Camelia, the Perl 6 bug

IRC log for #cdk, 2010-08-29

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All times shown according to UTC.

Time Nick Message
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11:10 egonw moin
11:10 zarah privet egonw
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18:40 CIA-50 cdk: Egon Willighagen master * rd070396 / (2 files): Skip inner classes for @cdk.module and @cdk.githash JavaDoc tests (fixes #3043084) - http://bit.ly/962RuN
19:17 CIA-50 cdk: Egon Willighagen cdk-1.2.x * r3ec1480 / src/main/org/openscience/cd​k/smiles/SmilesParser.java :
19:17 CIA-50 cdk: Upper case the first character to also properly recognize lower cased 'aromatic' two-character element symbols (fixes SMILES parsign of things like c1[se]ccccc1
19:17 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/aKFnld
19:20 CIA-50 cdk: Egon Willighagen cdk-1.2.x * r6ab74bc / src/main/org/openscience/cd​k/smiles/SmilesParser.java :
19:20 CIA-50 cdk: Added missing elements, fixing several problems reported in bug #3048501
19:20 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/dr0mBm
19:20 CIA-50 cdk: Egon Willighagen cdk-1.2.x * r5cf9334 / src/main/org/openscience/cd​k/smiles/SmilesParser.java :
19:20 CIA-50 cdk: A few more missing elements in the SMILES two-character element symbol parsing
19:20 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/czYvCi
19:22 CIA-50 cdk: Egon Willighagen cdk-1.2.x * rbf8defd / src/test/org/openscience/cdk/​smiles/SmilesParserTest.java :
19:22 CIA-50 cdk: Unit tests for SMILES parsing bugs reported in #3048501
19:22 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/aS3nMw
19:22 CIA-50 cdk: Egon Willighagen cdk-1.2.x * r31f7462 / src/test/org/openscience/cdk/​smiles/SmilesParserTest.java :
19:22 CIA-50 cdk: More missing elements for SMILES parsing problems reported in bug #3048501
19:22 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/bH5VL9
19:24 CIA-50 cdk: Egon Willighagen master * r9eb04e5 / src/main/org/openscience/cd​k/inchi/InChIGenerator.java :
19:24 CIA-50 cdk: Fixed annotation with TestMethod, not TestClass (fixes #3016632)
19:24 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/9v6lXm
19:26 CIA-50 cdk: Egon Willighagen master * r937c4c7 / src/main/org/openscience/cd​k/smiles/SmilesParser.java :
19:26 CIA-50 cdk: Use the PT class to see if something can be an element and removing the redundant element symbol info
19:26 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/9nP6N7
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20:04 CIA-50 cdk: Mark Rynbeek master * rf6fd82b / (4 files in 3 dirs):
20:04 CIA-50 cdk: MDLV2000 reader interprets D and T without M ISO line mandatory
20:04 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/cUATYV
20:04 CIA-50 cdk: Egon Willighagen master * r6760330 / src/main/org/openscience/c​dk/io/MDLV2000Reader.java :
20:04 CIA-50 cdk: Use the builder pattern to instantiate an IIsotope
20:04 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/atJpSC
20:04 CIA-50 cdk: Egon Willighagen master * rd4045cc / src/test/org/openscience/cdk​/io/MDLV2000ReaderTest.java :
20:04 CIA-50 cdk: Assert pattern has the expected value as first argument
20:04 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/c5ODPV
20:08 CIA-50 cdk: Egon Willighagen master * rf0256d0 / (11 files in 5 dirs):
20:08 CIA-50 cdk: Renamed MDLWriter into MDLV2000Writer (implements #3029447)
20:08 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/aWMGyw
20:18 CIA-50 cdk: Egon Willighagen master * r0de5777 / src/main/org/openscience/cdk/io/SMILESWriter.java :
20:18 CIA-50 cdk: Also take into account super classes
20:18 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/aExdZO
20:23 CIA-50 cdk: Egon Willighagen master * r5a2bc65 / (5 files in 5 dirs):
20:23 CIA-50 cdk: Introduced a helper class with info about the CDK library: the version number, which is read from the build.props which is now included in the cdk-core.jar
20:23 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/cUkD3H
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21:12 CIA-50 cdk: Egon Willighagen master * r8ec9ad4 / (79 files in 42 dirs):
21:12 CIA-50 cdk: Renamed get/setHydrogenCount() to get/setImplicitHydrogenCount(), per report #3020065
21:12 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/c5VT4c
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21:50 egonw_ ha s9asad!
