Camelia, the Perl 6 bug

IRC log for #cdk, 2008-07-17

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All times shown according to UTC.

Time Nick Message
00:29 CIA-33 cdk: rajarshi * r11605 /cdk/branches/rguha_vdw_removal/: Removed the VdW branch since the changes have been merged into trunk
00:36 CIA-33 cdk: rajarshi * r11606 /cdk/branches/rajarshi-descnames/:
00:36 CIA-33 cdk: Created a new branch in which the descriptor interface will be refactored to
00:36 CIA-33 cdk: allow retrieval of names without calculation and to make sure that no descriptor
00:36 CIA-33 cdk: throws an exception. Rather exceptions will be returned in the DescriptorValue
00:36 CIA-33 cdk: object
01:32 CIA-33 cdk: rajarshi * r11607 /cdk/branches/rajarshi-descnames/src/ (2 files in 2 dirs):
01:32 CIA-33 cdk: Updated DescriptorValue to have a field to hold an exception object. We
01:32 CIA-33 cdk: specifically hold only one exception object since anytime a descriptor throws an
01:32 CIA-33 cdk: exception we will be returning, so only that ezception need be stored
01:36 CIA-33 cdk: rajarshi * r11608 /cdk/branches/rajarshi-descnames/src/main/​org/openscience/cdk/qsar/IDescriptor.java:
01:36 CIA-33 cdk: Updated to provide a method to get descriptor names. This is useful, since it
01:36 CIA-33 cdk: will allow retrieval of names without a priori calculation. Obviously, the
01:36 CIA-33 cdk: number of names will depend on the parameter settings (if any). So if this is an
01:36 CIA-33 cdk: issue, make sure to set parameters and then call the method. Otherwise the names
01:36 CIA-33 cdk: are constructed from default parameters (if necessary)
01:42 CIA-33 cdk: rajarshi * r11609 /cdk/branches/rajarshi-descnames/src/main/org/o​penscience/cdk/qsar/IMolecularDescriptor.java: Modifed the definition of calculate() so that it does not throw an exception. All exceptions will be caught and returned via a DescriptorValue object
02:20 CIA-33 cdk: rajarshi * r11610 /cdk/branches/rajarshi-descnames/src/ (10 files in 2 dirs): Updated descriptors starting with A to conform to the new policy on not throwing exceptions and providing descriptor names without calculation
02:33 CIA-33 cdk: rajarshi * r11611 /cdk/branches/rajarshi-descnames/src/main/org​/openscience/cdk/qsar/descriptors/molecular/ (3 files): Updated descriptors starting with B to conform to the new policy on not throwing exceptions and providing descriptor names without calculation
03:13 CIA-33 cdk: rajarshi * r11612 /cdk/branches/rajarshi-descnames/src/main/org​/openscience/cdk/qsar/descriptors/molecular/ (6 files): Updated descriptors starting with C to conform to the new policy on not throwing exceptions and providing descriptor names without calculation
03:22 CIA-33 cdk: rajarshi * r11613 /cdk/branches/rajarshi-descnames/src/main/org​/openscience/cdk/qsar/descriptors/molecular/ (3 files): Updated descriptors starting with E, F and G to conform to the new policy on not throwing exceptions and providing descriptor names without calculation
03:31 CIA-33 cdk: rajarshi * r11614 /cdk/branches/rajarshi-descnames/src/main/org​/openscience/cdk/qsar/descriptors/molecular/ (2 files): Updated descriptors starting with H to conform to the new policy on not throwing exceptions and providing descriptor names without calculation
03:36 CIA-33 cdk: rajarshi * r11615 /cdk/branches/rajarshi-descnames/src/main/org​/openscience/cdk/qsar/descriptors/molecular/ (2 files): Updated descriptors starting with I and K to conform to the new policy on not throwing exceptions and providing descriptor names without calculation
03:58 CIA-33 cdk: rajarshi * r11616 /cdk/branches/rajarshi-descnames/src/main/org​/openscience/cdk/qsar/descriptors/molecular/ (4 files): Updated descriptors starting with L to conform to the new policy on not throwing exceptions and providing descriptor names without calculation
04:05 CIA-33 cdk: rajarshi * r11617 /cdk/branches/rajarshi-descnames/src/main/org​/openscience/cdk/qsar/descriptors/molecular/ (4 files): Updated descriptors starting with M and P to conform to the new policy on not throwing exceptions and providing descriptor names without calculation
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04:17 CIA-33 cdk: rajarshi * r11618 /cdk/branches/rajarshi-descnames/src/main/org​/openscience/cdk/qsar/descriptors/molecular/ (4 files): Updated descriptors starting with R, T and V to conform to the new policy on not throwing exceptions and providing descriptor names without calculation
04:37 CIA-33 cdk: rajarshi * r11619 /cdk/branches/rajarshi-descnames/src/main/org​/openscience/cdk/qsar/descriptors/molecular/ (6 files): Updated remaining descriptors to conform to the new policy on not throwing exceptions and providing descriptor names without calculation
04:46 rguha joined #cdk
04:46 egonw hi rguha
04:46 rguha hi
04:46 rguha how're things going?
