Camelia, the Perl 6 bug

IRC log for #cdk, 2008-02-05

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All times shown according to UTC.

Time Nick Message
00:41 CIA-18 cdk: miguelrojasch * r10028 /branches/miguelrojasch/reaction/src​/org/openscience/cdk/test/reaction/t​ype/BreakingBondReactionTest.java: added test which test all type of hybridization for C,N,O,F. Not finished.
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06:35 CIA-18 jmol: hansonr * r8950 /branches/v11_4/Jmol/src/org/jmol/ (5 files in 3 dirs):
06:35 CIA-18 jmol: 11.4.RC3 VERSION
06:35 CIA-18 jmol: # bug fix: antialias of images not functionally independent of antialias for display
06:35 CIA-18 jmol: # bug fix: label offset doubled for multiline labels with left/right/center alignment not specified
06:35 CIA-18 jmol: # bug fix: default label offsets mangled by default Front/Group
06:35 CIA-18 jmol: # bug fix: PDB files with missing amino acid carbonyl O cause exception
06:38 CIA-18 jmol: hansonr * r8951 /trunk/Jmol/src/org/jmol/ (29 files in 7 dirs): (log message trimmed)
06:38 CIA-18 jmol: 11.5.4 VERSION
06:38 CIA-18 jmol: # new feature: set delayMaximumMs sets the maximum delay that scripts will use, primarily for testing scripts
06:38 CIA-18 jmol: # new feature: set fontScaling TRUE/FALSE
06:38 CIA-18 jmol: # atom labels and 3D echos then scale properly.
06:38 CIA-18 jmol: # note that the current zoom affects the label size.
06:38 CIA-18 jmol: # bug fix: image writing does not scale fonts properly.
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07:15 rojasm moin
07:31 CIA-18 cdk: miguelrojasch * r10029 /branches/miguelrojasch/reaction/src/org/openscie​nce/cdk/reaction/type/BreakingBondReaction.java: Added some JavaDoc
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08:54 CIA-18 cdk: miguelrojasch * r10030 /branches/miguelrojasch/reaction/src​/org/openscience/cdk/test/reaction/t​ype/BreakingBondReactionTest.java: Added more tests for specific atomType, Mapping, CDKConstants.ACTIVE_CENTER etc..
08:55 rojasm moin
08:55 egonw moin
08:55 jonalv hi
08:56 * egonw is getting some chocolate...
09:11 CIA-18 cdk: miguelrojasch * r10031 /branches/miguelrojasch/reaction/src​/org/openscience/cdk/test/reaction/t​ype/BreakingBondReactionTest.java: added test for O and F cases
09:11 rojasm egonw: when you have time, could you take a look at the test BreakingBondReactionTest only. And discuss about all atomtype and theirs reaction that I put and make sense
09:11 rojasm Those cases that fails I will make a test in test.atomtype.ReactionStructureTest
09:12 egonw ok, hang on... will have a lookt now
09:12 egonw -t
09:21 egonw rojasm: I get 34 tests, 1 error, 7 failing...
09:21 egonw same as you get?
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09:22 rojasm yes! which are failing I will put in test.atomtype.ReactionStructureTest the expected products to see what is happen
09:23 egonw good
09:23 rojasm But one with error is because
09:24 rojasm the checker don't accept the [F+]C
09:24 rojasm but with the smiles is possible to create it
09:24 egonw ack
09:24 egonw ok, this is an excellent start...
09:24 rojasm LonePairChecker
09:24 egonw now I can start working on adding missing atom types...
09:26 egonw https://blueprints.launchpad.net/cdk/
09:27 rojasm :)
09:29 egonw rojasm: I saw prediction-protonation...
09:29 egonw does CDK have functionality to calculate protonation state?
09:30 egonw that is... protonation as function of pKa?
09:30 rojasm not yet
09:30 rojasm I have to intention to implement it
09:31 rojasm the same way as the ionizate thing
09:31 rojasm I think
09:31 egonw ah, ok
10:16 CIA-18 cdk: miguelrojasch * r10032 /branches/miguelrojasch/reaction/src​/org/openscience/cdk/test/reaction/t​ype/BreakingBondReactionTest.java: added in all test the method checkLonePair to put the correctly number of lone pair depending of the charge. Added creatSymbolAndChargeQueryContainer to look at the isomorphism.
