Camelia, the Perl 6 bug

IRC log for #cdk, 2008-08-06

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All times shown according to UTC.

Time Nick Message
03:37 CIA-34 cdk: rajarshi * r11922 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (12 files in 7 dirs): Updated remaining classes to use Iterable rather than Iterator
03:41 CIA-34 cdk: rajarshi * r11923 /cdk/branches/mesprague-iterators/​src/test/org/openscience/cdk/formu​la/MolecularFormulaRangeTest.java: Fixed the last test class to use Iterable and not Iterator. Everything compiles nicely :)
03:54 CIA-34 cdk: rajarshi * r11924 /cdk/branches/mesprague-iterator​s/src/main/org/openscience/cdk/ (2 files in 2 dirs): Spoke too soon. Fixed the last two
04:16 CIA-34 cdk: rajarshi * r11925 /cdk/branches/mesprague-iterators/src/main/org/ope​nscience/cdk/tools/diff/tree/IDifferenceList.java: Converted from Iterator to Iterable
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04:48 CIA-34 cdk: rajarshi * r11926 /cdk/branches/mesprague-iterators/src/ (6 files in 2 dirs): Converted from Iterator to Iterable and updated usage
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05:45 CIA-34 cdk: rajarshi * r11927 /cdk/branches/mesprague-iterators/s​rc/main/org/openscience/cdk/tools/ (23 files in 3 dirs): Updated code to use Java 1.5 idiom for Iterables
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05:53 CIA-34 jmol: hansonr * r9673 /trunk/Jmol/.classpath:
05:55 CIA-34 jmol: hansonr * r9674 /trunk/Jmol/src/org/jmol/ (22 files in 5 dirs): (log message trimmed)
05:55 CIA-34 jmol: version=11.6.RC1
05:55 CIA-34 jmol: # new feature: echo myecho IMAGE "filename"
05:55 CIA-34 jmol: # -- reads a JPG, GIF, or PNG image and displays it the
05:55 CIA-34 jmol: # same as text is displayed.
05:55 CIA-34 jmol: # new feature: echo myecho DEPTH xx
05:55 CIA-34 jmol: # -- sets the depth in percent (0% far back, 100% front) for the placement of the image
05:57 CIA-34 cdk: rajarshi * r11928 /cdk/branches/mesprague-iterators/src/ (4 files in 4 dirs): Converted Iterator to Iterable and fixed a few usage cases
05:58 CIA-34 jmol: hansonr * r9675 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: dev only
06:06 CIA-34 cdk: egonw * r11929 /cdk/trunk/src/test/org/openscience/cdk​/atomtype/CDKAtomTypeMatcherTest.java:
06:06 CIA-34 cdk: Added test for failing atom type recognition in
06:06 CIA-34 cdk: qsar.descriptors.atomic.PiElectronegativity​DescriptorTest.testPiElectronegativity1().
06:06 CIA-34 cdk: It fails because the SMILES parser sets the hydrogen Count to zero for the first
06:06 CIA-34 cdk: carbon at least, which is wrong...
06:09 CIA-34 jmol: hansonr * r9676 /trunk/Jmol/src/org/jmol/ (shape/Measures.java viewer/Jmol.properties): (log message trimmed)
06:09 CIA-34 jmol: version=11.6.RC1
06:09 CIA-34 jmol: # bug fix: measures were messed up
06:09 CIA-34 jmol: # new feature: echo myecho IMAGE "filename"
06:09 CIA-34 jmol: # -- reads a JPG, GIF, or PNG image and displays it the
06:09 CIA-34 jmol: # same as text is displayed.
06:09 CIA-34 jmol: # new feature: echo myecho DEPTH xx
06:15 CIA-34 jmol: hansonr * r9677 /trunk/Jmol/src/org/jmol/export/ (_MayaExporter.java _VrmlExporter.java):
06:19 CIA-34 cdk: egonw * r11930 /cdk/trunk/src/test/org/openscience​/cdk/qsar/descriptors/atomic/PiElec​tronegativityDescriptorTest.java: Fixed SMILES string: no Hx implies 0 hCount, resulting in bad valencies for the carbons
06:23 CIA-34 cdk: egonw * r11931 /cdk/trunk/src/main/org/openscience/c​dk/atomtype/CDKAtomTypeMatcher.java: Split out counts for easier debugging...
