Camelia, the Perl 6 bug

IRC log for #cdk, 2008-01-02

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All times shown according to UTC.

Time Nick Message
00:15 CIA-17 cdk: rajarshi * r9782 /trunk/cdk/src/org/openscience/cdk​/test/CoverageAnnotationTest.java: Updated to ensure that toString() methods also have a test method annotation
00:15 CIA-17 cdk: egonw * r9783 /trunk/cdk/src/org/openscience/cdk/ (4 files in 3 dirs):
00:15 CIA-17 cdk: Fixed the DescriptorEngineTest: 1. renamed methods to split up class
00:15 CIA-17 cdk: constructor, and descriptor loading, with better feedback; 2. assert that all
00:15 CIA-17 cdk: descriptor info bits are of equal length; 3. put in qsarmolecular so that it can
00:15 CIA-17 cdk: find all descriptors (FIXME: assumed qsarmolecular depends on qsaratomic and
00:15 CIA-17 cdk: qsarbond)
00:17 CIA-17 cdk: egonw * r9784 /trunk/cdk/src/org/openscience/cdk/t​est/qsar/DescriptorEngineTest.java: Protein descriptors are now treated differently, so no class proteinDescriptor anymore for the loaded MOLECULAR descriptors
00:29 CIA-17 cdk: egonw * r9785 /trunk/cdk/src/org/openscience/cdk/qsar/des​criptors/atomic/AtomDegreeDescriptor.java: Added unit test annotation (arghh... that's a lot of work...) and missing return value column names
00:55 CIA-17 cdk: egonw * r9786 /trunk/cdk/src/org/openscience​/cdk/qsar/descriptors/atomic/ (27 files): Added annotation for unit tests
01:31 CIA-17 cdk: egonw * r9787 /trunk/cdk/src/org/openscience/cdk/test/qsar/desc​riptors/atomic/RDFProtonDescriptor_GHRTest.java: Set the descriptor not the test :)
01:32 CIA-17 cdk: egonw * r9788 /trunk/cdk/src/org/openscience/cdk/test/qsar/​descriptors/atomic/AtomicDescriptorTest.java: Use the hydrogen to make the RDF descriptors happy... maybe they should simply return NaN for non-hydrogens? I wish there was a bit more policy here...
01:37 CIA-17 cdk: egonw * r9789 /trunk/cdk/src/org/openscience​/cdk/qsar/descriptors/atomic/ (5 files): Fixed returned parameters names to match implementation; return null when incorrect param name is passed, instead of zero
01:56 CIA-17 cdk: egonw * r9790 /trunk/cdk/src/org/openscience/cdk/test/qsar/desc​riptors/molecular/IPMolecularDescriptorTest.java: Fixes a NPE, because the local descriptor field was not set; use thes super.descriptor now
02:02 CIA-17 cdk: egonw * r9791 /trunk/cdk/src/org/openscience/​cdk/qsar/descriptors/molecular/ (19 files): Fixed descriptor type lengths
07:21 jbrefort joined #cdk
07:42 olas joined #cdk
09:03 jonalv joined #cdk
09:34 egonw joined #cdk
09:42 _thomas_k joined #cdk
09:42 _thomas_k moin
09:58 egonw hi _thomas_k
09:59 CIA-17 cdk: egonw * r9792 /trunk/cdk/src/org/openscience/cdk/test/qsar/​descriptors/atomic/AtomicDescriptorTest.java: Take a hydrogen to make the RDF unit tests happy (only works on protons)
10:13 CIA-17 cdk: egonw * r9793 /trunk/cdk/src/org/openscience​/cdk/qsar/descriptors/atomic/ (5 files): Fixed getParameterType methods
10:13 CIA-17 cdk: egonw * r9794 /trunk/cdk/src/org/openscience/cdk/test​/qsar/descriptors/DescriptorTest.java: More detailed testing
10:13 egonw all: happy new year
10:23 olas app
10:23 olas happy new year to you too, egonw!
10:27 _thomas_k happy new year to all
10:28 CIA-17 cdk: egonw * r9795 /trunk/cdk/src/org/openscience/cdk/qsar/desc​riptors/atomic/RDFProtonDescriptor_GSR.java: Create column names for descriptor values
10:28 egonw olas, _thomas_k: lot's of inconsistent QSAR descriptor code...
10:28 egonw olas: the Bioclipse code assumed that a descriptor would properly return the number of doubles
10:29 egonw to be able to calculate the descriptor matrix size
10:29 egonw but lot's of descriptors were not doing that properly...
10:29 olas I see
10:29 egonw which was causing the bugs when combining JOELib and CDK descriptors
10:30 olas is that a cdk bug or feature?
