Camelia, the Perl 6 bug

IRC log for #cdk, 2007-08-22

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All times shown according to UTC.

Time Nick Message
01:23 CIA-1 jmol: gutow * r8130 /branches/gutow-webmaker/ (15 files in 3 dirs): (log message trimmed)
01:23 CIA-1 jmol: All fixes to webexport:
01:23 CIA-1 jmol: fixes to ScriptButton and PopIn templates to make them consistent.
01:23 CIA-1 jmol: fixed panel element widths.
01:23 CIA-1 jmol: fixed code so that % spinner shows up for ScriptButton tab and height and width spinners show up for the PopIn tab.
01:23 CIA-1 jmol: changed time-stamp function to generate a stamp more appropriate to generation by a function within Jmol.
01:23 CIA-1 jmol: fixed errors leading to failure to create javascript only pages.
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06:45 rojasm Moin
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07:59 thomas_ku moin
08:01 egonw joined #cdk
08:01 egonw moin
08:05 thomas_ku moin egonw
08:05 thomas_ku Egonw:
08:05 egonw hi thomas_ku
08:05 egonw yes, we need to chat
08:05 thomas_ku If I want to revert a cvs commit how do I do this
08:05 egonw ah... don't think you can...
08:06 egonw but you can commit the reverse patch
08:06 egonw which is effectively the same
08:06 thomas_ku no it is for another projekt
08:06 thomas_ku so there is no reverse posibility?
08:06 egonw you should get the 'cvs diff -u' of the commit(s) you want to revert
08:06 egonw apply that with 'patch'
08:07 egonw and than commit again
08:07 thomas_ku ok so there is no easy way to do this! right?
08:08 egonw no
08:08 egonw it involves some manual work
08:09 thomas_ku ok thanks
08:10 thomas_ku I thought that this was possible easyly!
08:11 egonw well, you could 'merge' that merge directly...
08:12 thomas_ku I thought there of something linke undo And I thought that this kind of functionality is in such a version control system
08:12 thomas_ku linke = like
08:13 egonw no, sorry...
08:13 egonw not in svn or cvs
08:13 egonw a few other vcs's do have it, though
08:13 thomas_ku ok but it would be a cool feature
08:13 thomas_ku sourcesafe for example as far as I know
08:16 thomas_ku egonw is there something you want to chat with me?
08:18 egonw yes, I plan to make some CDK based webservices, mass spectroscopy oriented; interested?
08:18 thomas_ku yes of course
08:19 thomas_ku But I fear that I will have not much time to contribute stuff
08:19 egonw ok, good
08:19 egonw no worry...
08:19 egonw I will likely try them with Taverna, so might ask you to give it a go for some feedback at some point...
08:20 thomas_ku no prob
08:21 thomas_ku will be back in 20 min have to go to the bakery to get some bread because it is not raining currently
08:32 CIA-1 bioclipse: jonalv * r3711 /trunk/plugins/net.bioclipse.statistics/s​rc/net/bioclipse/editors/GridEditor.java: The hack for the index related bugg in Grid was needed on more places
08:38 thomas_ku egonw:what will the webservice do exactly?
08:38 egonw accurate mass to a list of molecular formula
08:38 egonw calculate accurate mass
08:38 egonw isotopic pattern calculation
08:39 egonw those three to start with...
08:39 thomas_ku ok great
08:39 thomas_ku will open these webservice to the public?
08:40 egonw not sure
08:40 egonw the source, of course
08:41 thomas_ku it is a question of hosting the webservice?
08:42 egonw yes
08:43 egonw but it could be deployed anywhere...
08:43 egonw and some redundancy would be good anyway...
08:44 thomas_ku yes of course, but this is everytime the problem if you have webservice which properly will need a lot of cpu resources...
08:47 egonw these three should be fairly cheap
09:11 CIA-1 blueobelisk: egonw * r91 /operator/ (11 files in 5 dirs): Placed my GPL3 Operator scripts online
09:12 CIA-1 blueobelisk: egonw * r92 /operator/tags/: Added missing tags/ dir
09:13 CIA-1 blueobelisk: egonw * r93 /operator/ (branches/1.0/ branches/1.1/ tags/1.0/ tags/1.1/): Moved to correct dir
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11:11 CIA-1 cdk: thomaskuhn * r8697 /trunk/cdk/src/org/openscience/cdk/isomorphi​sm/matchers/QueryAtomContainerCreator.java: Add a method to the query atom container creator which creates an queryatomcontainer. This replaces each pseudoatom to an anyatom.
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11:29 egonw http://neksa.blogspot.com/200​7/08/mdl-sd-file-support.html
11:29 lambdabot2 Title: Chemistry and Biology support, KDE/Strigi GSoC project: MDL SD file support
11:30 egonw carsten: alexandrs first result blog with screenshots :)
11:33 carsten Moin folks
11:33 egonw hi :)
11:38 carsten nice blog, nice technologie
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11:40 egonw hi neksa
11:41 egonw http://kemistry-desktop.blogspot.com/2007/08​/mdl-sd-files-as-folders-opening-single.html
11:41 lambdabot2 Title: kemistry desktop environment: MDL SD files as folders: opening a single molfile, http://tinyurl.com/3bvlyj
11:42 neksa hi egonw
11:43 neksa egonw: there is one more post about PNG
11:44 egonw yes, reading it now
11:45 neksa I made SD post as a tutorial, because it's not that easy to get the idea of how it all works once you want to write your own stream provider and/or analyzer