04:47 egonw in general, or something in particular?
04:47 * egonw hates 'how are you' questions...
04:47 egonw never get them properly
04:47 rguha ha ha
04:47 rguha just generally
04:47 rguha btw when are you moving to Uppsala?
04:47 egonw september
04:48 rguha JArl's group?
04:48 egonw yes
04:48 rguha nice
04:48 egonw so, working hard now gettings things finished in Wageningen
04:48 rguha aah
04:49 egonw who are, btw, looking for a qualified bio/chemoinformatician
04:49 egonw seen the ad in my blog?
04:49 rguha yes, saw that
04:49 egonw you were looking in USA, but wanted to mentioned it nevertheless
04:49 rguha your replacemnent :)
04:49 egonw and of Mark Fiers
04:49 egonw our workflow dude
04:49 rguha thanks, but I'll ahve to stay here
04:49 rguha aah
04:49 egonw he wrote, singlehanded, a workflow tool, Cyrille2
04:49 egonw web based
04:50 egonw looks quite nice
04:50 egonw but no community like Taverna
04:50 egonw and very performant
04:50 egonw they use it for large scale sequence annotation and sorts
04:50 egonw see BMC BioInf
04:50 egonw [06:49] <rguha> thanks, but I'll ahve to stay here
04:50 egonw at Indiana?
04:50 rguha the US
04:51 egonw did they manage an extension, fixed position, or so?
04:51 rguha impressive!
04:51 egonw ah, ok
04:51 rguha things wll get settled by the end of August
04:51 egonw ok, will ask then :)
04:51 rguha :)
04:51 rguha btw, did you se the mail wrt names for non-molecular descriptors?
04:52 egonw anyway... if you happen to know someone, post-doc range, who might be interested, and who knows his way around in workflows...
04:52 egonw please let me know
04:52 egonw I hope at least Thomas will apply... (hint hint ;)
04:52 rguha sure
04:54 egonw will file the RFE now
04:54 egonw on that performance issue
04:55 rguha thanks
04:55 CIA-33 cdk: rajarshi * r11620 /cdk/branches/rajarshi-descnames/src/ma​in/org/openscience/cdk/qsar/descriptors​/protein/TaeAminoAcidDescriptor.java: Updated descriptor to conform to the new policy on not throwing exceptions and providing descriptor names without calculation
04:55 egonw ok, got to go and catch a train
04:55 jbrefort joined #cdk
04:56 rguha bye
04:56 egonw bbl
04:56 egonw bye
04:58 CIA-33 cdk: rajarshi * r11621 /cdk/branches/rajarshi-descnames/src/main/org​/openscience/cdk/qsar/IAtomicDescriptor.java: Updated interface to emove exceptions on calculate()
05:03 bag joined #cdk
05:10 CIA-33 jmol: hansonr * r9605 /trunk/Jmol/src/org/jmol/ (shapespecial/Draw.java util/Quaternion.java): new Quaternion algorithm uses double precision
05:11 CIA-33 jmol: hansonr * r9606 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: new Quaternion algorithm uses double precision
05:15 CIA-33 cdk: rajarshi * r11622 /cdk/branches/rajarshi-descnames/src/main/o​rg/openscience/cdk/qsar/descriptors/atomic/ (4 files): Updated atom descriptors starting with A, to not throw eceptions and to return names outside of calculate()
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06:55 thomas_ku moin
07:01 rojasm joined #cdk
07:05 egonw hi rojasm, thomas_ku
07:05 egonw and masak
07:05 masak egonw: hiya
07:05 egonw rojasm: please check the discussion on the QSAR API... and the commits from Rajarshi in the branch
07:30 egonw joined #cdk
08:35 zarah joined #cdk
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09:59 malick joined #cdk
10:57 zarah joined #cdk
10:59 zarah joined #cdk
11:00 zarah joined #cdk
12:22 steinbeck joined #cdk
12:22 steinbeck shk3: around?