10:30 egonw bug, in my opinion
10:30 olas ok
10:30 olas then good we gound it out so it can be fixed
10:30 olas found
10:31 CIA-17 cdk: egonw * r9796 /trunk/cdk/src/org/openscience​/cdk/qsar/descriptors/atomic/ (5 files): No need for these methods to be public
10:31 egonw indeed
10:31 egonw porting to cdk-1.0.x/ will be difficult though
10:31 egonw because more and more code in trunk/ is Java5...
10:31 olas then it will be fixed in BC2
10:32 egonw yes, that would suite me much better...
10:32 olas regarding Bioclispe I mean
10:32 egonw btw, we need to update teh svn:externals for Jmol
10:32 egonw to point to the new 11_4 branch
10:32 olas oh?
10:32 olas could you please?
10:32 olas I have no idea how to do that
10:32 egonw pleaes file a bug report
10:32 olas ok
10:32 egonw with copy/paste of these lines here in IRC or so
10:32 egonw it's damn easy
10:33 egonw just google for it..
10:33 egonw plenty of examples
10:35 CIA-17 cdk: egonw * r9797 /trunk/cdk/src/org/openscience/cdk/qsar/desc​riptors/atomic/RDFProtonDescriptor_GSR.java: Time that I wake up... :(
10:46 CIA-17 cdk: egonw * r9798 /trunk/cdk/src/org/openscience​/cdk/qsar/descriptors/atomic/ (4 files): More missing column names
10:52 jpansanel moin
10:57 egonw hi jpansanel
10:58 jbrefort hi jpansanel
10:58 jbrefort jpansanel, what about adding CAS to structures?
10:59 egonw jbrefort: not allowed without written permission
10:59 jbrefort ok, I did not know
10:59 egonw CAS number should not be promoted anyway
10:59 egonw imprecise
11:00 egonw CAS numbers may indicate a mixture, something without known stereochemistry...
11:00 CIA-17 cdk: egonw * r9799 /trunk/cdk/src/org/openscience​/cdk/qsar/descriptors/atomic/ (2 files): Fixed parameter specs
11:04 jpansanel jbrefort : it's a good idea
11:04 jpansanel for some products
11:04 jpansanel but as egonw says, CAS can not be used freely
11:05 egonw jbrefort: why do you want it anyway?
11:05 egonw there is InChI...
11:05 jpansanel egonw : I'll release a 2.1.5 version of Structures today or tomorrow
11:05 CIA-17 cdk: egonw * r9800 /trunk/cdk/src/org/openscience/cdk/qsar/descrip​tors/atomic/PartialSigmaChargeDescriptor.java: Placed in the correct module
11:08 CIA-17 bioclipse: ospjuth * r4592 /branches/bioclipse2/test/:
11:09 CIA-17 bioclipse: ospjuth * r4593 /branches/bioclipse2/test/olaRepo1/: Initial import.
11:10 CIA-17 bioclipse: ospjuth * r4594 /branches/bioclipse2/test/olaRepo1/qsar.xml: added file
11:11 CIA-17 bioclipse: ospjuth * r4595 /branches/bioclipse2/test/olaRepo1/ (11 files): Added more files
11:18 CIA-17 cdk: egonw * r9801 /trunk/cdk/src/org/openscience/c​dk/test/qsar/descriptors/atomic/ (5 files): Removed sysout calls
11:29 jbrefort egonw, just somebody asked me
11:29 egonw write a greasemonkey script :)
11:30 egonw to get the CAS from PubChem/ChemSpider and add it to the Structure Repository website
11:30 egonw that's what those scripts are for
11:31 CIA-17 cdk: egonw * r9802 /trunk/cdk/src/org/openscience/cdk/test/qsar/des​criptors/molecular/MolecularDescriptorTest.java: Fixed test to take into account the new *Type classes: was now often incorrectly failing because DoubleArrayResult notEquals DoubleArrayResultType
11:34 CIA-17 cdk: egonw * r9803 /trunk/cdk/src/org/openscience/cdk/test/qsar/d​escriptors/molecular/BCUTDescriptorTest.java: Some better feedback than just 'null'
11:39 simbot_ joined #cdk
11:39 egonw hi simbot_
11:40 simbot_ hi egonw,
11:40 egonw are you a true bot?
11:41 simbot_ no, sorry, the name is probably misleading
11:41 egonw no worries
11:41 egonw just making sure :)
11:41 egonw every now and then a spam bot shows up
11:41 egonw not so often here, fortunately
11:41 simbot_ ah yes, the terrors of the internet
11:42 simbot_ Is there a faster way to get the molecular formula from a SMILES expression than using the SmilesParser and then the MFAnalyser?
11:42 egonw no
11:42 simbot_ as it took 4 hours to convert 4000 expressions.