21:51 egonw_ got time to help me out?
21:51 s9asad Hi
21:51 zarah hi s9asad
21:51 s9asad Sure
21:51 s9asad let me know
21:51 egonw_ please tell me what needs to be changed in build.xml for your SMSD patch
21:51 egonw_ your 0003 patch was too dirty to apply
21:52 egonw_ mostly whitespace changes; impossible for me to see what changed, so could not fix it myself
21:52 egonw_ is now known as egonw
21:52 s9asad Smsd depends on signature
21:52 s9asad .jar
21:52 egonw that's the only change?
21:52 egonw that I can do
21:52 egonw nothing else?
21:53 egonw if not, I'll try that now
21:53 s9asad And I think one more lob
21:53 egonw lob?
21:53 s9asad Lib
21:53 egonw 3rd party lib?
21:53 s9asad I guess cdk valency checker
21:53 s9asad Let me start my laptop
21:54 s9asad Plz give me 5 mins
21:54 egonw np
21:54 egonw (no problem)
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21:59 asad_ Hi
21:59 zarah hi asad_
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21:59 asad_ is now known as s9asad
21:59 s9asad so
22:00 s9asad its basically
22:00 s9asad smsd depends on the signature.jar
22:00 egonw but that's all defined in the src/META-INF/ files anyway
22:01 egonw so, in the build.xml it's just the compile time reordering of signature and smsd?
22:01 egonw I will try that now
22:01 s9asad while compiling it has to compile after cdk-signature.jar
22:01 s9asad sure
22:01 egonw yes, I understand
22:07 egonw ok, compiling
22:07 s9asad super
22:10 egonw hang on...
22:10 egonw found a unrelated problem
22:11 s9asad ?
22:11 egonw CDK.java patch that hit master today break compilation
22:12 egonw only just noticed that
22:12 egonw fixing that now
22:12 s9asad oh
22:12 egonw rajarshi is standing by to apply review the patch and apply it
22:13 s9asad looks like you guys are out and about for bug squashing session
22:14 egonw yeah, seems so :)
22:14 s9asad :-)
22:20 egonw so, why does smsd actually depend on the signature module?
22:21 s9asad well I use signature to canonise the atom container
22:22 egonw please go on
22:22 egonw why is canonisation needed?
22:23 CIA-50 cdk: Egon Willighagen master * re2c8329 / src/main/org/openscience/cdk/CDK.java :
22:23 CIA-50 cdk: Use the factory to not depend on an implementation
22:23 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/bDEquq
22:25 s9asad canonisation-: this part of the code was need to make sure that of two graphs are isomorphic then the atom container too should have similar index (sequential mappinf index)
22:25 egonw ah, ok
22:25 s9asad if* two graphs*
22:25 egonw sounds like a good use
22:26 s9asad thanks
22:27 egonw mmm... had to rebase your patch
22:27 egonw one conflict
22:27 egonw resolved that one manually
22:28 s9asad great
22:28 s9asad which one?
22:28 egonw one class change implementation
22:28 s9asad Oh
22:28 egonw but the old code was using IAtom.getHydrogenCount()
22:28 egonw which is now getImplicitHydrogenCount()
22:29 egonw but your new code was not using the hydrogenCount code anymore anyway...