12:35 egonw carsten: btw, OSRA is now on SourceForge... so, if you feel like a bit of cmake magic...
12:35 egonw or otherwise daniel might beat you to it with some autotools magic
12:36 carsten yeah, autotools are great for this, that make platform indepent hacking so easy. I let him do the autohell dance :)
12:44 jpansanel moin
13:04 CIA-1 cdk: fichte01 * r500 /trunk/protonprediction/Data/ (8 files in 2 dirs):
13:24 CIA-1 jmol: nicove * r8131 /trunk/Jmol-FAH/projects/p3731.xyz.gz: Folding@Home
13:26 CIA-1 blueobelisk: pansanel * r94 /structures/trunk/tools/ (cmlhandler.py cmlwriter.py): Handle new identifier tag
13:31 jpansanel egonw : how would you translate 'Monoisotopic weight' in Dutch ?
13:32 egonw no idea
13:32 egonw we talk too much in ENglish here
13:32 jpansanel :)
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13:57 CIA-1 cdk: mario_baseda * r8698 /trunk/cdk-taverna/src/main/java/org/openscience/​cdk/applications/taverna/qsar/model/weka/action/ (10 files): Add some comment
14:01 CIA-1 cdk: egonw * r8699 /trunk/cdk/src/data/mdl/shortest_path_test.mol: Added test file by Volker (see cdk-user) for the shortest path problem
14:18 CIA-1 cdk: egonw * r8700 /trunk/cdk/src/org/openscience/cd​k/test/graph/PathToolsTest.java: JUnit test provided by Volker Haehnke (haehnke - bioinformatik uni-frankfurt de), somewhat rewritten.
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16:44 CIA-1 jmol: nicove * r8132 /trunk/Jmol-FAH/projects/p3695.xyz.gz: Folding@Home
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17:02 CIA-1 cdk: steinbeck * r8701 /trunk/cdk/src/org/openscien​ce/cdk/graph/PathTools.java: Renamed a variable to comply with http://en.wikipedia.org/wiki/Dijkstra's_algorithm
17:02 lambdabot2 Title: Dijkstra's algorithm - Wikipedia, the free encyclopedia
17:03 steinbeck joined #cdk
17:03 steinbeck H folks
17:03 steinbeck h==Hi
17:05 egonw hi steinbeck
17:05 * egonw is not really here...
17:09 steinbeck Hi egonw
17:09 steinbeck did my commit show up here?
17:10 steinbeck thought you could see it. Was just a min ago or so
17:24 egonw yes it was
17:24 steinbeck thanks
17:24 egonw [2007-08-22 19:02:34] <CIA-1> cdk: steinbeck * r8701 /trunk/cdk/src/org/openscien​ce/cdk/graph/PathTools.java: Renamed a variable to comply with http://en.wikipedia.org/wiki/Dijkstra's_algorithm
17:24 egonw [2007-08-22 19:02:35] <lambdabot2> Title: Dijkstra's algorithm - Wikipedia, the free encyclopedia
17:24 lambdabot2 Title: Dijkstra's algorithm - Wikipedia, the free encyclopedia
17:30 steinbeck thanks
17:32 egonw steinbeck: how was the BO meeting/dinner ?
17:33 steinbeck will be in 5 hours :-)
17:33 egonw oh... I thought Tue
17:35 egonw btw: http://neksa.blogspot.com/
17:35 lambdabot2 Title: Chemistry and Biology support, KDE/Strigi GSoC project
17:36 egonw latest two blogs are very cool
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17:46 steinbeck That looks extremely cool indeed!!!
18:01 CIA-1 cdk: egonw * r501 /trunk/schematron/ (33 files in 3 dirs): Added Schematron-based NMRShiftDB convention, as used in the CMLSpect article
18:15 neksa steinbeck: thanks for your chemistry classes in CUBIC :)
18:18 * egonw is going to relocate to hist laptop again
18:18 egonw brb
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18:26 steinbeck neksa: welcome :-)
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19:39 CIA-1 cdk: shk3 * r502 /trunk/protonprediction/Data/input/dataX.txt: new dataX
19:44 neksa egonw: why do you think there should not be SMILES in Strigi-chemical? obsolete?
19:44 egonw neksa: was actually away... watching Bones..
19:45 egonw but it's a break now :(
19:45 egonw s/:(/:)/
19:45 egonw SMILES is not unique...
19:45 neksa nice regexp
19:45 egonw a SMILES can start with any of the atoms inthe molecules...
19:45 egonw and the arbitrarily pick the next neighbor
19:46 egonw so some N^2 possibilities at least or so
19:46 egonw regexp or anything like that will never work
19:46 egonw that's why we use finger prints
19:47 egonw OK, back to TV
19:47 neksa thanks
19:47 neksa egonw: InChI for unique queries only?
19:47 egonw yes
19:47 egonw because InChI does not allow substructure search
19:47 egonw or similarity search
19:48 egonw ok, really back to tv now
19:57 shk3 tv?
19:57 shk3 better do some hacking...
20:12 * egonw has done enough hacking for today...
20:30 egonw actually... going to bed...
20:30 egonw shk3: did you get my comments on the proof?
20:31 shk3 yes
20:31 egonw ok, good
20:31 shk3 I will submit them all together, next week or so
20:31 egonw ack
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21:48 CIA-1 cdk: shk3 * r503 /trunk/protonprediction/Data/input/ (data.txt dataX.txt dataY.txt): new data
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22:44 CIA-1 cdk: shk3 * r504 /trunk/nmrshiftdb/src/vmtemplat​es/portlets/html/user-order.vm: made the assignment button a link
22:55 CIA-1 cdk: shk3 * r8702 /trunk/cdk/src/org/openscience/c​dk/smiles/SmilesGenerator.java: added my changes (use of aromaticity possible) to trunk
22:56 CIA-1 cdk: shk3 * r8703 /branches/cdk-1.0.x/src/org/openscie​nce/cdk/smiles/SmilesGenerator.java: added rajarshis changes to 1.0 branch

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