11:42 simbot_ dear
11:42 egonw because you need to figure out the hydrogen counts
11:43 egonw ah, you're using CDK 1.0.x I assume?
11:43 egonw that's caused by the use of the AllRingsFinder...
11:43 simbot_ yes I am,
11:43 egonw which shows very bad performance for certain compounds...
11:43 egonw sorry about that...
11:43 egonw try the trunk/ version
11:43 simbot_ No problems, I will
11:44 egonw that should behave much better for this task
11:44 simbot_ thanks
11:44 egonw you know where you can download the prebuild .jar ?
11:44 egonw build last night...
11:45 egonw http://cheminfo.informatics.india​na.edu/~rguha/code/java/nightly/
11:45 simbot_ not off the top of my head,
11:45 simbot_ thanks
11:45 egonw cdk-svn-20080102.jar
11:46 simbot_ what time zone are most of the people in this room? I'm GMT+10. Just curious when I'm likely to catch people
11:47 egonw EU day time most likely...
11:47 egonw Rajarshi is US-based, but not often online
11:58 simbot_ wow, it takes about 5 seconds now,
12:00 egonw :)
12:05 CIA-17 cdk: egonw * r9804 /trunk/cdk/src/org/openscienc​e/cdk/qsar/IDescriptor.java: Added note on the fact that the descriptor length may only depend on parameters and not the IAtomContainer input
12:06 egonw simbot_: are all atom types perceived correctly?
12:06 simbot_ no
12:06 egonw if not, the hydrogen counts may be inaccurate...
12:07 egonw if you like, you can email me SMILES for which atom types are not correctly detected
12:07 egonw possibly, a SMILES fragment with just the failing atom and its direct neighbors
12:08 simbot_ ok, that is easy enough.
12:22 simbot_ Here is some of the ones which failed. They go SMILES, then the error messages on the following lines. http://www.nigelsim.org/non-percieved.txt
12:26 egonw OK, I can live with the [S+2]([O-])([O-]) problems...
12:26 egonw no sure why that is not simple O=S=O...
12:26 egonw but fair :)
12:26 egonw what about the Cl+3 ?
12:27 egonw that's a ionized bond representation for chlorates?
12:28 egonw simbot_: is this report confidential?
12:28 egonw that is, can I post is as a bug report?
12:28 egonw or the, some 6-7, representable examples...
12:33 CIA-17 cdk: egonw * r9805 /trunk/cdk/src/org/openscience/cdk/qsar/descript​ors/molecular/LengthOverBreadthDescriptor.java: Added a workaround for situations when atom types have been perceived (see #1862142)
12:36 CIA-17 cdk: egonw * r9806 /trunk/cdk/src/org/openscience/cdk/ (5 files in 2 dirs): Addressed a few inconsistencies
12:40 simbot_ post it as you wish
12:54 CIA-17 cdk: egonw * r9807 /trunk/cdk/src/org/openscience/cdk/ (3 files in 3 dirs): Added atom type perception for: Zn (e.g. ZnCl2), Zn2+ and [Cl+3] as in [Cl+3]([O-])([O-])([O-])[O-]
12:56 jpansanel egonw : I've updated Chemical Structure website
12:56 jpansanel http://chem-file.sourceforge.net/
12:56 jpansanel Last structures are now available
13:00 jpansanel and the site is fully xhtml 1.0 valid
13:02 egonw good
13:03 CIA-17 cdk: egonw * r9808 /trunk/cdk/src/org/openscience/cdk/ (3 files in 3 dirs): Added perception of S.onyl.charged, as in [S+2]([O-])([O-])([O-])[O-]
13:03 egonw simbot_: OK, that should cover most of those atom typing problems
13:03 simbot_ excellent, much appreciated
13:03 egonw likewise...
13:03 simbot_ When do the nightly builds occur?
13:03 egonw bug reports of this quality are much appreciated
13:04 egonw at night :)
13:04 simbot_ Well, it's 11pm here :)
13:04 egonw yeah, I think it's midnight UCT+6 or so
13:05 simbot_ right
14:09 CIA-17 bioclipse: jonalv * r4596 /branches/bioclipse2/ (7 files in 5 dirs): Attempts at getting recording of API calls to work. It is not yet working...
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14:39 CIA-17 bioclipse: ospjuth * r4597 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.qsar/ (24 files in 7 dirs): Added NewQSARProjectWizard that creates folders 'molecules', 'descriptors', and file qsar.xml from template.
14:42 CIA-17 bioclipse: ospjuth * r4598 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.qsar/ (3 files in 2 dirs): Renamed file
14:46 CIA-17 bioclipse: ospjuth * r4599 /branches/bioclipse2/chemoinformatics/​net.bioclipse.qsar/src/net/bioclipse/q​sar/wizards/NewQSARProjectWizard.java: Name on subtasks
14:51 CIA-17 bioclipse: ospjuth * r4600 /branches/bioclipse2/misc/net.bioclipse.pkpd/: Initial import.
