Camelia, the Perl 6 bug

IRC log for #cdk, 2007-10-31

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All times shown according to UTC.

Time Nick Message
02:30 CIA-16 jmol: hansonr * r8547 /trunk/Jmol/src/org/ (2 files in 2 dirs):
02:30 CIA-16 jmol: version=11.3.40_dev
02:30 CIA-16 jmol: # POV-Ray fix for number formatting width > 999
07:05 jbrefort joined #cdk
07:06 rojasm joined #cdk
07:25 egonw joined #cdk
07:25 egonw moin
07:41 rojasm moin
08:12 * egonw is playing with git-svn
08:12 egonw http://www.flavio.castelli.​name/howto_use_git_with_svn
08:15 egonw rojasm: around?
08:16 egonw just looked at your r9269 patch
08:16 egonw one small comment, one question
08:16 egonw assertEquals(46.96885268,totalExactMass,0.001);
08:16 egonw that error of 0.001 could be much smaller... say 0.00000001
08:16 egonw nto?
08:17 egonw not?
08:18 egonw the question is about getTotalNaturalAbundance(IAtomContainer)...
08:18 egonw should that not be normalized?
08:18 egonw that is...
08:19 egonw return abundance/100**atomContainer.getAtomCount() ?
08:20 egonw oh... saw commit 9270 too now..
08:20 egonw so you do normalize :)
08:20 egonw but not correctly...
08:20 masak joined #cdk
08:22 egonw anyway, rather nice/interesting patches
08:39 CIA-16 cdk: egonw * r9271 /trunk/cdk/.classpath: Removed jars no longer in SVN.
08:40 egonw cool :)
08:40 egonw that was my first commit using git/git-svn
08:40 CIA-16 bioclipse: ospjuth * r4102 /trunk/playground/plugins/net.bioclips​e.biomoby.ui/src/net/bioclipse/biomoby​/ui/views/MobyViewLabelProvider.java: Removed status added by labelprovider
08:42 masak egonw: cool indeed. any special reason you're trying out git?
08:42 egonw yes
08:43 masak I've been curious about it myself for a while
08:43 egonw because git allows me to make commits when I am offline
08:43 masak very good reason
08:43 egonw and then I can commit the changes later to SVN
08:43 egonw with git-svn
08:43 masak I've been using svk for offline committing, mainly
08:43 egonw so I can work on the train, while maintaining my normal commit behaviour
08:43 egonw commit soon, commit often
08:43 masak verily
08:44 CIA-16 bioclipse: ospjuth * r4103 /trunk/playground/plugins/net.bioclipse.bio​moby.ui/src/net/bioclipse/biomoby/ui/prefs/ (BioMobyPrefsInitializer.java RegistryPage.java): Updated the preference page and initializer. Still doesn't run on first startup.
08:44 CIA-16 bioclipse: ospjuth * r4104 /trunk/playground/plugins/net.bioclipse.bio​moby.ui/src/net/bioclipse/biomoby/ui/model/ (3 files): Updated ViewObjects for new child creation process based on cached info
08:45 CIA-16 bioclipse: ospjuth * r4105 /trunk/playground/plugins/net.biocli​pse.biomoby.ui/src/net/bioclipse/bio​moby/ui/model/MobyViewCentral.java: New child creation process based on cached impl
08:45 CIA-16 bioclipse: ospjuth * r4106 /trunk/playground/plugins/net.biocl​ipse.biomoby.ui/src/net/bioclipse/b​iomoby/ui/BioclipseMobyModel.java: Use new cache dir in prefs page
09:34 rojasm joined #cdk
09:35 rojasm ooo
09:35 rojasm you are with the error
09:39 rojasm with the normalization I don't understand why abundance/100**atomContainer.getAtomCount()
09:39 rojasm egonw!
09:40 egonw because which atom you multiply by 100 (max)
09:40 egonw 90*74*88 results in something in the domain [0,1000000] == [0, 100^3]
09:41 rojasm ok
09:41 rojasm I see
09:41 rojasm I summit again
09:47 CIA-16 cdk: miguelrojasch * r9272 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): correctly normalized == abundance/(100^atomContainer.getAtomCount())
09:51 rojasm egonw. it is not possible to create a int[9437184][22]
09:51 rojasm is to big?
09:52 rojasm in java of course
09:52 egonw sound like a memory problem
09:52 rojasm I have problem of OutOfMemoryError
09:52 rojasm :)
09:52 rojasm Is there some solution or I have to go to R for that
09:54 egonw rojasm: need to go shopping now...