22:29 egonw but you are at many other places :)
22:29 egonw OK, me is hacking...
22:29 s9asad yeah, indeed that was a very good patch, who so ever suggested, thanks to him
22:29 egonw trivial fixes :)
22:29 egonw ola spjuth @ uppsala
22:31 s9asad Once this SMSD patch is done I would like to discuss few improvements in the SMART code
22:31 egonw please start doing that on the cdk-devel@ mailing list
22:31 s9asad good idea
22:31 egonw I'm not the best person to discuss that with
22:31 egonw but others on the ML are
22:38 CIA-50 cdk: Syed Asad Rahman master * r7217e82 / (166 files in 37 dirs): (log message trimmed)
22:38 CIA-50 cdk: Latest SMSD code 1.2.0: Major changes are:
22:38 CIA-50 cdk: b) Optimised Substructure search
22:38 CIA-50 cdk: c) Hanser Ring detection
22:38 CIA-50 cdk: f) MolHandler fixed
22:38 CIA-50 cdk: e) Matchers introduced
22:38 CIA-50 cdk: f) Canonical Signatures used
22:38 CIA-50 cdk: Egon Willighagen master * r7d5fc9d / build.xml : The smsd module now depends on the signature module - http://bit.ly/cFTdoY
22:38 CIA-50 cdk: Egon Willighagen master * r0f64e4d / (6 files in 2 dirs): Updates for the getImplicitHydrogenCount() renaming - http://bit.ly/9gZ3yi
22:39 egonw s9asad: btw, did you post those statistics on how much faster the SMARTS matching is when based on your code, compared to the current implementation?
22:39 egonw I have not seen those yet
22:39 s9asad I can only do that once I have these patches done.
22:40 s9asad else my numbers don't make sense
22:40 egonw how so?
22:40 egonw I mean, you have the patch, right?
22:40 s9asad Hence I am drafting a mail for changes in the SMART itself
22:40 egonw what does patch 3052052 do then?
22:41 s9asad The present smartcode itself can be improved
22:41 s9asad aha, that patch has to be ignored, as I need to discuss few things on the mailing list
22:41 s9asad this will really improve the speed
22:42 egonw ok, then please close the bug report
22:42 s9asad how to do that
22:42 egonw go to the bug report
22:42 egonw set Resolution to: Invalid
22:42 egonw and Status to: Closed
22:43 egonw these Resolution you can use to:
22:43 egonw Rejected
22:43 egonw and: Out of Data
22:43 egonw and: Out of Date
22:43 egonw E
22:43 egonw and make sure to give some text in the comment as to why it is such
22:48 s9asad done
22:49 s9asad just sent a mail on the dev
22:57 s9asad so
22:57 s9asad does the smsd patch work?
22:58 egonw I hope you checked
22:58 egonw I just applied it
22:58 s9asad aha sorry i was away
22:59 s9asad i have added a function turbo substructure search, which might be of use in smarts as its looks for first match only
23:00 egonw sounds interesting
23:01 egonw OK, I'm off to bed now
23:01 s9asad so are you back in eu
23:01 s9asad :-)
23:01 egonw yes
23:01 egonw bad not in the right rythm yet
23:01 s9asad aha will read your blog about the meeting
23:02 egonw yeah, if I ever write that up... (we'll see...)
23:02 s9asad biological clock will takr its own time
23:02 egonw otherwise, feel free to review one or two more of my patches in the Patches tracker
23:02 s9asad take*
23:02 s9asad sue will do that 2row
23:03 s9asad see 2row
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23:04 s9asad thanks egon
23:04 s9asad left #cdk
23:10 CIA-50 cdk: Egon Willighagen cdk-1.2.x * ra01de91 / src/main/org/openscience/cdk/​dict/data/cdk-atom-types.owl :
23:10 CIA-50 cdk: Fixed hybridization information: these are sp3 hybridized systems
23:10 CIA-50 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/dmwn92
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