Camelia, the Perl 6 bug

IRC log for #cdk, 2007-11-16

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All times shown according to UTC.

Time Nick Message
03:02 CIA-16 jmol: hansonr * r8627 /trunk/Jmol/src/org/jmol/ (3 files in 3 dirs): version=11.3.45_dev # bug fix: new boundbox command with small numbers of atoms
03:18 CIA-16 jmol: hansonr * r8628 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.45 VERSION
03:50 Conrad joined #cdk
04:19 CIA-16 jmol: hansonr * r8629 /trunk/Jmol/src/org/jmol/viewer/Viewer.java: 11.3.45 VERSION
06:26 jbrefort joined #cdk
06:37 rojasm joined #cdk
07:30 CIA-16 cdk: miguelrojasch * r9442 /branches/miguelrojasch/mf/src​/org/openscience/cdk/formula/ (IMolecularFormula.java IMolecularFormulaSet.java): added more methods in interface MolecularFormula
08:05 egonw joined #cdk
08:18 egonw rojasm: around?
08:20 jpansanel joined #cdk
08:21 rojasm moin egonw
08:21 rojasm yes I am
08:21 egonw I'm sending you an email...
08:21 rojasm ok
08:23 egonw sent
08:24 egonw I will relocate to my other desk now...
08:24 egonw will be back in some 15 minutes...
08:24 rojasm perfect
08:39 egonw joined #cdk
08:44 egonw rojasm: did you get my email?
08:45 egonw no, you did not...
08:45 egonw miguel...
08:45 egonw please update your forward email address for your SF account...
08:46 egonw it still tries to send email to the CUBIC
09:09 egonw coffee time
09:28 rojasm Sorry egonw now I am here. I received
09:29 egonw OK good...
09:29 egonw btw, got news on a possible visit days?
09:30 rojasm I don't think it is good idea to have too many Interfaces
09:31 rojasm I didn't ask I ask now and I came in 5 minutes with the data :).
09:31 egonw I prefer more, but clean interfaces...
10:11 rojasm egonw: 7 should be perfect for us
10:11 rojasm 7th
10:11 rojasm December
10:21 jonalv joined #cdk
10:32 egonw rojasm: I think that should be fine...
10:32 egonw what style? regular work meeting, or a bit more formal?
10:36 rojasm I think better regular work meeting like you are here
10:39 egonw OK, good
10:39 egonw then 7th is fine
10:39 rojasm :)
11:03 jpansanel egonw : I've open a 3MB PDB structure (DNA) strand with Jmol.
11:03 jpansanel It's very fast
11:03 jpansanel incredible
11:35 egonw :)
11:35 egonw how many atoms?
12:18 jonalv joined #cdk
12:18 masak joined #cdk
12:29 CIA-16 blueobelisk: egonw * r162 /cb/trunk/generate_summaries.pl: Some feedback on what it is doing, and only delete the old when really needed... which should keep the website more populated during updates which take rather long
12:31 jpansanel egonw : 50743 (without hydrogens)
12:52 egonw not quite the limit yet
13:39 masak egonw: does cdk do something w/ InChI? or is it all SMILES?
13:39 egonw InChI is supported
13:39 masak ok, good
13:53 CIA-16 blueobelisk: egonw * r163 /cb/trunk/get_inchikey.pl: Added a time-out
13:54 CIA-16 blueobelisk: egonw * r164 /cb/trunk/parse_wp_links.pl: First test cheapest (=fastest) + more descriminative (moved test for wikipedia link to SQL statement)
14:34 egonw masak: what do you plan to do?
14:38 masak egonw: on my spare time, I'm writing on this alkane naming program which I might have told you about
14:39 egonw ah...
14:39 masak I started working on it before I found SMILES so it uses a homegrown format for describing molecules
14:39 egonw yes, I think you did...
14:39 egonw yeah, try opensmiles.com
14:39 masak in the weekend I plan to convert it to using SMILES
14:39 egonw or .org...
14:39 masak egonw: yep, I know
14:40 masak so I'm mainly just curious about what this other InChI, that I just found, is all about
14:57 CIA-16 cdk: rajarshi * r9443 /trunk/cdk/src/org/openscience/cdk​/renderer/progz/TestRenderer.java: Got rid of smiles parsing since it's in a different moduke
15:10 steinbeck joined #cdk
15:10 egonw hi steinbeck