09:54 rojasm no problem
09:55 egonw solution: depends on what you want to acchieve
09:55 rojasm is nice to go shopping
09:55 rojasm :)
09:55 masak rojasm: are you sure you need all that space?
09:55 masak if not, sounds like a job for a sparse matrix
09:56 rojasm may be
09:56 masak rojasm: also, you might not need to keep all in memory at once
09:56 rojasm they are all possible combinations creating Isotopes pattern
09:56 masak ok
09:56 masak and what is the algorithm you want to perform on them?
09:57 rojasm first I create the matrix for Br2 is
09:57 rojasm brom has 2 isotopes
09:57 egonw rojasm: what about storing only those with a 'abundance' of 0.1% or more?
09:57 rojasm 11
09:57 rojasm 12
09:57 rojasm 21
09:57 rojasm 22
09:58 egonw no, differently...
09:58 egonw what do you store in the matrix?
09:58 egonw is it indeed sparse?
09:58 rojasm ja that could be now I am using 0.001
09:58 rojasm ok
09:58 egonw that is... are all values filled, or only some?
09:58 rojasm all
09:58 masak :/
09:58 egonw ok, cu later
09:59 masak egonw: cu
09:59 masak rojasm: ok, so you've built this matrix of isotope-combined-with-isotope. what do you do with it?
10:01 rojasm Then with this matrix I create IAtomContainer with atoms which have the correct Isotope mass
10:01 rojasm that help me after for find the isotpe pattern
10:02 masak so you have as many IAtomContainers as you have elements in the array?
10:02 rojasm It works but now I have the problem with C5H13N2O2
10:02 rojasm that is already too big
10:02 masak ok
10:02 rojasm mmm
10:02 rojasm :(
10:02 masak I'm thinking you could maybe eliminate the big array somehow
10:03 rojasm ok
10:03 masak does that seem possible? do you access each element in the array only once?
10:03 rojasm yes
10:04 masak great
10:04 masak and then you loop over the array using for loops?
10:04 rojasm yes
10:04 masak excellent
10:04 masak ditch the array
10:05 rojasm ok thanks i will try
10:05 masak calculate the value of each element as you need it
10:05 masak good luck :)
10:52 CIA-16 cdk: miguelrojasch * r9273 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): correction in power operator
11:16 CIA-16 cdk: egonw * r9274 /trunk/cdk/src/org/openscience/cdk/ (5 files in 5 dirs): Removed interruptable SMILES parser. The AllRingsFinder is no longer used, so no timeout feature requirred.
11:16 CIA-16 cdk: egonw * r9275 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): Moved CDKHueckelAromaticityDetector to 'standard' to fix the compile errors.
12:37 CIA-16 bioclipse: ospjuth * r4107 /trunk/playground/plugins/net.bioclipse.biomoby.ui​/src/net/bioclipse/biomoby/ui/views/MobyView.java: Added search field that filters tree based on service name
12:50 dleidert joined #cdk
13:13 CIA-16 bioclipse: ospjuth * r4108 /trunk/playground/plugins/net.biocli​pse.biomoby.ui/src/net/bioclipse/bio​moby/ui/model/MobyViewCentral.java: Replaced search bar with patternfFilter. Much nicer filtering now.
13:23 CIA-16 cdk: rajarshi * r9276 /trunk/cdk/tools/nightly.py: Put back Egons edits
13:32 CIA-16 bioclipse: ospjuth * r4109 /trunk/playground/plugins/net.bioclipse.biomoby.ui​/src/net/bioclipse/biomoby/ui/views/MobyView.java: Filtered on whole name, not just from beginning
14:03 rguha joined #cdk
14:19 rojasm egonw! experience with jri
14:19 rojasm ?
14:19 rojasm or somebody
14:19 egonw what's jri again? the bridge to R?
14:19 rojasm yes
14:20 egonw rojasm: ask bjarni on #bioclipse
14:20 egonw or rajarshi
14:20 rojasm ok
15:08 jbrefort joined #cdk
15:16 rguha joined #cdk
15:16 egonw hi rguha
15:16 rguha egonw: hi - a student had come over
15:16 egonw I am just writing up some findings on the failing test...
15:16 rguha hence my vaishing
15:16 egonw ah :)
15:17 rguha tests are looking good!
15:17 egonw huh?
