Camelia, the Perl 6 bug

IRC log for #cdk, 2008-07-23

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All times shown according to UTC.

Time Nick Message
00:46 CIA-33 jmol: hansonr * r9628 /trunk/Jmol/src/org/jmol/ (9 files in 6 dirs): code simplification/cleaning
00:58 CIA-33 cdk: rajarshi * r11707 /cdk/trunk/ (110 files in 19 dirs): merged changes fro rajarshi-descanmes r11605:11706 intro trunk
02:23 CIA-33 cdk: rajarshi * r11708 /cdk/trunk/src/main/org/openscienc​e/cdk/qsar/descriptors/molecular/ (4 files): Updated so that all atom typing exceptions are caught properly
02:29 CIA-33 cdk: rajarshi * r11709 /cdk/trunk/src/main/org/openscience/cdk/qsar/descr​iptors/molecular/LengthOverBreadthDescriptor.java: Updated an error message
02:47 CIA-33 cdk: rajarshi * r11710 /cdk/trunk/src/main/org/openscienc​e/cdk/qsar/descriptors/molecular/ (4 files): Damn sleepiness. Fixed more typos
03:47 azeem_ joined #cdk
04:59 CIA-33 cdk: rajarshi * r11711 /cdk/trunk/tools/nightly.py: Updated to include the descriptor summary page
05:04 bag joined #cdk
05:21 rojasm joined #cdk
06:03 jbrefort joined #cdk
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07:28 CIA-33 jmol: hansonr * r9629 /trunk/Jmol/src/org/jmol/ (shapespecial/Draw.java viewer/Jmol.properties): version=11.5.50_dev # bug fix: $ptx[2] notation broken in 11.5.49
07:33 masak joined #cdk
07:51 thomas_ku moin
07:51 zarah hi thomas_ku
07:59 egonw hi thomas_ku
08:24 olas joined #cdk
08:25 CIA-33 cdk: ospjuth * r11712 /cdk/trunk/ (META-INF/MANIFEST.MF build.properties): Added new jumbo5.4.2 to MANIFEST.
08:53 egonw_ joined #cdk
09:07 zarah joined #cdk
09:16 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 7285, 73 fails + 49 errors (1.67%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk | CDK News paper online on pharmacophores: http://www.cdknews.org/
10:03 CIA-33 cdk: egonw * r11713 /cdk/branches/cdk-1.0.x/sr​c/org/openscience/cdk/io/ (16 files in 4 dirs): Use system's line.separator instead of hardcoded '\n'
10:26 CIA-33 cdk: egonw * r11714 /cdk/trunk/src/main/org/openscience/cdk/io/ (16 files in 4 dirs): Ported patch r11713: Use system's line.separator instead of hardcoded '\n'
12:47 jonalv @seen shk3
12:47 zarah I have not seen shk3
12:50 masak joined #cdk
13:46 egonw joined #cdk
15:17 CIA-33 cdk: rajarshi * r11715 /cdk/trunk/src/main/org/openscience/cd​k/fingerprint/FingerprinterTool.java: Fixed a Javadoc
15:31 CIA-33 cdk: rajarshi * r11716 /cdk/trunk/src/ (2 files in 2 dirs): Added a fingerprint that just looks for EState fragments. Note that it only records their presence, since the EState fragment decriptor already does counts
15:36 CIA-33 cdk: rajarshi * r11717 /cdk/trunk/src/main/org/openscience/cdk/qsar/desc​riptors/molecular/KierHallSmartsDescriptor.java: Updated descriptor to use the proper names. We add a prefix to the standard EState notation, so that these fragg counts canbe differentiated from the eState indices (when they get implemented)
15:42 CIA-33 cdk: rajarshi * r11718 /cdk/trunk/src/main/org/openscience/cdk/qsar/desc​riptors/molecular/KierHallSmartsDescriptor.java: Fixe a typo in the Javadocs
15:59 CIA-33 cdk: rajarshi * r11719 /cdk/trunk/src/ (2 files in 2 dirs): Fixed some more isses with naming. NOTE: Though a String[] canbe static final, the contents of the array can still be modified. Ideallly static final String[] should be replaced by some form of immutable Collection
16:25 CIA-33 jmol: gutow * r9630 /trunk/Jmol/src/org/ (2 files in 2 dirs): # bug fix: was reading server path for local path from history in Webexport
16:28 CIA-33 jmol: gutow * r9631 /branches/v11_4/Jmol/src/org/ (2 files in 2 dirs): # bug fix: was reading server path for local path from history in Webexport
17:25 CIA-33 cdk: rajarshi * r11720 /cdk/trunk/src/main/org/opens​cience/cdk/fingerprint/data/ (. maccs.txt): Added MACCS key definitions
