Camelia, the Perl 6 bug

IRC log for #cdk, 2007-11-01

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All times shown according to UTC.

Time Nick Message
03:34 CIA-16 cdk: rajarshi * r9309 /trunk/cdk/src/org/openscience/cdk/qsar/d​escriptors/molecular/TPSADescriptor.java: Updated to use new aromaticity calculator. Also throw an exception if we get a null for implicit H count
04:11 CIA-16 cdk: rajarshi * r9310 /trunk/cdk/src/org/openscience/cdk/qsar/d​escriptors/molecular/TPSADescriptor.java: Updated to count an unset implicit H count as zero rather than throw an exception
04:12 CIA-16 cdk: rajarshi * r9311 /trunk/cdk/src/org/openscience/cdk/test/qsar/d​escriptors/molecular/TPSADescriptorTest.java: Separated individual tests so easier to track things. Also uncommented the various tests so that various atom types are checked
04:20 CIA-16 cdk: rajarshi * r9312 /trunk/cdk/src/org/openscience/cdk/test/qsar/d​escriptors/molecular/TPSADescriptorTest.java: Forgot to use the count of implicit H's properly in the loop, so now prevents NPE. Also added a few more tests
04:20 CIA-16 cdk: rajarshi * r9313 /trunk/cdk/src/org/openscience/cdk/qsar/d​escriptors/molecular/TPSADescriptor.java: Forgot to use the count of implicit H's properly in the loop, so now prevents NPE. Also added a few more tests
07:25 jbrefort joined #cdk
07:29 rojasm joined #cdk
07:35 rojasm moin
07:53 masak joined #cdk
08:32 egonw joined #cdk
08:37 egonw moin
08:38 masak moin
08:52 rojasm moin
10:01 CIA-16 bioclipse: ospjuth * r4111 /trunk/playground/plugins/net.bioclipse.​biomoby.ui/src/net/bioclipse/biomoby/ui/ (BioMobyConstants.java BioclipseMobyModel.java): Caching of ontologies now works.
10:01 CIA-16 bioclipse: ospjuth * r4112 /trunk/playground/plugins/net.bioclipse.bio​moby.ui/src/net/bioclipse/biomoby/ui/prefs/ (4 files): Started working on preference page for multiple BioMoby Registries
10:02 CIA-16 bioclipse: ospjuth * r4113 /trunk/playground/plugins/net.bioclipse.​biomoby.ui/src/net/bioclipse/biomoby/ui/ (3 files in 3 dirs): Adapted to use cached registry.
11:01 egonw lunch time
11:58 CIA-16 cdk: egonw * r9314 /trunk/cdk/src/org/openscience/​cdk/interfaces/IAtomType.java: Forgot to remove the prefixes for the SP3D* hybridization types.
12:02 CIA-16 cdk: egonw * r9315 /trunk/cdk/src/org/openscience/cdk/s​miles/smarts/parser/SMARTSParser.jj: Fixed copyright line; I hope it also now properly picks up the :$ stuff
12:03 egonw no, it does not :(
12:09 CIA-16 cdk: egonw * r9316 /trunk/cdk/src/org/openscien​ce/cdk/smiles/smarts/parser/ (9 files): Removed autogenerated files from SVN
12:32 CIA-16 cdk: egonw * r9317 /trunk/cdk/src/org/openscien​ce/cdk/smiles/smarts/parser/ (SMARTSParserTreeConstants.java SMARTSParserVisitor.java): Deleted too many files. But these too are marked autogenerated... ??
12:33 dleidert joined #cdk
12:33 egonw hi dleidert
12:33 dleidert hi
12:43 CIA-16 cdk: rajarshi * r9318 /trunk/cdk/src/org/openscience/cdk/t​est/tools/CDKHydrogenAdderTest.java: Fixed a typo in the hyb state
12:56 CIA-16 cdk: egonw * r9320 /trunk/cdk/src/org/openscience/cdk/tes​t/gui/smiles/SmilesGeneratorTest.java: Fixed a compile error
13:07 CIA-16 jmol: hansonr * r8552 /trunk/Jmol/src/org/jmol/viewer/ (6 files):
13:07 CIA-16 jmol: version=11.3.40_dev # new feature: set xxxx where xxxx is not a Jmol variable causes ERROR
13:07 CIA-16 jmol: # code: privatized Token to avoid null value problem in Eval.statementAsString()
13:42 CIA-16 cdk: egonw * r9322 /trunk/cdk/src/ (3 files in 3 dirs): Removed crappy file. 10 bonds?? No, the file has 11. Uncharged 5-valent carbon??
