Camelia, the Perl 6 bug

IRC log for #cdk, 2008-05-25

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All times shown according to UTC.

Time Nick Message
04:23 CIA-31 jmol: hansonr * r9418 /branches/v11_4/Jmol/src/org/jmol/ (shapespecial/LcaoCartoon.java viewer/Jmol.properties): 11.4.4_dev # bug fix: lcaoCartoon naming for multiple centers
04:28 CIA-31 jmol: hansonr * r9419 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs):
04:28 CIA-31 jmol: 11.5.38 VERSION
04:28 CIA-31 jmol: # bug fix: lcaoCartoon naming for multiple centers
04:28 CIA-31 jmol: # new feature: [draw|pmesh|isosurface] xxx* [on|off|delete]
04:28 CIA-31 jmol: # -- turns on, turns off, or deletes all objects of the type starting with "xxx"
04:28 CIA-31 jmol: hansonr * r9420 /trunk/Jmol/src/org/jmol/s​hape/MeshCollection.java:
04:28 CIA-31 jmol: 11.5.38 VERSION
04:28 CIA-31 jmol: # bug fix: lcaoCartoon naming for multiple centers
04:28 CIA-31 jmol: # new feature: [draw|pmesh|isosurface] xxx* [on|off|delete]
04:28 CIA-31 jmol: # -- turns on, turns off, or deletes all objects of the type starting with "xxx"
04:43 CIA-31 jmol: hansonr * r9421 /branches/v11_4/Jmol/src/org/​jmol/viewer/Jmol.properties: 11.4.4 VERSION
04:54 jbrefort joined #cdk
05:04 CIA-31 jmol: hansonr * r9422 /trunk/Jmol/src/org/jmol/viewer/Eval.java: 11.4.4 VERSION (better coding)
05:09 CIA-31 jmol: hansonr * r9423 /trunk/Jmol/src/org/jmol/viewer/Eval.java: 11.4.4 VERSION (better coding)
05:16 CIA-31 jmol: hansonr * r9424 /trunk/Jmol/src/org/jmol/mo​delsetbio/BioPolymer.java: 11.4.4 VERSION (better coding)
07:38 egonw joined #cdk
07:53 CIA-31 cdk: egonw * r11144 /cdk/trunk/src/main/org/opens​cience/cdk/io/MDLWriter.java: Use newLine() to use Win newlines on Win.
08:03 CIA-31 cdk: egonw * r11145 /cdk/branches/cdk-1.0.x/src/org/o​penscience/cdk/io/MDLWriter.java: Use newLine() to use Win newlines on Win.
08:43 CIA-31 cdk: egonw * r11146 /cdk/branches/cdk-1.0.x/src/ME​TA-INF/jchempaint.libdepends: Added missing dependency
08:44 rojasm joined #cdk
08:44 egonw hi rojasm
08:44 egonw good morning
08:45 rojasm good morning egonw
08:51 CIA-31 cdk: miguelrojasch * r11147 /cdk/trunk/src/main/org/openscience/c​dk/dict/data/reaction-processes.owl: added as reference new information in the file ontology reactions
08:52 CIA-31 jmol: nicove * r9425 /trunk/Jmol-FAH/ (9 files in 3 dirs): Folding@Home
09:02 * egonw is playing with the new webdav upload system of SF
09:02 CIA-31 cdk: miguelrojasch * r11148 /cdk/branches/miguelrojasch-IP/ (82 files in 36 dirs): Synchronized with trunk the branches.miguelrojasch-IP, Rev=11098:11147
09:03 rojasm making again the difference between trunk and branch
09:03 egonw ok
09:03 egonw hope this works...
09:03 egonw there seems to be an atom type problem introduced for carbons or oxygens...
09:03 rojasm I hope too
09:03 egonw not sure yet
09:04 egonw I hope this does not interfere with the IP stuff
09:25 CIA-31 jmol: nicove * r9426 /trunk/Jmol-FAH/projects/ (p4540.xyz.gz p4547.xyz.gz p4548.xyz.gz): Folding@Home
09:26 * egonw is uploading CDK 1.0.3
09:26 egonw with a few minor bug fixes
09:31 carsten joined #cdk
09:52 egonw rojasm: ping
09:55 thomas_ku joined #cdk
09:56 egonw hi thomas_ku
09:56 thomas_ku moin
10:01 bag joined #cdk
10:02 egonw hi bag
10:02 bag hi egonw
10:02 * egonw wonders who bag and mansu are
10:02 rojasm egonw ping
10:02 egonw rojasm: replied
10:03 egonw I edited the patch a small bit
10:03 egonw and send you a new version
10:03 rojasm perfect!