17:56 CIA-33 cdk: rajarshi * r11721 /cdk/trunk/src/ (2 files in 2 dirs): Updated module membership of EState fp's to extra
17:57 CIA-33 cdk: rajarshi * r11722 /cdk/trunk/src/META-INF/ (experimental.datafiles extra.datafiles): Updated data file deps for the new fingerprints
17:58 bag joined #cdk
18:32 CIA-33 cdk: rajarshi * r11723 /cdk/trunk/src/ (5 files in 4 dirs): Updated module membership to experimental, since putting it in extra is leading to circular dependencies
19:04 CIA-33 cdk: rajarshi * r11724 /cdk/trunk/src/ (2 files in 2 dirs): Fixed yet more compile time dependencies. Also corrected the class passed to the logger
19:06 CIA-33 cdk: rajarshi * r11725 /cdk/trunk/src/ (2 files in 2 dirs): Implementation of 166 bit MACCS keys. Patterns taken fron RDKit. Some patterns checked for manually, since the SMARTS parser doesn't handle those features
19:19 CIA-33 cdk: djiao * r11726 /cdk/trunk/src/main/org/opensci​ence/cdk/smiles/smarts/parser/ (11 files):
19:19 CIA-33 cdk: Added the following elements to smarts parser:
19:19 CIA-33 cdk: Pu, Am, Cm, Bk, Cf,
19:19 CIA-33 cdk: Es, Fm, Md, No, Lr
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20:12 CIA-33 cdk: egonw * r11727 /cdk/trunk/src/main/org/opensci​ence/cdk/smiles/smarts/parser/ (7 files): Removed autogenerated files again
20:31 CIA-33 cdk: egonw * r11728 /cdk/trunk/src/main/org/openscie​nce/cdk/io/MDLV2000Reader.java: Fixed firing of the interpretHydrogenIsotopes setting.
20:35 CIA-33 jmol: nicove * r9632 /trunk/Jmol-FAH/projects/p2662.xyz.gz: Folding@Home
20:46 CIA-33 jmol: hansonr * r9633 /branches/v11_4/Jmol/src/org/jmol/viewer/ (Jmol.properties Viewer.java): version=11.4.6_dev # bug fix: vibration thread not closing down for applet destroy when applet is off-screen
20:47 CIA-33 jmol: hansonr * r9634 /trunk/Jmol/src/org/jmol/viewer/ (Jmol.properties Viewer.java): version=11.5.50_dev # bug fix: vibration thread not closing down for applet destroy when applet is off-screen
20:51 CIA-33 jmol: hansonr * r9635 /trunk/Jmol/src/org/openscience/jvxl/ (calc/ data/ readers/ util/): removal of unnecessary classes for Jvxl.Java
20:52 CIA-33 jmol: hansonr * r9636 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.5.50 VERSION
20:52 CIA-33 jmol: hansonr * r9637 /branches/v11_4/Jmol/src/org/​jmol/viewer/Jmol.properties: 11.4.6 VERSION
21:05 CIA-33 jmol: nicove * r9638 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
21:08 CIA-33 cdk: egonw * r11729 /cdk/trunk/src/ (3 files in 3 dirs): Added missing force3DCoords setting for the iterating MDL reader (closes #2025785)
21:11 CIA-33 jmol: nicove * r9639 /branches/v11_4/Jmol/src/org/​jmol/viewer/Jmol.properties: Version
21:18 CIA-33 jmol: hansonr * r9640 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Viewer.java): thread shutdown on initialize()
21:56 CIA-33 cdk: rajarshi * r11730 /cdk/trunk/src/main/org/opensci​ence/cdk/smiles/smarts/parser/ (4 files): Removed some of the autogenerated files, since we can now correctly generate and process them via the build script
21:57 CIA-33 cdk: rajarshi * r11731 /cdk/trunk/build.xml: Added ant tasks to correctly generate the SMARTS jj parser from the tree spec and perform the required massaging so that everything compiles OK. This allows us to allows compile from the tree spec
22:06 bag joined #cdk
22:25 CIA-33 cdk: rajarshi * r11732 /cdk/trunk/src/main/org/openscience/cdk​/smiles/smarts/parser/SMARTSParser.jjt: Added some more missing element symbols: Np,Ce,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu,Pr
22:27 CIA-33 cdk: rajarshi * r11733 /cdk/trunk/src/test/org/openscience/cdk/sm​iles/smarts/parser/SMARTSSearchTest.java: Added a test to check for wolfram

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