07:00 CIA-34 jmol: hansonr * r9678 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Jmol.properties):
07:37 rojasm joined #cdk
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07:57 jpansanel moin
07:57 zarah hi jpansanel
07:58 jpansanel moin zarah
07:58 egonw hi jpansanel
08:50 carsten joined #cdk
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08:54 shk3 good morning
08:54 shk3 egonw: a question
08:54 shk3 ?
08:54 egonw ha shk3
08:54 egonw yes
08:54 egonw I got time now :)
08:54 shk3 ok, I worked on the fingerprinter, which is in extra.
08:55 shk3 nightly says for extra module:
08:55 shk3 Testsuite: org.openscience.cdk.modulesuites.MextraTests
08:55 shk3 Tests run: 37, Failures: 0, Errors: 0, Time elapsed: 1.319 sec
08:55 shk3 result-extra.txt in reports says (on my machine):
08:55 shk3 Testsuite: org.openscience.cdk.modulesuites.MextraTests
08:55 shk3 Tests run: 90, Failures: 3, Errors: 1, Time elapsed: 3.096 sec
08:56 shk3 What is happening here?
08:56 masak joined #cdk
08:57 egonw so, summary inconsitent with individual reports?
08:57 egonw you should discuss that with Rajarshi
08:57 egonw but not good indeed
08:58 shk3 but they should be the same?
08:58 shk3 so I am not totally wrong with this assumption?
09:01 egonw they should indeed be the same
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10:42 CIA-34 cdk: shk3 * r11932 /cdk/trunk/src/ (2 files in 2 dirs): modified extendedfingerprinter not to use allringsfinder any more.
10:45 egonw shk3: please check that commit
10:45 egonw I think you are reverting things you do not want to revert, such as:
10:45 egonw - * Generates an extended fingerprint for a given {@link IAtomContainer}, that
10:45 egonw - * extends the {@link Fingerprinter} with additional bits describing ring
10:45 egonw + * Generates an extended fingerprint for a given AtomContainer, that
10:45 egonw + * extends the Fingerprinter with additional bits describing ring
10:45 egonw - * @cdk.module     fingerprint
10:45 egonw + * @cdk.module     extra
10:46 egonw also, please use types List:
10:46 egonw -    public BitSet getFingerprint(IAtomContainer ac, IRingSet rs) throws Exception {
10:46 egonw +    public BitSet getFingerprint(IAtomContainer ac, IRingSet rs, List rslist) throws Exception {
10:46 egonw make that third argument List<Something>
11:03 shk3 ah, wasn't sure about this
11:03 shk3 we use generics in trunk?
11:07 egonw yes
11:17 shk3 on cdk-user, there was a question about lost doublebonds
11:17 shk3 did anybody answer this?
11:17 shk3 if not, I think I should have a look.
11:17 egonw please fix those changes I mentioned earlier first
11:18 egonw particularly the @cdk.module mix up will mess up compililation on NIghtly, I think
11:20 shk3 working on that
11:22 egonw ok, thanx
11:24 shk3 egonw: a problem
11:24 shk3 if no List is given, one is calculated via
11:24 shk3 partitionRings in RingPartitioner
11:25 shk3 this just returns a List
11:25 egonw ok, hang on
11:25 shk3 so if I make the parameter List<x>, I can't assign to it
11:28 shk3 changing the ringpartitioner shouldn't be too hard
11:28 egonw just done
11:28 shk3 this would be a welcome clean up anyway, i suppose
11:28 egonw commit pending
11:28 egonw yes
11:28 shk3 ah
11:29 egonw quite a few of such clean ups have been made in trunk already...
11:29 CIA-34 cdk: egonw * r11933 /cdk/trunk/src/main/org/openscience/​cdk/ringsearch/RingPartitioner.java: Update List to List<IRingSet>.
11:29 egonw but there is a lot of code :)
11:29 egonw ok, try now
11:30 CIA-34 cdk: shk3 * r11934 /cdk/trunk/src/main/org/openscience/cdk/​fingerprint/ExtendedFingerprinter.java: unwanted reverts, better commentary, use of generics
11:31 egonw the cdk.module fix is missing
11:32 shk3 grrrr
11:32 shk3 copied in wrong bit
11:32 * shk3 is to lunch
11:33 CIA-34 cdk: shk3 * r11935 /cdk/trunk/src/main/org/openscience/cdk/​fingerprint/ExtendedFingerprinter.java: unwanted reverts, better commentary, use of generics
11:36 egonw mmm... SF stats webpages are back online... but no backlog processed yet...