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12:24 CIA-18 jmol: hansonr * r8952 /trunk/Jmol/src/org/jmol/ (5 files in 2 dirs): debug comments out
12:34 rojasm egonw: how I can set again atom.hybridization CDKConstants.UNSET. The reason is after the clonation it copies the hybridization too
12:34 egonw setHybridization(CDKConstants.UNSET)?
12:34 rojasm it doesn't work
12:35 egonw how so?
12:35 rojasm only accepts Object in this case IHybrization I would say
12:35 egonw ah...
12:35 rojasm sorry IAtom.Hybridization
12:35 egonw try:
12:35 egonw setHybridization(null)?
12:36 rojasm than the checke in findMatchingAtomType fails
12:36 egonw good
12:36 rojasm must be CDKConstants.UNSET
12:36 egonw that means that it setting works...
12:36 egonw you get a NPE?
12:36 rojasm :)
12:36 egonw that would be a bug
12:38 egonw anyway...good reason to have a IAtomType.Hybridization.UNSET
12:40 rojasm It could be possible to commit that in branches/miguelrojasch/reaction
12:40 rojasm :)
12:41 rojasm I tried allready. But I try again
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13:45 egonw hi dleidert
13:45 dleidert hi
13:48 CIA-18 jmol: hansonr * r8953 /trunk/Jmol/src/org/jmol/ (3 files in 3 dirs): version=11.5.4 # new feature: Spartan input files read as Odyssey format
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14:07 carsten egonw: funny results in the jave vs. other langs shootout
14:07 carsten here every single java app I testes is slow as hell
14:07 egonw why funny?
14:07 egonw ah
14:07 egonw what libs are you using?
14:07 egonw that can make things slow
14:07 carsten egonw: whatever opensuse installs at default
14:07 egonw ah...
14:07 egonw right
14:08 egonw well, one JVM is faster than the other
14:08 egonw the free ones have some way to go
14:08 egonw particularly in the area of graphics...
14:08 egonw AWT using Classpath is known to be slow
14:08 carsten java version "1.5.0_13"
14:08 carsten Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_13-b05)
14:08 carsten Java HotSpot(TM) Client VM (build 1.5.0_13-b05, mixed mode)
14:09 egonw that should be fast enough
14:09 carsten Eclipse is slow as hell for example.
14:09 egonw what program?
14:09 egonw ah,... eclipse
14:09 carsten eg eclipse uzsing bioclipse
14:09 egonw are you sure eclipse is being run with the Sun JVM?
14:09 egonw try:
14:09 carsten I didn't test it recenctly, don't have BC installed here
14:09 egonw bioclipse -vm /path/to/su/java/bin/java
14:09 egonw or
14:09 egonw eclipse -vm /path/to/su/java/bin/java
14:09 egonw su=sun
14:10 carsten tried it some time ago, it was always next to unusable. Recently I tested some kind of git@java application.
14:10 carsten soooooooooooo slow.
14:10 egonw eclipse is rather memory eating...
14:10 egonw not your children, but surely your DIMMs
14:10 carsten yes, my new RAM will arrive tomorrow or the day after
14:10 carsten OOo is also verrrrry mem-hungy
14:11 dleidert carsten: eclipse has a different Java setup!
14:11 * carsten knows nothing about those thing
14:11 carsten s
14:11 dleidert /etc/eclipse/java_home
14:12 dleidert check that you a) use Sun Java there or b) use Eclipse with native compiled code and GIJ - both are very fast
14:12 carsten Is Java now completly OpenSource, by the way?
14:12 egonw dleidert: did you see my blog post today?
14:12 dleidert People are working on Ide(d)Tea, yes
14:12 carsten as in: Can I run eg BC or Eclipse without touch non-OSS software?
