learn in the process
09:48 jonalv egonw: you lost me...
09:51 egonw nvm :)
10:02 olass jonalv: explain
10:02 * olass is cooking lunch
11:18 olass joined #bioclipse
11:51 * jonalv is back from lunch with claes
11:52 jonalv olass: well, it's easy to calculate properties if you know their name
11:52 jonalv it's difficult to get all properties for a molecule
11:52 jonalv and it's not so obvious what the possible proerty names are
11:53 olass ?
11:53 olass context?
11:53 olass sdf?
11:53 olass smiles?
11:53 jonalv IMolecule
11:53 olass please make a long explanation starting from scratch
11:53 * olass has no idea
11:53 olass what jonalv is talking about
11:53 jonalv I am trying to write a test for the bug you gave me
11:54 olass smiles bug?
11:54 jonalv yea
11:54 jonalv so I read in the molecules from the smiles file
11:54 jonalv then I try to look at the molecule and see if they have properties or not
11:54 jonalv only, there is no obvious wayu to do that
11:54 olass sorry, no time, need to be in a TC now
11:54 jonalv lol
11:54 olass bye
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13:39 CIA-120 bioclipse.cheminformatics: jonalv 2.5.x * r25456bb / (2 files in 2 dirs): test for bug: 3055 - http://git.io/vg4rFA
13:39 zarah bug #3055 | http://tinyurl.com/3txtdds
14:40 jonalv egonw: Bioclipse seems to have SMARTS validation but no SMILES validation do you know if that is because CDK lacks functionlaity for doing that?
14:41 egonw maybe there was no need yet
14:42 egonw moreover, CDK does not provide great SMILES validation feedback
14:42 jonalv okey
14:42 jonalv I am trying to figure out how to do a miles files parser
14:42 jonalv that handles the stupid amount of differnet files formats around
14:42 jonalv I am not sure I am familiar with all standards yet
14:43 egonw :)
14:43 egonw I am not familiar with SMILES file standards
14:43 jonalv the blueoblisk++ shapade has a question on the topic so I am rading up there
14:43 egonw good :)
14:44 jonalv blueobelisk++ I mean
14:56 jonalv Bioclipse seems to have very many smiles formats supported...
15:58 CIA-120 bioclipse.cheminformatics: jonalv 2.5.x * rf336398 / (4 files in 3 dirs): fixed bug 3055 - http://git.io/YvzoNQ
15:58 zarah bug #3055 | http://tinyurl.com/3txtdds
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