11:36 egonw CDK has seen *a lot of* development... so does Bioclipse...
11:37 egonw really interesting to see their new SF rankings
11:38 egonw also wondering about the metware ranking
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14:14 CIA-34 cdk: egonw * r11936 /cdk/trunk/src/main/org/opensci​ence/cdk/tools/IDCreator.java: Ported the IDCreator patch from Aleksey from cdk-1.0.x/ to trunk (closes #2011204)
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14:40 CIA-34 jmol: hansonr * r9679 /trunk/Jmol/src/org/jmol/ (5 files in 3 dirs):
14:40 CIA-34 jmol: version=11.6.RC1 (pointgroup enhancements)
14:40 CIA-34 jmol: # new feature: write/show pointgroup gives counts and tab-separated listing;
14:40 CIA-34 jmol: # new feature: write pointgroup draw delivers draw commands
14:40 CIA-34 jmol: # new feature: better draw pointgroup
14:40 CIA-34 jmol: # new feature: no saving of point group -- just recalculated each time
14:41 CIA-34 jmol: # bug fix: measures were messed up
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14:49 Technetium3 hey everyone is someone here
14:49 egonw yes
14:49 Technetium3 azeem
14:50 Technetium3 yay
14:50 Technetium3 tell me what do u study
14:50 egonw ummm... who are you?
14:51 Technetium3 im just a guy looking for some help with a publication im trying to access
14:51 Technetium3 who are u
14:52 egonw what brings you here?
14:52 egonw you're a CDK user?
14:53 Technetium3 no i dont really know what cdk is i searched google for chemistry chat rooms and found this
14:53 Technetium3 im a master student in chemistry looking for someone who has access to  a journal
15:04 azeem hrmpf
15:07 CIA-34 jmol: hansonr * r9680 /trunk/Jmol/src/org/jmol/symmetry/UnitCell.java: comment
15:09 CIA-34 jmol: hansonr * r9681 /trunk/Jmol/src/org/jmol/adapter​/readers/cifpdb/CifReader.java: comment
15:09 carsten joined #cdk
15:14 egonw hi carsten
15:15 carsten Moin moin
15:18 egonw crap
15:18 egonw I hate it when I do manage to get anything done in the afternoon
15:18 egonw (other than some catching up with reading...)
15:18 azeem s/do/don't/ I assume
15:18 egonw hahah
15:18 egonw umm, indeed
15:21 olas left #cdk
15:25 CIA-34 jmol: hansonr * r9682 /trunk/Jmol/src/org/jmol/ (4 files in 3 dirs):
15:25 CIA-34 jmol: version=11.6.RC1 (c)
15:25 CIA-34 jmol: # bug fix: LOAD "..." nn loading of model numbers for PDB files should read real model number, not sequentially.
16:02 CIA-34 jmol: hansonr * r9683 /trunk/Jmol/src/org/jmol/shape/Measures.java: unnecessary message removed.
16:42 CIA-34 jmol: hansonr * r9684 /branches/v11_4/Jmol/src/org/jmol/ (3 files in 2 dirs):
16:42 CIA-34 jmol: version=11.4.7_dev
16:42 CIA-34 jmol: # bug fix: H1, H2, H3 in DNA not backbone
16:42 CIA-34 jmol: # bug fix: longstanding exception: isosurface fullylit --> isosurface backlit --> isosurface frontlit
16:56 malick left #cdk
18:07 CIA-34 jmol: hansonr * r9685 /trunk/Jmol/src/org/jmol/ (symmetry/PointGroup.java viewer/Jmol.properties): version=11.6.RC1 # bug fix: D3h point group
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19:48 egonw @tell rojasm if he can let me know if he has time to check the iterable patch
19:48 zarah Consider it noted.
20:19 CIA-34 jmol: nicove * r9686 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
20:36 CIA-34 jmol: nicove * r9687 /trunk/Jmol-FAH/projects/ (p4510.xyz.gz p4517.xyz.gz): Folding@Home
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