15:18 CIA-16 cdk: egonw * r9277 /trunk/cdk/src/org/openscience/cdk/test​/smiles/smarts/parser/ParserTest.java: Added a convenience method to dump the atom types
15:18 rguha relatively small fraction of failure/errors
15:18 CIA-16 cdk: egonw * r9278 /trunk/cdk/src/org/openscience/cdk​/atomtype/CDKAtomTypeMatcher.java: Don't perceive based on hybridization if nitrogens are charged
15:18 egonw ah, just 50 output some 300 right..
15:18 CIA-16 cdk: egonw * r9279 /trunk/cdk/src/org/openscience/cdk/test​/smiles/smarts/parser/ParserTest.java: Also dump the aromaticity flag (and look at next failing test)
15:18 egonw that was git-svn in action :)
15:19 rguha where id git come from?
15:20 egonw http://chem-bla-ics.blogspot.com/2007/10/o​ffline-cdk-development-using-git-svn.html
15:21 rguha aah, very sweet
15:21 rguha got to take a look at thi
15:22 egonw it's great...
15:22 dleidert egonw: Linux surname is Torvalds ... maybe you should fix that in the blog entry ;)
15:23 dleidert s/Linux/Linus
15:24 egonw dleidert: fixed, thanx for letting me know!
15:24 dleidert no problem :)
15:24 egonw rguha: email sent regarding the failing tests..
15:25 egonw dleidert: any progress on the packaging side?
15:26 dleidert gcu is currently prepared (goffice0.4 will arrive in Sid soon)
15:26 dleidert we have several packages waiting (ghemical, bkchem, ...)
15:26 egonw yes, I saw that news on debian-science
15:26 dleidert but I did not yet find time to work on CDK
15:26 egonw ack
15:27 dleidert I already tested, how to extract the svn-commits/logs, ... from the pkg-java SVN and how to inject it into the debichem SVN - just for the case
15:27 dleidert however ... I also read your mail to Steffen Moeller about Jmol ... but the same here ... no time atm
15:28 egonw ack
15:28 egonw same here...
15:28 egonw but at least I managed to get the new CDK atom typing online...
15:28 egonw and seems to be doing a rather well job...
15:28 egonw much cleaner code... much easier debugging of problems
15:29 egonw .deb packages has lower priority, because I can contribute less unique things to the opensource community
15:31 dleidert no problem ... no package is waiting for CDK atm ... I hope, I'll find some more time this month
15:31 egonw yeah, that's a pity...
15:31 egonw bioclipse should be waiting for it :)
15:31 dleidert ... and I hope, Debian will create the uploaders keyring for non-DDs ... would make things easier and faster
15:32 dleidert well, haven't tested bioclipse yet, so I have no clue, how easy or difficult packaging it will be
15:33 egonw should be quite the same as any eclipse plugin...
15:33 egonw but I know it's non-trivial...
15:34 egonw we worked on it in the past... but I lack time and the important details...
15:49 CIA-16 cdk: rajarshi * r9280 /trunk/cdk/src/org/openscience/cdk/​smiles/smarts/SMARTSQueryTool.java: Updated to use CDKHueckelAromaticityDetector
15:55 egonw rguha: might you rerun nightly with the updated SMARTSQueryTool?
15:55 CIA-16 cdk: rajarshi * r9281 /trunk/cdk/src/org/openscience/cdk/test​/smiles/smarts/parser/ParserTest.java: Fixed the test for the R2 smarts suince the target molecule has 2 ring atoms that are part of two rings
15:55 rguha it'll run in 5 minutes :)
15:56 egonw ah :)
16:01 CIA-16 cdk: djiao * r9282 /trunk/cdk/ (54 files in 6 dirs):
16:01 CIA-16 cdk: Cleaned classes in org.openscience.cdk.isomorphism.matches. Removed unnecessary
16:01 CIA-16 cdk: classes after the removal of JavaCC based smarts parser. Also cleaned code in
16:01 CIA-16 cdk: org.openscience.cdk.smiles.s​marts.parser.SMARTSParser.jj and javacc generated
16:01 CIA-16 cdk: classes.