15:11 CIA-16 bioclipse: carl_masak * r4253 /trunk/playground/plugins/net.bioclipse.base2/: Initial import.
15:13 CIA-16 bioclipse: carl_masak * r4254 /trunk/playground/plugins/net.bioclipse.base2/ (19 files in 9 dirs): Initial import.
15:21 steinbeck hi egonw
15:21 steinbeck egonw: just saw that the PI for this nih grant does not need be US-based
15:21 egonw cool
15:22 egonw yes, let's do that
15:24 steinbeck Put the deadline for the letter of intent in my calendar. Will have to study how that should look like. Would be helpful to see if Rajarshi and David have experience with the procedure.
15:25 egonw right
15:26 * steinbeck is in Heidelberg at EMBL
15:27 steinbeck Got to leave for the next meeting
15:27 steinbeck cheers
15:27 egonw bye
15:27 steinbeck left #cdk
15:43 CIA-16 cdk: egonw * r9444 /trunk/cdk/build.xml: Added detection of Java 1.7
15:46 CIA-16 cdk: egonw * r9445 /branches/egonw/remove-non-cdkatomtype-code/ (3 files in 3 dirs): Synched with trunk up to rev 9444
16:28 CIA-16 bioclipse: jonalv * r4255 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (6 files in 2 dirs): Made mock implementation of tree view.
16:44 CIA-16 bioclipse: ospjuth * r4256 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (8 files in 2 dirs): Updated intro page a little...
16:45 CIA-16 bioclipse: ospjuth * r4257 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (4 files in 3 dirs): Completed refactoring to net.bioclipse.ui
18:40 egonw joined #cdk
20:17 rguha joined #cdk
20:17 rguha hi
20:18 rguha either the nightly code is buggy or else commit 9445 is scary :)
20:18 egonw hi rguha
20:18 egonw 9445 was J1.7 support?
20:18 egonw what error message do you get?
20:19 rguha No. old fails fixed since r9445 = 1
20:19 rguha No. new fails since r9445 = 107
20:19 egonw weird...
20:19 rguha yes, individual module stats look OK
20:19 egonw 9445 was only in branches/egonw/remove... :
20:19 egonw http://cdk.svn.sourceforge.net/vie​wvc/cdk?view=rev&revision=9445
20:20 egonw 9444 was in trunk
20:20 rguha right, but subversion will increment the version for any change to the repo
20:20 egonw and 9443 was yours to fix that module problem
20:20 rguha right
20:20 egonw yeah, sure
20:20 rguha probably a bug in the nightly code
20:20 egonw so the build.xml update must have caused it
20:20 rguha can't see how that'd happen
20:21 egonw http://cdk.svn.sourceforge.net/viewvc/cdk/trunk/c​dk/build.xml?r1=9444&r2=9443&pathrev=9444
20:21 egonw indeed... patch seems rather clean
20:22 rguha ah well I'll look at nightl
20:29 CIA-16 jmol: nicove * r8630 /trunk/Jmol/src/org/jmol/vi​ewer/PropertyManager.java: Warning
20:43 CIA-16 jmol: nicove * r8631 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
20:52 CIA-16 cdk: egonw * r9446 /branches/egonw/remove-non-cdkatomtyp​e-code/src/org/openscience/cdk/charge​s/GasteigerPEPEPartialCharges.java: Perception already done, don't mess it up... maybe a good idea to add that as extra test: add explicit hydrogens, do another perception and test if things still work out nicely...
21:05 CIA-16 cdk: egonw * r9447 /branches/egonw/remove-non-cdkatomtype-code.patch: Patch to remove the HueckelAromaticityDetector
21:22 CIA-16 cdk: egonw * r9448 /branches/miguelrojasch/mf​/src/org/openscience/cdk/ (5 files in 2 dirs): Renamed blaElement() to blaIsotope(), cleaned IAdductFormula interface (by cherry picking only those methods from IMolecularFormula which are appropriate) and update the two implementing classes
22:11 CIA-16 cdk: egonw * r9449 /trunk/cdk/src/org/openscience/cdk​/atomtype/CDKAtomTypeMatcher.java: Added perception of isolated O atoms (=water)
22:27 CIA-16 cdk: egonw * r9450 /branches/egonw/remove-non-cdkatom​type-code/src/org/openscience/cdk/​atomtype/CDKAtomTypeMatcher.java: Synched with trunk 9449

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