10:03 egonw I removed some patches to build.xml etc, which should not be applied to trunk/
10:03 egonw otherwise, please apply to trunk/
10:03 rojasm perfect
10:03 rojasm I do now
10:03 egonw good
10:03 bag egonw: cooking a meal :)
10:04 egonw bag seems to be from germany
10:05 bag yes near Berlin :)
10:05 egonw indeed
10:05 egonw my ping was routed via dusseldorf, frankfurth and berlin :)
10:06 egonw bag: what brings you here? have you emailed to one of the lists earlier?
10:06 bag long way ...
10:07 rojasm egonw for the question:
10:07 rojasm Reversed (or previously applied) patch detected!  Assume -R? [n]
10:07 rojasm enter or I should write yes
10:07 egonw which java file?
10:07 rojasm IPBondDescriptor
10:08 rojasm but I guess it will be more of one this question
10:08 egonw ah, that might have to do because you 'remove' the file...
10:08 egonw I mean... that class does not exist in the branch, right?
10:08 rojasm right
10:08 egonw ok, make a note on paper to remove this file from trunk with 'svn remove' later...
10:08 egonw as the patch won't do that..
10:08 egonw then type "yes"
10:08 bag egonw: no i'm fairly new to CDK, indeed i use openbabel but the openbabel channel is non existent ;)
10:08 rojasm perfect
10:08 egonw to apply the reverse patch
10:09 egonw bag: ah, ic
10:09 egonw well, welcome ! :)
10:09 bag egonw: Where do you come from?
10:09 bag egonw: thanks!
10:10 egonw niederlande
10:10 egonw bag: http://chem-bla-ics.blogspot.com/
10:10 bag a neighbor, nice
10:13 bag nice blog, so much interesting stuff
10:13 egonw thanx
10:14 bag and KDE User ;)
10:15 egonw 100%
10:15 egonw even a bit of KDE developer
10:15 egonw not much, just a bit
10:15 egonw was GSoC mentor for KDE last year
10:15 egonw for Strigi
10:16 bag sounds great
10:17 egonw we have a chemistry project for Strigi
10:17 bag I'm a Tracker user, but i know the Strigi Project and a few devs from irc
10:17 egonw so that metadata and even chemistry for chemical formats gets indexed too
10:17 bag yeah, i'm reading the blog to that topic :)
10:17 egonw ha, who do you know on #strigi?
10:18 bag no only if the strigi devs pop up on #tracker or on xesam list :)
10:18 bag are you a bioinformatics-student?
10:19 egonw no, a chemoinformatics post-doc
10:19 egonw now in the field of bioinformatics, though
10:19 egonw small molecule bioinformatics
10:19 egonw metabolomics to be precise
10:21 bag PostDoc, congratulation :)
10:22 bag oh i think i must go back in the kitchen ;) see you later
10:22 egonw ok, cu
10:23 * egonw has to leave soon too
10:23 egonw but anxiously waiting for patches from miguelrojasch and vedina
10:23 CIA-31 cdk: egonw * r11149 /cdk/branches/cdk-1.0.x/build.props: Made CDK 1.0.3 and JChemPaint 2.3.3 releases
10:25 CIA-31 cdk: egonw * r11150 /cdk/tags/jchempaint-2.3.3/: Tagged JCP 2.3.3.
10:26 CIA-31 cdk: egonw * r11151 /cdk/tags/cdk-1.0.3/: Tagged CDK 1.0.3.
10:26 egonw OK, lunch time here too
10:27 egonw bbl
10:43 CIA-31 jmol: nicove * r9427 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
10:50 CIA-31 jmol: nicove * r9428 /branches/v11_4/Jmol/src/org/​jmol/viewer/Jmol.properties: Version
11:01 edrin joined #cdk
11:34 egonw joined #cdk
11:37 egonw rojasm: how are things getting along?