16:01 CIA-16 cdk: rajarshi * r9283 /trunk/cdk/src/org/openscience/cdk/test​/smiles/smarts/parser/ParserTest.java: Updted the expected property for C@C in benzene - there are 12 matches but 6 USA matches. Since the matcher is not looking at USA matches we should check that the expcted count is 12, not 6
16:18 CIA-16 cdk: rajarshi * r9284 /trunk/cdk/src/org/openscience/cdk/test​/smiles/smarts/parser/ParserTest.java: Updated single bond count tests - matches daylight depictmatch
16:23 CIA-16 cdk: rajarshi * r9285 /trunk/cdk/src/org/openscience/cdk/test​/smiles/smarts/parser/ParserTest.java: Updated more tests so that use the proper expected match count for non-USA matching
16:32 CIA-16 cdk: egonw * r9286 /trunk/cdk/src/org/openscience/cdk/ (5 files in 5 dirs): Added O.planar3 atom type as found in furan; added JUnit test for furan
16:33 CIA-16 cdk: egonw * r9287 /trunk/cdk/src/org/openscience/cdk/ (5 files in 5 dirs):
16:33 CIA-16 cdk: Revert "Added O.planar3 atom type as found in furan; added JUnit test for furan"
16:33 CIA-16 cdk: This reverts commit 98d32817e7f8f38d800ecc98e1e7122dbd00bf6c.
16:33 CIA-16 cdk: egonw * r9288 /trunk/cdk/src/org/openscience/cdk/ (3 files in 3 dirs): Added O.planar3 atom type as found in furan; added JUnit test for furan
16:34 egonw OK, dinner time...
16:34 egonw will be back later
16:35 rguha bye
16:45 CIA-16 bioclipse: ospjuth * r4110 /trunk/playground/plugins/net.bioclipse.biomoby/ (10 files in 3 dirs): Updated to new BioMoby 2007-10-31 and added some tests
17:04 rojasm joined #cdk
17:42 CIA-16 cdk: rajarshi * r9290 /trunk/cdk/src/org/openscience​/cdk/smiles/SmilesParser.java: Removed incorrect Javadoc
18:08 CIA-16 jmol: pimpimpim * r8548 /trunk/Jmol/src/org/ (3 files in 3 dirs): povray: caps on slabbed atoms, matte finish for translucenct objects
18:09 egonw joined #cdk
18:09 rguha hi
18:13 rguha egonw: is it the job of the atom type macther to set hybridization?
18:15 egonw no
18:15 rguha ok
18:15 egonw that only does the perception...
18:15 rguha then the hucekl detector needs some work
18:15 egonw use the AtomTypeManipulator.configure()
18:15 rguha since it will never add 2 e for the O in furan
18:15 egonw was just reading your bug report...
18:15 egonw will explain...
18:15 rguha because it has no hybridization set
18:15 egonw the method name is misleading...
18:16 egonw no, it should not...
18:16 egonw let me explain..
18:16 rguha ok
18:16 egonw O.planar != O.sp2
18:16 egonw that's one thing...
18:16 rguha yes, I realized that
18:16 egonw the second has 1 electron available for p_z
18:16 egonw OK, good :)
18:16 egonw while O.planar 2 electrons because the lone pair...
18:16 rguha right
18:16 egonw I don't want to go the *.aromatic way...
18:17 egonw because aromaticity is not well defined...
18:17 rguha ok that's fine
18:17 egonw the method name is inaccurate...
18:17 egonw allSP2 is wrong...
18:17 rguha which method?
18:17 rguha oh right, yes I agree
18:17 egonw actually...
18:17 rguha but where you check for N.planar3, S.2 etc I added a check for O.planar3
18:17 egonw if you check the code, you should already find the method to be OK with N.planar3...
18:17 egonw right
18:18 rguha but the problem is the code will never get to that part
18:18 egonw OK, that's good
18:18 rguha because the hyb for the O atom is null
18:18 rguha where does the hyb get set?
18:18 rguha for N.plana3 cdk_atomtypes.xml provides a hybridization value
18:19 rguha but not for O.planar3
18:19 egonw I though I had added that...
18:19 egonw mom...
18:20 egonw ah...
18:20 egonw well.. the XML is fine...
18:20 egonw the XML parsing is not...
18:20 rguha ?
18:20 rguha the XML doc has planar for the hyb
18:20 rguha is that a valid CDK constant?
18:21 egonw guess not yet... :)
18:21 rguha aah
18:21 rguha so something called CDKConstants.PLANAR
18:22 egonw Yeah, but let's make this a proper Enum
18:22 rguha ok
18:22 rguha i'll hold of on the hueckel class commit till the constant is added
18:22 egonw mom...
18:24 egonw oh, well...
18:24 egonw how much can get broken :)
18:24 rguha ?
18:25 egonw changing the signature of getHybridzation() ...
18:26 egonw remember I suggested IBond.Order as Enum ?
18:26 egonw could idea...
18:26 rguha right
18:26 egonw but one big ugly patch...