14:53 CIA-17 bioclipse: ospjuth * r4601 /branches/bioclipse2/misc/net.bioclipse.pkpd/ (27 files in 11 dirs): Stub for a PK/PD plugin with a non-implemented builder for pkpd.xml.
14:57 CIA-17 bioclipse: ospjuth * r4602 /branches/bioclipse2/misc/net.bioclips​e.pkpd/src/net/bioclipse/pkpd/builder/ (PKPDBuilder.java PKPDNature.java): lowercase in ids
15:21 CIA-17 bioclipse: jonalv * r4603 /branches/bioclipse2/ (3 files in 3 dirs): More attempts at getting recodring to work. It fails silently now. (The worst kind...)
15:49 CIA-17 bioclipse: ospjuth * r4604 /branches/bioclipse2/misc/net.bioclipse.pkpd/ (plugin.xml src/net/bioclipse/pkpd/editors/PKPDEditor.java): Cleanup of editor
15:51 CIA-17 bioclipse: ospjuth * r4605 /branches/bioclipse2/misc/net.bioclipse.pkpd/s​rc/net/bioclipse/pkpd/editors/PKPDEditor.java: Some cleanup in doc
16:16 CIA-17 bioclipse: jonalv * r4606 /branches/bioclipse2/bioinformatics/plugi​ns/net.bioclipse.biojava.business.tests/ (6 files in 3 dirs): Wrote a test for loading of fasta sequence
16:23 CIA-17 bioclipse: jonalv * r4607 /branches/bioclipse2/bioinformatic​s/plugins/net.bioclipse.biojava.bu​siness/src/net/bioclipse/biojava/ (4 files in 2 dirs): renamed file
16:27 CIA-17 bioclipse: jonalv * r4608 /branches/bioclipse2/core/plugins/net.b​ioclipse.recording.tests/src/net/biocli​pse/recording/tests/RecordingTest.java: Test code currently not working but which might work with RC2 of Spring-dm project
16:33 CIA-17 bioclipse: jonalv * r4609 /branches/bioclipse2/core/plug​ins/net.bioclipse.recording/: clearing up some strange naming
16:33 CIA-17 bioclipse: jonalv * r4610 /branches/bioclipse2/core/plugins/ (net.bioclipse.record/ net.bioclipse.recording/): clearing up some strange naming
17:26 CIA-17 bioclipse: jonalv * r4611 /branches/bioclipse2/ (14 files in 6 dirs): Added copyright text to my classes
17:32 CIA-17 cdk: rajarshi * r9809 /trunk/cdk/tools/nightly.py: Updated to process the pmd migration results
19:17 olas left #cdk
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20:13 egonw joined #cdk
20:44 CIA-17 jmol: nicove * r8902 /trunk/Jmol/src/org/jmol/translation/Jmol/et.po: Translation: estonian (et)
20:52 CIA-17 jmol: nicove * r8903 /branches/v11_4/Jmol/src/org/​jmol/translation/Jmol/et.po: Translation: Estonian (et)
21:14 CIA-17 jmol: nicove * r8904 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
21:16 jbrefort joined #cdk
21:24 CIA-17 cdk: rajarshi * r9810 /trunk/cdk/src/org/openscience/cdk/co​nfig/atomtypes/AtomTypeHandler.java: Fixed some PMD errors
21:49 CIA-17 cdk: rajarshi * r9811 /trunk/cdk/src/org/openscience/cdk/ (3 files in 3 dirs): Updated to use Junit 4 and added test class/method annotations
21:54 CIA-17 cdk: rajarshi * r9812 /trunk/cdk/src/org/openscience​/cdk/geometry/BondTools.java: Fixed a typo and added a missing annotation
22:01 CIA-17 cdk: rajarshi * r9813 /trunk/cdk/src/org/openscience/cdk/ (3 files in 3 dirs): Updated to JUnit 4 and added test class/method annotations. Some source methods that look empty either need to be removed, made private or tested
22:01 edrin joined #cdk
22:14 CIA-17 cdk: rajarshi * r9814 /trunk/cdk/src/org/openscience/cdk/ (5 files in 3 dirs): Updated to JUnit 4 and added test class/method annotations.
22:30 CIA-17 bioclipse: edrin_t * r4612 /trunk/xws-client/src/net/bioclipse/xws/client/ (4 files in 4 dirs): some minor bugfixes (especially of invokeSync!)
22:31 CIA-17 cdk: rajarshi * r9815 /trunk/cdk/src/org/openscience/cdk/ (3 files in 3 dirs): Updated to JUnit 4 and added test class/method annotations.

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