13:46 CIA-16 jmol: hansonr * r8553 /trunk/Jmol/src/org/jmol/viewer/ (Compiler.java Jmol.properties): version=11.3.40_dev # bug fix: @{} for within(1.0,point,@{....})
14:02 CIA-16 cdk: egonw * r9323 /trunk/cdk/src/org/openscience/cdk/test/isom​orphism/UniversalIsomorphismTesterTest.java: Use the new aromaticity detector
14:04 CIA-16 jmol: hansonr * r8554 /trunk/Jmol/src/org/jmol/viewer/Compiler.java: version=11.3.40_dev # new feature: set xxxx where xxxx is not a Jmol variable causes ERROR
14:23 CIA-16 cdk: egonw * r9324 /trunk/cdk/src/org/openscience/cdk/ (5 files in 4 dirs): No need for IAtomType.Hybridization.UNSET when we got 'null' aka CDKConstants.UNSET (per Rajarshis comment :)
14:26 CIA-16 cdk: egonw * r9325 /trunk/cdk/src/org/openscience/cdk/tools/ (SmilesValencyChecker.java ValencyHybridChecker.java): Forgot to remove these two Hybridization.UNSETs
14:44 rguha joined #cdk
14:44 egonw hi rguha
14:44 rguha hi
14:44 rguha can ant-contrib go into SVN?
14:45 egonw yes, develjar/
14:45 egonw its Apache license, so fine
14:45 rguha k
14:46 rguha looks like SMARTS is working perfectly - just one last atom type to consider: dative N-O
14:46 egonw explain...
14:46 CIA-16 cdk: rajarshi * r9326 /trunk/cdk/develjar/ant-contrib-1.0b3.jar: Added ant-contrib
14:47 egonw e.g. example structure?
14:47 rguha O=n1ccccc1
14:47 rguha [O+][n-]1ccccc1
14:48 egonw the first SMILES is ugly
14:49 egonw blast... the first N is a N.planar *without* a lone pair...
14:49 rguha :)
14:50 egonw no, this is plain stupid...
14:50 rguha I thought dative bonds were problematic for any chemical  rep system
14:50 egonw the charge separated has a nitrogen with 10 electrons!
14:50 egonw I think you mean:
14:50 egonw [O-][n+]1ccccc1
14:51 rguha oops sorry
14:51 egonw :)
14:51 egonw not sure what to do with the first...
14:53 egonw how is that supposed to work anyway?
14:53 egonw a nitrogen, planar, two double bonds?
14:53 egonw two 'p_z' orbitals?
14:53 egonw the first is crap...
14:54 egonw I see that depict accepts it...
14:54 egonw but it's crap
14:54 rguha hmm
14:54 egonw no way you can work that out in reasonable terms...
14:54 egonw or can you?
14:54 egonw that is, in terms of orbitals and hybridization state
14:55 * egonw is going to check what PubChem has to say on this
14:56 egonw that has the charged separated form...
14:56 rguha my understanding is that the two are interchangable
14:56 rguha the O double bond is delocalzed with the ring
14:57 egonw not as far as I know...
14:57 egonw that would break aromaticity
14:58 egonw anyway... look at it like this:
14:58 egonw two double bonds both attached to the nitrogen... how can that be delocalized?
14:58 egonw the answer should come from mopac, of course...
14:58 rguha hmm, true
14:58 egonw run a QM calculation on it...
14:58 egonw and visualize the MOs
14:59 egonw I don't think the pz of the oxygen will participate with the MO of the ring system...
14:59 egonw this makes an excellent blog item :)
14:59 rguha yes
15:00 rguha is there any quick GUI to do a QM run? forgotten the MOPAC / Gaussian command set
15:00 egonw yes...
15:00 egonw ghemical
15:01 rguha oh right
15:02 rguha it'll be inetersting to see
15:08 egonw OK, I'm not going to worry about the first SMILES form for now...
