Camelia, the Perl 6 bug

IRC log for #cdk, 2008-02-21

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All times shown according to UTC.

Time Nick Message
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08:09 jpansanel moin
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11:49 egonw moin
11:50 egonw de_maas: 3D builder is having trouble with the fingerprint db it is using...
11:50 egonw the current fingerprinter creates incompatible prints compared to those in the database...
11:50 egonw de_maas: hence, look up of 3D templates for ring structures in the db fails...
11:50 egonw about bc_ghemical...
11:50 egonw not sure about the status of that...
11:51 egonw I only know that no one is maintaining it...
11:51 egonw so likely broken...
12:00 Annzi joined #cdk
12:04 de_maas Hi Egon, thanks
12:04 de_maas Had some problems getting smi23d working but I will contact Rajashi about that one.
12:15 egonw ack
12:15 egonw would be nice to have that integrated in Bioclipse...
12:16 egonw I wish a had a big pile of money to bootstrap a Bioclipse-based company...
12:16 de_maas Well there is an opertunity.
12:20 CIA-48 bioclipse: Annzi * r4906 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.moss/ (4 files in 2 dirs): Layout changes
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13:20 CIA-48 bioclipse: ospjuth * r4907 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.moss/ (6 files in 3 dirs): Added empty help to MOSS
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13:59 jpansanel pouet
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16:29 CIA-48 bioclipse: Annzi * r4908 /branches/bioclipse2/chemoinformatics/ne​t.bioclipse.moss/src/net/bioclipse/moss/ (4 files in 2 dirs): Hash table modifications
16:32 Annzi left #cdk
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17:58 CIA-48 cdk: rajarshi * r10198 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs):
17:58 CIA-48 cdk: Added a method for atom pol calculation that accepts a topo distance matrix. So
17:58 CIA-48 cdk: if we're getting values for multiple atoms in the same molecule, no need to do
17:58 CIA-48 cdk: BFS each time we're called - just do a lookup. Also updated BCUT code to use
17:58 CIA-48 cdk: this mehtod - 2x speedup :)
18:19 CIA-48 cdk: rajarshi * r10199 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): Cleaned up some unused arguments
18:29 CIA-48 cdk: rajarshi * r10200 /trunk/cdk/src/org/openscience/cdk/q​sar/descriptors/molecular/Autocorrel​ationDescriptorPolarizability.java: Updated for faster polarizability calculations
18:38 egonw joined #cdk
18:39 rguha hi
18:41 egonw hi rguha
18:42 egonw rguha: I found how to get call coutns....
18:42 egonw if you go to run profile run dialog...
18:42 egonw check the J5 profiling system
18:42 rguha aah ok, i'll take a look at that
18:43 rguha one thing I noticed, read() in MDLV2000Reader takes up a big chunk of time - something to focus on for optimization
18:43 egonw yeah...
18:43 egonw have been thinking about the reader too...
18:43 egonw java.nio should be used...
18:43 egonw maybe
18:43 egonw is said to be faster
18:44 rguha hmm, i've never used nio
18:44 egonw neither have I
18:44 egonw so no clue about how to do it...
18:44 rguha btw, the nightly build is failing because of qsar-weka.libdepends not being found
18:44 rguha can you committ that?
18:45 egonw hang on..
18:47 egonw btw, how are things in Indiana?
18:47 rguha in what context? :)
18:47 rguha cold weather and uncertain future
18:47 egonw more like the department, research etc...
18:48 rguha aah
18:48 rguha interesting projects going on, submitted a grant
18:48 rguha but not clear if i'll stay on beyond december
18:53 rguha i can see your messages, can't you see mine?
18:54 egonw no
18:54 rguha just found out my nick is not registered that's why
18:55 egonw ah, ack
18:55 egonw skype?
18:55 egonw jabber?
18:56 rguha i'm on gtalk (rajarshi.guha@gmail.com)
19:08 CIA-48 cdk: rajarshi * r10201 /trunk/cdk/ (build.props build.xml): Updated build.xml to pick up the correct libdepends file for qsar-weka
19:09 egonw he... was already fixing that !
19:09 egonw :)
19:10 rguha build is running
19:12 CIA-48 cdk: egonw * r10202 /trunk/cdk/ (6 files in 2 dirs): qsarweka libdepends fixes
19:13 rguha going to lunch
19:14 egonw ok, I'll go offline soon...
19:14 egonw cu later
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23:10 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 5214, 77 fails + 44 errors (2.3%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk

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