Camelia, the Perl 6 bug

IRC log for #cdk, 2009-10-05

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All times shown according to UTC.

Time Nick Message
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06:15 slyrus_ egonw: so I looked at the supposed data model support for E/Z configurations... there's not much to speak of.
06:15 egonw moin
06:15 zarah hello egonw, you fantastic person you
06:15 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
06:15 slyrus_ morning
06:16 slyrus_ the problem, in my eyes. with what's there is that the configuration is coded in terms of the spatial coords, rather than some abstract e/z specification
06:16 egonw well, I guess there is not much to E/Z anyway
06:16 slyrus_ which means that you need to have a spatial representation to begin with before representing e/z
06:16 egonw there is a E/Z stereolabeling patch ready for master...
06:16 egonw mom
06:17 egonw ah, wait... you should have that
06:17 egonw IBond.Stereo
06:17 egonw from jcp-prim
06:18 slyrus_ yeah, but what that gives is: "/** Indication that this double bond has a fixed, but unknown E/Z * configuration." and "/** Indication that this double bond has a fixed configuration, defined * by the 2D and/or 3D coordinates."
06:19 egonw ummm...
06:19 egonw there should be E and Z too...
06:19 egonw not yet?
06:19 slyrus_ I think the Bond class itself should know something about the configuration
06:20 * egonw making a mental note to add E and Z ...
06:22 slyrus_ I'll just whistle a little tune and pretend that i didn't just think about how nasty trying to represent allene stereochemistry must be...
06:22 slyrus_ s/stereochemistry/geometric configuration/ (?)
06:22 slyrus_ something like that...
06:22 egonw ah, yes
06:23 egonw that lot is in the grant application :)
06:23 slyrus_ spiro too?
06:23 egonw yeah, same thing
06:23 egonw from a greometry point of perspecitve
06:23 slyrus_ ok
06:23 egonw and thing like BINAP too
06:23 egonw I think it's BINAP...
06:24 egonw yes, BINAP
06:26 slyrus_ ok, well I'm sure you don't need any additional motivation for this problem, but the lack of SMILES -> 2d structure graphs that preserve E/Z will prevent me from using CDK for real work :( (and, to be far, was one of the missing hard bits that I was afraid of getting around to implementing for my lisp-based chemistry package)
06:26 slyrus_ s/far/fair/
06:29 egonw yeah, sorry about that
06:29 egonw it *is* a blocker
06:29 egonw I know
06:33 slyrus_ alright, thanks. gnight!
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10:21 egonw mmm...
10:21 egonw ioformats is not being tested... :(
10:40 CIA-68 cdk: mark_rynbeek * r14919 /jchempaint/trunk/ (3 files in 2 dirs):
10:50 CIA-68 cdk: mark_rynbeek * r14920 /jchempaint/trunk/build.shrink.xml:
11:01 CIA-68 cdk: Egon Willighagen cdk-1.2.x * r56289e2 / build.xml : Added ioformats to modules to test - http://bit.ly/2lQRUD
11:15 CIA-68 cdk: Egon Willighagen cdk-1.2.x * r8759481 / (2 files): Added missing dependencies - http://bit.ly/2U2qMY
13:05 CIA-68 cdk: mark_rynbeek * r14921 /jchempaint/trunk/src/main/org/openscien​ce/jchempaint/action/SaveAsAction.java: indentation only fixed
13:10 jbrefort joined #cdk
13:23 CIA-68 cdk: shk3 * r14922 /jchempaint/trunk/src/test/​org/openscience/jchempaint/ (JCPEditorAppletDrawingTest.java JCPEditorAppletMenuTest.java): some slight improvements in tests
13:23 CIA-68 cdk: shk3 * r14923 /jchempaint/trunk/.classpath: the project setup contained absolute paths
13:38 CIA-68 cdk: shk3 * r14924 /jchempaint/trunk/src/test/​org/openscience/jchempaint/ (JCPEditorAppletDrawingTest.java JCPEditorAppletMenuTest.java): more tests
13:54 CIA-68 cdk: mark_rynbeek * r14925 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (action/SaveAsAction.java application/JChemPaint.java): Takes care of flipped MOL files
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15:39 CIA-68 cdk: goglepox * r14926 /jchempaint/trunk/src/main/org/openscience/jc​hempaint/undoredo/SwingUndoRedoFactory.java: Fixed undo for IEdit operations
15:58 CIA-68 cdk: shk3 * r14927 /jchempaint/trunk/src/test/org/openscience/jchemp​aint/matchers/ComboBoxTextComponentMatcher.java: the saveAs tests now also work in windows
15:58 egonw joined #cdk
16:28 CIA-68 cdk: shk3 * r14928 /jchempaint/trunk/src/test/org/openscience/jchemp​aint/matchers/ComboBoxTextComponentMatcher.java: the saveAs tests now also work in windows
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