15:09 egonw I'll run the calculation... and might blog about it...
15:09 egonw will be interesting indeed...
15:09 egonw we can extract info from NMRShiftDB, CrystalEye, etc...
15:09 egonw but ghemical's partial charges will already do a good first guess
15:10 rguha yes
15:11 egonw brilliant...
15:11 egonw I attached one hydrogen to each carbon
15:11 egonw and Ghemical thinks they are sp3 carbons :(
15:13 jbrefort add double bonds ;)
15:13 egonw jbrefort: that seems broken
15:14 egonw but now running a QM job
15:14 egonw that seems to do the right thing
15:14 egonw jbrefort: any idea how I can get the partial atom charges?
15:15 CIA-16 cdk: rajarshi * r9327 /trunk/cdk/build.xml: Updated build script to include the ant contrib tasks
15:16 jbrefort no, I'm not very competent about ghemical use :(
15:19 egonw OK, found it
15:19 egonw ESP population analysis
15:19 egonw partial charge: -0.4736
15:21 egonw on the oxygen
15:22 rguha ok
15:22 egonw now, how to interpret the value ... :)
15:24 egonw OK, doing O=N-C-C-C-C now
15:25 egonw oxygen -> -0.1337
15:26 rguha seems to make sense
15:26 egonw and now O-n1ccccc1
15:26 egonw make that:
15:27 egonw and now O-n1cccc1
15:28 egonw calculating partial charges
15:28 egonw oxygen: -0.2492
15:28 egonw I'm convinced
15:30 rguha to compile ghemical do I need to compile libghemical and ghemical? Or just ghemical?
15:30 egonw funny: http://wwmm.ch.cam.ac.uk/blogs/corbett/?p=44
15:30 egonw "Also, try: precious metals such as diamonds" :)
15:31 rguha :)
15:34 CIA-16 cdk: egonw * r9328 /trunk/cdk/src/org/openscience/cdk​/atomtype/CDKAtomTypeMatcher.java: Pick up O.planar3 if hybridization was set
15:36 egonw rguha: might you please rerun Nightly on trunk/
15:36 egonw ?
15:36 rguha ok
15:37 CIA-16 bioclipse: ospjuth * r4114 /trunk/playground/plugins/​net.bioclipse.biomoby/lib/ (jmoby-dashboard.jar jmoby-others.jar jmoby.jar): Updated to latest BioMoby: 2007-11-01
15:37 CIA-16 bioclipse: ospjuth * r4115 /trunk/playground/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/biom​oby/tests/TestRegistryCache.java: The cache test passes now.
15:39 CIA-16 bioclipse: ospjuth * r4116 /trunk/playground/plugins/net.bioclipse.biomoby/ (.classpath META-INF/MANIFEST.MF build.properties): Updated for latest BioMoby: 2007-11-01
15:52 egonw rguha: you let me know when nightly is updated?
16:00 rguha will have to wait a bit since the scheduled run just started
16:05 egonw ack
16:11 CIA-16 cdk: egonw * r9329 /branches/cdk-1.0.x/ (9 files in 5 dirs): Removed SMARTS from the 1.0.x branch. Users will need to use trunk/; this SMARTS release is not mature enough
16:16 CIA-16 cdk: rajarshi * r9330 /trunk/cdk/build.xml: Cleaned up handling of presence/absence of autogenerated files, so no more warnings
16:37 egonw OK, going offline for basketball
16:37 egonw cu later
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20:53 rojasm joined #cdk
20:53 rojasm hi egonw
20:54 rojasm left #cdk
20:54 rojasm joined #cdk
20:59 egonw hi rojasm
21:07 rojasm for tomorrow what time you have spected to come
21:08 egonw mom
21:10 egonw 11:00 ?
21:14 rojasm when you want!
21:16 rojasm We take a bier 5 oclock if you want. But each two or three week i make sangria. You know I don't like much the Bier
21:16 rojasm And this week I will take again
21:16 rojasm Also You could prove the sangria. dat ist lecker
21:17 egonw i'm sorry... but I don't think I can stay that late tomorrow...
21:18 rojasm o
21:18 rojasm If you want to cancel I can understand that
21:19 rojasm We can leave for other day.
21:19 egonw no, but I only can't stay until the sangria :)
21:46 rojasm left #cdk

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