14:12 egonw dleidert: really don't understand why the did not use gcj tom compile it to native code
14:13 dleidert egonw: who? (did not yet read your post)
14:13 egonw carsten: java1.7.0 will be... but that's still in alpha/beta though packaged for debian/ubuntu
14:13 dleidert if you speak about eclipse: there is an howto for Eclipse + native code + GCJ/GIJ
14:13 carsten egonw: ah, ok. Will try to remembver that
14:14 carsten Did you read this (FAH @ PS3) http://golem.de/0802/57485.html
14:15 egonw yeah, saw something
14:18 egonw coffee time... bbl
14:32 egonw back
14:34 carsten egonw: I got a gps device (eTrex) and will start contributing to OSM :)
14:34 egonw oh cool
14:34 egonw was is expensive?
14:35 egonw how do you use that on linux?
14:35 carsten with gpsbabel
14:35 carsten http://cgi.ebay.de/ws/eBayISAPI.dll?Vi​ewItem&rd=1&item=230217388184&​amp;ssPageName=STRK:MEWN:IT&ih=013
14:35 carsten egonw: ^^^
14:36 carsten http://www.gpsbabel.org/
14:44 CIA-18 jmol: hansonr * r8954 /trunk/Jmol/src/org/jmol/ (5 files in 2 dirs): # new feature: font [type] [size] [face] [weight] [scaleReference (Angstroms per pixel)]
15:21 CIA-18 cdk: miguelrojasch * r10033 /branches/miguelrojasch/reaction/src​/org/openscience/cdk/test/reaction/t​ype/BreakingBondReactionTest.java: added some miss setting formalCharge
15:24 CIA-18 cdk: miguelrojasch * r10034 /branches/miguelrojasch/reaction/src/org/openscien​ce/cdk/test/atomtype/ReactionStructuresTest.java: added more tests from reaction structures
15:36 CIA-18 jmol: hansonr * r8955 /trunk/Jmol/src/org/jmol/ (7 files in 5 dirs): version=11.5.4 # bug fixes -- font scaling
15:39 jpansanel hehe
15:39 jpansanel Chemical Structures is on Freshmeat
15:41 CIA-18 cdk: miguelrojasch * r10035 /branches/miguelrojasch/reaction/src/org/openscie​nce/cdk/reaction/type/BreakingBondReaction.java:
15:41 CIA-18 cdk: added some special case when the bond is remove (Not finish. waiting to create
15:41 CIA-18 cdk: IAtomType.Hybridization.Unset). In this case the hybridization change when the
15:41 CIA-18 cdk: order of the bond decreased. Eg: C[N+]=C -> CN + [C+]. N atomType going from
15:41 CIA-18 cdk: N.sp2 to N.sp3. But clonation process copy the same hybridization too and it is
15:41 CIA-18 cdk: not possible to chage afterwards.
15:53 egonw rojasm: will fix that bug now...
15:53 egonw and update the branch with trunk afterwards...
16:01 rojasm oh perfect
16:01 rojasm thanks
16:02 rojasm I am playing with zotero a plugin for firefox
16:02 rojasm nice. I think I change against jabref to
16:18 egonw rojasm: pending a resolution on the Hybridization.UNSET, please use: atom.setHybridization(null);
16:19 egonw that works properly
16:19 egonw will commit a unit test for that
16:19 CIA-18 cdk: egonw * r10036 /trunk/cdk/src/org/openscienc​e/cdk/test/AtomTypeTest.java: Added a unit test for unsetting the hybridization
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16:37 CIA-18 jmol: hansonr * r8956 /trunk/Jmol/src/org/jmol/shape/ (5 files): version=11.5.4 # bug fixes -- font scaling
17:05 CIA-18 jmol: hansonr * r8957 /trunk/Jmol/src/org/jmol/vie​wer/TransformManager11.java: debug comments out
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17:44 * egonw is going home
17:44 egonw bye all
17:45 rojasm cu
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18:56 CIA-18 jmol: nicove * r8958 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
19:05 CIA-18 jmol: nicove * r8959 /branches/v11_4/Jmol/src/org/​jmol/viewer/Jmol.properties: Version
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20:02 CIA-18 jmol: aherraez * r8960 /trunk/Jmol-web/source/doc/ (index_en.xml index_es.xml): add Spartan spinput format to list
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22:08 CIA-19 jmol: nicove * r8962 /trunk/Jmol-FAH/projects/p2585.xyz.gz: Folding@Home

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