12:33 egonw he was just at #bioclipse
12:33 shk3 we already met
12:45 egonw ack
13:03 thomas_ku hi steinbeck
13:13 steinbeck Hi thomas_ku
13:45 egonw steinbeck: no, that did not help
13:45 egonw same error on cdknews.org
13:46 steinbeck Same error but with different number?
13:46 egonw no, don't think so
13:46 steinbeck hm - mom
13:47 egonw I don't seem able to make steinbeck an admin
13:47 egonw ah, wait, I think I can
13:47 egonw that does not solve the missing admin pwd though :)
13:48 egonw ok, the steinbeck account should now be journal manager too
13:48 steinbeck well, the username should be enough. Is it "admin"
13:48 egonw well, 'steinbeck' is journal manager now too
13:48 egonw which should allow you to reproduce the problem with #31
13:49 steinbeck what was the url again? Just deleted your mail :-)
13:49 egonw http://www.steinbeck-molecular.de/cdknew​s/index.php/CDKNews/editor/submission/31
13:49 zarah egonw's link is also http://tinyurl.com/6x33x6
13:49 steinbeck thought I had solved it :-)
13:51 steinbeck I can open this sdf
13:51 egonw pdf, you mean?
13:51 egonw I still can't even see the details...
13:52 egonw Fatal error: Allowed memory size of 8388608 bytes exhausted (tried to allocate 58368 bytes) in /var/www/cdknews/lib/smarty​/Smarty_Compiler.class.php on line 1380
13:52 steinbeck yes, pdf
13:52 steinbeck have you tried it again?
13:53 egonw yes
13:53 steinbeck weird. works for me
13:54 egonw really, weird...
13:54 egonw and rather annoying
13:54 steinbeck I now adjusted all php.ini in question
13:54 steinbeck maybe a session problem?
13:54 egonw I just tried logging out, and relogin
13:54 egonw did not help
14:00 steinbeck anyone here ever had to do the "Laptop Drive of Shame"? :-)
14:00 steinbeck http://www.networkworld.com/community/node/29791
14:00 zarah steinbeck's link is also http://tinyurl.com/55v6el
14:00 egonw that's the advantage of having a separate desktop machine :)
14:01 egonw umm.. now also tried with a different browser
14:01 egonw same problem
14:08 * steinbeck is going for a run
14:08 steinbeck left #cdk
14:21 egonw outcome SF SVN upgrade info: http://sourceforge.net/community/forum/topic.​php?id=2892&amp;page&amp;replies=1#post-6659
14:21 zarah egonw's link is also http://tinyurl.com/5m9d5s
14:21 CIA-33 jmol: hansonr * r9607 /trunk/Jmol/src/org/jmol/ (5 files in 4 dirs):
14:21 CIA-33 jmol: version=11.5.48_dev sheetsmoothing, messageCallback
14:21 CIA-33 jmol: # bug fix: sheetsmoothing not consistent among structures in multi-chain systems
14:21 CIA-33 jmol: # bug fix: messages not sent to messageCallback
15:07 CIA-33 jmol: hansonr * r9608 /trunk/Jmol/src/org/jmol/viewer/ (Jmol.properties ScriptManager.java Viewer.java): version=11.5.48_dev # bug fix: queue thread termination when applets are off screen
15:24 malick joined #cdk
17:00 rojasm joined #cdk
17:24 bag joined #cdk
17:28 malick joined #cdk
19:16 egonw joined #cdk
19:18 CIA-33 jmol: hansonr * r9609 /trunk/Jmol/src/org/jmol/ (4 files in 3 dirs):
19:18 CIA-33 jmol: version=11.5.48_dev quaternion arrows;connect aromatic auto
19:18 CIA-33 jmol: # bug fix: quaternion derivative DRAW arrows placed on residue i+1 instead of residue i
19:18 CIA-33 jmol: # bug fix: connect aromatic auto; select connected([bond type],...)