18:26 egonw had to change the whole CDK code :)
18:26 rguha yuk
18:26 egonw spent two hours before I gave up :)
18:26 rguha how long will getHybridization take to fix? :)
18:27 rguha should be easier than bond orders!
18:27 egonw right
18:27 egonw mom
18:31 egonw OK, changed the API...
18:31 egonw 160 problems
18:32 rguha hmm
18:32 rguha what's the new API?
18:36 egonw IAtomType.setHybridization(IAtomType.Hybridization hybridization)
18:37 rguha what does the Hybridization enum look like?
18:37 egonw much like the Enum in IBond
18:37 rguha oh ok
18:38 rguha do you want to pactch it all? or will you committ and I can handle some classes
18:39 rguha also IAtom.getHybridiztion needs to be updated
18:42 egonw OK, sounds good...
18:42 egonw hang on...
18:42 egonw will commit what I changed now...
18:45 CIA-16 cdk: egonw * r9291 /trunk/cdk/src/org/openscience/cdk/ (4 files in 4 dirs): Start of IAtomType.Hybridization Enum.
18:46 egonw I'll do the CDKAtomTypeMatcher
18:46 egonw can you start with cdk.test?
18:47 egonw oh... argh...
18:47 egonw forgot to remove the H11N prefix for SP3D4_bla hybridizations...
18:53 rguha i'll work on cdk.test
18:53 rguha don't you also need to change IAtom?
18:54 egonw no, don't think so...
18:55 rguha oh right
18:55 rguha btw, I'm updatingthe hueckel class for the new enum
18:56 egonw already did that
18:57 rguha did you committ?
18:57 egonw not yet
18:58 rguha oh ok
19:08 egonw ha, look a this marvolous bit of code:
19:08 egonw int oldHCount = atom.getHydrogenCount() == null ? 0 : atom.getHybridization().intValue();
19:08 egonw hehehe
19:13 rguha mine, I think :(
19:13 egonw to fix, or who did it?
19:13 egonw I could have done it too...
19:14 egonw it's the autocomplete...
19:14 egonw this is one reason why these Enums are so great...
19:14 egonw the constant has a type
19:14 rguha I think I did that - though why I would do intValue() I don't know!
19:14 rguha btw, can you comit the hueckel code - I can't compile beyond that
19:14 egonw oh...
19:15 egonw really?
19:15 egonw Eclipse has no problem with that :)
19:15 egonw ok, hang on
19:15 rguha it's difficult to find out errors without looking at individual files
19:16 egonw rigth
19:16 egonw doing it one by one too
19:16 CIA-16 jmol: pimpimpim * r8549 /trunk/Jmol/src/org/jmol/ex​port/_PovrayExporter.java: fix to small copy/paste mistake in povray slab capping
19:17 CIA-16 cdk: egonw * r9292 /trunk/cdk/src/org/openscience/cdk/ (10 files in 7 dirs): Some IAtomType.Hybridization fixes
19:19 CIA-16 cdk: rajarshi * r9293 /trunk/cdk/src/org/openscience/cdk/test/ (2 files in 2 dirs): Updaetd to use the new Hybridization enum type
19:21 CIA-16 cdk: rajarshi * r9294 /trunk/cdk/src/org/openscience/cdk/aromat​icity/CDKHueckelAromaticityDetector.java: Updated to take into account the O.plana3 type when adding electrons
19:22 egonw mmm...
19:23 egonw there are a number of 'errors' not poping up...
19:23 rguha i'm working on valency hybrid checker
19:23 egonw atom.getHybridization() == CDKConstants.UNSET
19:23 egonw the latter == null
19:23 egonw which results in OK code...
19:23 egonw but the proper equation should be:
19:23 egonw atom.getHybridization() == Hybridization.UNSET
19:24 rguha I think a single UNSET is OK
19:24 rguha why specialize UNSET's?
19:25 egonw can't think of a reason, really
19:25 rguha btw, is there any way to use a switch statement and enum values?
19:26 egonw no, not really...
19:26 egonw that's a bit dissappointing...
19:26 egonw brb
19:30 rguha See http://www.javacamp.org/designPattern/enum.html
19:30 rguha actually that's not a good idea for our situation
19:35 egonw OK, seems I'm done with the non cdk.test classes
19:35 rguha just fixed smilesparser :)
19:35 CIA-16 cdk: egonw * r9295 /trunk/cdk/src/org/openscience/cdk/ (4 files in 4 dirs): Some more IAtomType.Hybridization fixes
19:35 rguha aargh!