12:23 mansu joined #cdk
12:51 edrin joined #cdk
13:16 CIA-31 jmol: nicove * r9429 /trunk/Jmol-FAH/projects/p4551.xyz.gz: Folding@Home
13:33 rojasm egonw almost finish
13:34 rojasm finished
13:34 rojasm it is just in commit process
13:35 rojasm But there is a new test testCalculate_NoModifications which produces some errors
13:36 rojasm and I also modified the build.xml file which it was missed to pack the ionpot module
13:36 CIA-31 cdk: miguelrojasch * r11152 /cdk/trunk/ (77 files in 23 dirs): Merged from brunch to trunk: miguelrojasch-IP -> trunk/
14:14 CIA-31 cdk: archvile18 * r11153 /cdk/trunk/src/main/org/openscience/cdk/arom​aticity/CDKHueckelAromaticityDetector.java: Made CDKHueckelAromaticityDetector aware of atom type "N.minus.planar3". Fixes test case SmilesParserTest.testPyrroleAnion1().
14:51 edrin where is egon?
14:51 CIA-31 cdk: vedina * r11154 /cdk/trunk/src/ (6 files in 2 dirs):
14:51 CIA-31 cdk: Random file access. Reads the file as a text and builds an index file in a
14:51 CIA-31 cdk: temporary directory, if the index file doesn't already exist. The index stores
14:51 CIA-31 cdk: offset, length and a third field reserved for a future use. Subsequent access
14:51 CIA-31 cdk: for a record N uses this index to seek the record and return the molecule.
14:51 CIA-31 cdk: Useful for large files.
15:00 edr1n joined #cdk
15:14 carsten joined #cdk
15:14 carsten Moin. Anyone here doing Folding at Home?
15:36 egonw joined #cdk
15:39 rojasm egonw: I commited!
15:39 egonw yes, I saw
15:39 egonw congrats!
15:39 rojasm some remarks that it is failing
15:39 egonw and a big step closer to CDK 1.2
15:40 edr1n hi egonw
15:40 egonw hi edr1n
15:40 edrin egonw: did you review the proposal to send it to stpeter?
15:41 egonw with the comments that I mention applied?
15:41 rojasm what is test testCalculate_NoModifications supposed to do
15:41 egonw edrin: I did not have time to apply my changes :(
15:41 egonw rojasm: make sure the input is not changed...
15:42 rojasm because in charge calculation was applied in each atom
15:42 edrin egonw: when will you have time to make the changes?
15:42 egonw right, so I clone must be used in the QSAR descriptor
15:42 egonw edrin: can't say
15:43 rojasm egonw: ok! it should be cloned those container to be calculate the descriptor
15:43 egonw or the original charges restored afterwards...
15:44 egonw but clone is easier
15:45 egonw edrin: I'll try to make some time tomorrow...
15:45 * egonw has to go offline to make dinner
15:46 egonw won't be online tonite, so cu tomorrow
15:46 edrin egonw: i will do it
15:46 egonw edrin: ok, thanx
15:46 edrin today or tomorrow
15:46 edrin according to your mail
15:46 edrin and then send it to stpeter
15:46 egonw ok
15:46 edrin egonw: it is not final then anyway
15:47 edrin we can still change things
15:47 egonw I know
15:47 egonw ok, bye all
15:49 CIA-31 cdk: egonw * r11155 /cdk/trunk/src/test/org/openscience/cdk​/atomtype/CDKAtomTypeMatcherTest.java: Added a test for a fail in the ChiPathDescriptor: CDK atom types are perceived correctly.
15:49 CIA-31 cdk: egonw * r11156 /cdk/trunk/src/main/org/ope​nscience/cdk/Molecule.java: Added missing ',' in toString() output
15:52 CIA-31 cdk: miguelrojasch * r11157 /cdk/branches/miguelrojasch-IP/: Removed branch to closed project IP
16:00 CIA-31 cdk: miguelrojasch * r11158 /cdk/branches/miguelrojasch-ReactionOntology/: Copied new branch.miguelrojasch-ReactionOntology. Definition: The reactions handled from ontology dictionary.
16:03 carsten_ joined #cdk
16:26 rojasm joined #cdk
17:40 CIA-31 cdk: miguelrojasch * r11159 /cdk/branches/miguelrojasch​-ReactionOntology/.project: changed name project
18:12 CIA-31 cdk: vedina * r11160 /cdk/trunk/src/main/org/openscience/c​dk/io/random/RandomAccessReader.java: fixed to get tmp dir via System.getProperty("java.io.tmpdir")
20:49 bag joined #cdk
21:18 mansu egnow what time are you usually around?
22:28 CIA-31 joined #cdk

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