Camelia, the Perl 6 bug

IRC log for #cdk, 2011-03-22

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All times shown according to UTC.

Time Nick Message
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09:47 egonw__ moin
09:47 zarah saluton egonw__
09:47 egonw__ is now known as egonw
09:47 egonw moin
09:47 zarah hi egonw
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09:56 maclean hi
09:57 zarah saluton maclean
09:59 egonw hi maclean
09:59 maclean saluton egonw : how's the grant proposing?
09:59 egonw sent
10:00 egonw one down... four to go :/
10:00 maclean 4!!
10:00 egonw the more the merrier
10:00 maclean Well, indeed. Or "The more, the more likely to be merry" I suppose.
10:01 maclean Not as catchy.
10:02 maclean So would now be a good time to ask about CIP? I think that I already know the answer : I'm just checking...
10:02 egonw indeed :)
10:02 egonw yes, it would indeed
10:03 maclean Ok, so here's the situation : I'm trying to convert wedge bonds to R/S assignments (at least).
10:04 maclean So, I have a way to recognise (say) UDNN or UDUD (U = Up, D = Down)
10:04 egonw mmm... ambitious
10:04 maclean Well, it's going ok so far.
10:04 * egonw strongly suggest to validate input, and report problems
10:04 egonw that would be very useful, in fact
10:04 maclean It should be possible to do that, yes.
10:04 maclean But there is the pattern UNN and DNN.
10:05 maclean In other words, a stereo with an implicit hydrogen.
10:06 maclean So my question is : is it really not possible to specify an implicit hydrogen to the CIP tool when used outside the package?
10:07 maclean Because LigancyFourChirality is package protected. There is a CIPTool method that takes atomIndices (with -1 meaning implicit H) but it returns a LFC...
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10:17 maclean Anyway, I think the solution may be either a) make LFC public or b) provide CIPTool with a method that takes 5 int indices and a Stereo and returns a CIP_CHIRALITY.
10:18 maclean I'll file a feature request. Anyway, got to go : bye! Sorry to ask and run :)
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10:24 egonw sorry... was called afk
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11:54 maclean back. https://github.com/gilleain/stereo/blob/mast​er/img/kegg_compounds/direct/C00008.mol.png
11:55 maclean 0 : R, 2 : R, 7 : R, 11 : R, 12 : S.
12:02 egonw 0 = R?
12:02 egonw that's the nitrogen, right?
12:02 egonw that one is not chiral
12:03 maclean hmmm. well doesn't it have hydrogen?
12:03 egonw agreeing with 2,7,11
12:03 egonw no hydrogen
12:03 maclean No, it's part of the planar ring, right.
12:03 egonw moreover, it's not charged
12:04 maclean What's happening is that it looks at N0's bonds (N0:C3, N0:C1, N0:C2) and determines that matches the UNN pattern.
12:05 maclean It should be charged?
12:05 egonw no, don't think so
12:05 egonw if it did have a hydrogen, then it would have needed that
12:05 maclean Right.
12:06 maclean So unfortunately, I'm going to have to notice the direction of the wedges....
12:06 egonw yes, crucial
12:08 egonw mmm... 12 is tricky...
12:08 egonw but the verdict is:
12:08 maclean Well, my pattern matching system should be able to handle this.
12:08 egonw R
12:08 maclean Oh?
12:08 egonw which doesn't match your report
12:09 egonw I think 7 takes precedence over 11
12:09 egonw or not
12:09 egonw wait
12:09 egonw damn CIP rules
12:10 maclean 7 = C(C(ON)O), 11 = C(C(C)O(C))
12:11 maclean Which is not helpful, I suppose.
12:11 egonw yeah, I got that far
12:11 egonw so, up to this they are equals:
12:11 egonw 7 = C(OC), 11 ? C(OC)
12:11 egonw 7 = C(OC), 11 = C(OC)
12:12 egonw so, for the third layer, we need to first look at the O
12:12 egonw so, we get:
12:12 egonw 7 = C(O(ON)C), 11 = C(OC)
12:12 egonw so, 7 is higher
12:12 egonw so 12 is indeed S
12:13 maclean Right, cool.
12:13 maclean Will probably verify with balloon/StereoTool, but takk :)
12:14 maclean Or, actually, the crystal coords of ATP, since I expect it appears in a protein or two.
12:14 egonw taCk
12:16 maclean Bah. I am listening to the Sigur Rós album "Takk...", so nyah.
12:17 maclean Hah. And I bet 'Me∂ Bló∂nasir' means "with a bloody nose" :)
12:21 maclean Right. It's either my mouse or my mobile plugin, so I'm off. Laters taters.
12:21 maclean Thankyou for your analysis egonw.
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