19:20 CIA-33 cdk: rajarshi * r11623 /cdk/branches/rajarshi-descnames/src/main/o​rg/openscience/cdk/qsar/descriptors/atomic/ (4 files): Updated atom descriptors starting with B,C,D,E, to not throw eceptions and to return names outside of calculate()
19:21 egonw moin
19:36 CIA-33 cdk: egonw * r11624 /cdk/branches/egonw-atowl/src/main/org/opens​cience/cdk/dict/data/cdk-sybyl-mappings.owl: Added template for CDK2Sybyl atom typing mapping
19:41 CIA-33 cdk: rajarshi * r11625 /cdk/branches/rajarshi-descnames/src/main/o​rg/openscience/cdk/qsar/descriptors/atomic/ (6 files): Updated atom descriptors starting with I, to not throw eceptions and to return names outside of calculate()
20:52 CIA-33 jmol: nicove * r9610 /trunk/Jmol-FAH/projects/p2175.xyz.gz:
20:54 CIA-33 cdk: rajarshi * r11626 /cdk/branches/rajarshi-descnames/src/main/or​g/openscience/cdk/qsar/DescriptorValue.java: removed a deprecated constructor since it has been cleaned up
20:55 CIA-33 cdk: rajarshi * r11627 /cdk/branches/rajarshi-descnames/s​rc/main/org/openscience/cdk/qsar/ (2 files in 2 dirs): Updated atom pair descriptors to conform to the new descriptor policy
20:55 rguha joined #cdk
20:57 CIA-33 cdk: rajarshi * r11628 /cdk/branches/rajarshi-descnames/src/main/o​rg/openscience/cdk/qsar/descriptors/atomic/ (16 files): Updated remaining atom descriptors according to the new descriptor policy
21:19 CIA-33 cdk: rajarshi * r11629 /cdk/branches/rajarshi-descnames/s​rc/main/org/openscience/cdk/qsar/ (7 files in 2 dirs): Updated bond descriptors according to the new descriptor policy
21:19 CIA-33 jmol: nicove * r9611 /trunk/Jmol/ (17 files in 4 dirs): Translation: Russian (ru)
21:23 CIA-33 cdk: rajarshi * r11630 /cdk/branches/rajarshi-descnames/src/test/org/open​science/cdk/qsar/descriptors/DescriptorTest.java: Some minor cleanups
21:28 CIA-33 cdk: rajarshi * r11631 /cdk/branches/rajarshi-descnames/src/test/org/open​science/cdk/qsar/descriptors/DescriptorTest.java: Added a test to check that we can get descriptor names without calculating and that the return array is not null and length >= 1
21:37 CIA-33 cdk: rajarshi * r11632 /cdk/branches/rajarshi-descnames/src/tes​t/org/openscience/cdk/qsar/descriptors/ (3 files in 3 dirs): Updated test superclasses to ensure that the calculate() method never throws an exception
21:41 CIA-33 cdk: rajarshi * r11633 /cdk/branches/rajarshi-descnames/src/test/​org/openscience/cdk/qsar/descriptors/molec​ular/MomentOfInertiaDescriptorTest.java: Updated test since descriptors now shouldn't throw an exception
21:49 CIA-33 cdk: rajarshi * r11634 /cdk/branches/rajarshi-descnames/src/tes​t/org/openscience/cdk/qsar/descriptors/ (3 files in 3 dirs): Added a test to the descriptor test superclasses to check that the names obtained directly from the decsriptor clas matches the names from the decsriptor value object
22:45 CIA-33 cdk: rajarshi * r11635 /cdk/branches/rajarshi-descnames/src/​main/org/openscience/cdk/qsar/descrip​tors/molecular/CPSADescriptor.java: Made descriptor names into static final
23:10 CIA-33 cdk: rajarshi * r11636 /cdk/branches/rajarshi-descnames/src/main/org​/openscience/cdk/qsar/descriptors/molecular/ (34 files): Made descriptor names into static final String[] where applicable
23:15 CIA-33 cdk: rajarshi * r11637 /cdk/branches/rajarshi-descnames/src/main/org​/openscience/cdk/qsar/DescriptorEngine.java: Updated to take into account new descriptr policies
23:26 CIA-33 cdk: rajarshi * r11638 /cdk/branches/rajarshi-descnames/src/main/org​/openscience/cdk/io/cml/QSARConvention.java: Updated to take into account new descriptr policies

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