Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-07-27

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All times shown according to UTC.

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07:44 sneumann_ Hi, I just came across
07:44 sneumann_ http://umbbd.msi.umn.edu/predict/
07:45 sneumann_ Sounds similar to metaprint2d
07:46 egonw yes
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08:53 edrin hello
09:20 sneumann_ ni hao, edrin :-)
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10:38 egonw hi edrin
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10:40 egonw hi maclean
10:40 maclean hi egonw
10:40 maclean how goes it?
10:41 egonw lot of conf call today :)
10:41 egonw just got back from a coffee break
10:42 maclean No doubt you will be updating wikis and irc-ing at the same time as conf calling, though :)
10:42 egonw I should be able to make a .jar with stereotool today
10:42 egonw well, I hope :)
10:42 maclean cool.
10:42 maclean I added a convenience method that takes 4 atoms in order, and returns StereoTool.TetrahedralDescriptor.{R,S}
10:42 egonw might you glance over the bug/patch report I wrote on cdk-devel about?
10:43 egonw your input would be appreciated
10:43 maclean which is kind of overkill, but still.
10:43 maclean the Bonds.clone? sure.
10:43 egonw maclean: yeah, sounds good
10:43 egonw why StereoTool.TetrahedralDescriptor.{R,S} instead of the CIP ones?
10:43 maclean well, partly to avoid me having to apply the 160-cip branch...
10:44 maclean but I could say that it is so that you get what the StereoTool 'means' by R/S
10:45 maclean Feel completely free to patch it so that it returns the CIP enum values instead.
10:46 maclean also, it could maybe go in the o.o.cdk.stereo package, rather than tools?
10:47 egonw yeah, sounds good to me
10:50 maclean actually, I will try rebasing on 160-cip and making those changes.
10:51 egonw great
11:07 maclean egonw : what module should the stereotool go in? Cip? or...
11:07 egonw good question
11:07 maclean (currently, I optimistically put it in a non-existent module called "stereo")
11:07 egonw I guess if you factor out the R,S designation, it should go into cdk.stereo
11:07 egonw ummm...
11:07 maclean no, that's package - I meant module.
11:08 egonw yes, sorry
11:08 egonw :)
11:08 egonw standard sounds fine to me
11:08 maclean ok
11:15 maclean wait, wait, wait. using CIP.R/CIP.S in stereotool will make the standard module dependent on the cip module!
11:16 egonw ah, right
11:16 egonw ok, cip module then
11:16 maclean ok
11:16 egonw but I do not think stereo tool should use CIP R S anyway
11:16 egonw it should work with the default CDK data model
11:16 egonw so, ITetrahedralChirality, etc
11:17 egonw and we have to CIP tool to convert that into R,S
11:17 maclean ahh. right.
11:20 maclean hmmm. no, that can't be right. ITetrahedralChirality defines Stereo.{Clockwise Anticlockwise} not {R,S}.
11:21 maclean That's not what is being calculated...
11:22 egonw that is correct
11:22 maclean I think this conversation is being split across github comments and irc. :)
11:22 egonw do you have problems with that? :)
11:23 egonw anyway...
11:23 maclean no, no. just don't move it to science 2.0 as well.
11:23 egonw CW and ACW are objectvie...
11:23 egonw R,S is subjective...
11:23 egonw the last depends on the algorithm to be correct
11:23 egonw the first is merely an absolute definition
11:23 maclean well, it depends on the order.
11:23 egonw yes, but that order is explicitly given
11:24 maclean so StereoTool.getTetrahedralDescriptor takes 4 atoms in order (not a set of atoms) and returns R or S depending on whether the first three are CW/ACW and the fourth is above/below the plane.
11:24 egonw put differently... CW/ACW is exact, R,S is an approximation
11:25 maclean not really.
11:25 egonw maclean: I'm actually tempted to say that the input should be five atoms, for tetrahedral chirality
11:25 maclean hmmm.
11:25 egonw which would be convenient and needed for setting up an ITetrahedralChirality anyway...
11:26 egonw it would also define the 'normal' as the bond between the central atom, and the atom looked from
11:26 maclean I'm pretty certain that given an order over 4 atoms it is possible to unambiguously return R/S.
11:27 maclean the normal in the stereotool is from the plane formed by the 3 highest priority atoms in ACW order.
11:28 maclean so, if the fourth atom is on the same side as this normal, it is R, otherwise S.
11:30 egonw mom, I phone
11:30 egonw I -> phone
11:31 maclean I spartacus?
11:36 egonw arg...
11:36 egonw anywya... I no phone anymuch
11:36 maclean er, ok.
11:36 egonw :)
11:36 * maclean is starting to make an image of this, to better explain...
11:37 maclean (r/s cw/ccw)
11:37 egonw I'm sure you can input priorities
11:37 egonw but, do those priorities always map to R, S
11:37 egonw ?
11:37 egonw anyway...
11:38 maclean well, the proof of the pudding is in the eating. It needs to be tested with stereochemicals with 3D coords.
11:38 egonw my point is... I like to keep the functionality as simple as possible...
11:38 egonw and the data model is ITetrahChir...
11:38 egonw so, anything that just spits that, suits me best
11:40 maclean sigh. ok, will think about it while I go and do stuff.
11:44 egonw e.g. it would remove any dependency on the cip module
12:08 maclean http://gilleain.tumblr.com/post/865805384
12:11 egonw we should have a taglet to point to images in the JavaDoc...
12:11 egonw {@cdk image foo/bar.png}
12:11 egonw {@cdk.image foo/bar.png}
12:12 maclean that would be excellent.
12:12 maclean especially for 3D geometry!
12:12 egonw yeah, and many other things actually...
12:12 maclean (oh, and I second your comments about jmol's javadocs - they are abysmal!)
12:13 egonw :)
12:13 maclean but they do at least have some ASCII art diagrams.
12:15 egonw oh, bugger... I wish someone would just fund my cheminformatics research...
12:15 egonw someone, please...
12:20 maclean egonw : would you prefer StereoTool.methodName(atom1, atom2, ...) or StereoTool.methodName(atom[])?
12:20 maclean (with the latter taking 5 atoms, as you say)
12:21 egonw atom1, atom2, ...
12:21 maclean ok
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