19:35 rguha forgot to update
19:35 egonw :)
19:36 rguha test is fixed
19:38 egonw commit is pending?
19:38 rguha no committed
19:39 rguha but the furan O problem is still there
19:39 rguha hyb is set to Hybridization.UNSET
19:39 egonw right...
19:39 egonw next step...
19:39 egonw please commit
19:40 rguha I did commit the test code
19:40 egonw all?
19:40 rguha I only found two places - let me check - a recompile is running
19:40 egonw ah... that's why I love Eclipse...
19:40 egonw it will give me all compile errors....
19:41 rguha aah, one sec
19:42 egonw OK, got to go now...
19:43 rguha ok, bye
19:43 egonw those autogenerated files should not go in SVN...
19:43 egonw please fix it like this:
19:43 egonw (for now)
19:43 egonw modify the code of net.sf.cdk.tools.MakeJavafilesFiles.java
19:44 egonw so that it places classes in the cdk.smiles.smarts package in the smarts module...
19:44 egonw bit ugly...
19:44 egonw but will think about a better solution...
19:44 rguha ok
19:44 egonw this workaround is basically the result of things going into extra by default...
19:45 egonw having autogenerated files in SVN will give nasty SVN errors like:
19:45 egonw ...
19:45 egonw U    src/org/openscience/cdk/smiles/smar​ts/parser/SMARTSParserVisitor.java
19:45 egonw U    src/org/openscience/cdk/smiles​/smarts/parser/SMARTSParser.jj
19:45 egonw svn: Failed to add file 'src/org/openscience/cdk/smiles/smarts/​parser/SMARTSParserTokenManager.java': object of the same name already exists
19:45 egonw and break off of the svn update process :(
19:45 egonw OK, email me further problems you encounter...
19:45 egonw cu later
19:45 rguha sure
19:47 CIA-16 cdk: rajarshi * r9296 /trunk/cdk/src/org/openscience/cdk/test/ (3 files in 2 dirs): Fixed for the new hybridization enum
19:58 CIA-16 cdk: rajarshi * r9297 /trunk/cdk/src/org/openscience/cdk/test/tools/ (3 files): Fixed for the new hybridization enum
20:01 CIA-16 cdk: rajarshi * r9298 /trunk/cdk/src/org/openscience/cdk/test/ (2 files in 2 dirs): Fixed for the new hybridization enum
20:10 CIA-16 cdk: rajarshi * r9299 /trunk/cdk/src/org/openscience/cdk/co​nfig/atomtypes/AtomTypeHandler.java: Added code to handle the planar3 hybridization state
20:23 CIA-16 cdk: rajarshi * r9300 /trunk/cdk/src/org/openscience/cdk/AtomType.java:
20:23 CIA-16 cdk: Updated so that unset hybridization uses CDKConstants.UNSET, since there is no
20:23 CIA-16 cdk: real need for specialization of UNSET. If osmethingis UNSET it means it's not
20:23 CIA-16 cdk: set(!) and so that something should be done. There is really no difference
20:23 CIA-16 cdk: between an unset hyb or an unset charge
20:29 CIA-16 cdk: rajarshi * r9301 /trunk/cdk/src/org/openscience/cdk/aromat​icity/CDKHueckelAromaticityDetector.java: Cleaned up code
20:33 CIA-16 jmol: nicove * r8550 /trunk/Jmol-FAH/projects/ (p4103.xyz.gz p4112.xyz.gz): Folding@Home
21:19 rguha joined #cdk
21:19 rguha can somebody put me out of my confusion: what is the hybridizat of the ring N in pyrrole?
21:25 jbrefort sp2
21:28 CIA-16 jmol: hansonr * r8551 /trunk/Jmol/src/org/jmol/ (export/_PovrayExporter.java viewer/Jmol.properties): version=11.3.40_dev # POV-Ray clipping codeing minor tweak
21:57 CIA-16 cdk: rajarshi * r9302 /trunk/cdk/src/org/openscience/cdk​/atomtype/CDKAtomTypeMatcher.java:
21:57 CIA-16 cdk: Added a fix to percieveNitrogens so that if an atom with SP2 hyb comes in then
21:57 CIA-16 cdk: the code will check whether it might be a N.planar3 rather than assume that it
21:57 CIA-16 cdk: is a N.sp2. This fixes the case of pyrrole nitrogens - but I'm not sure whether
21:57 CIA-16 cdk: this ends up being too specific or there is a way to generalize this,
22:01 CIA-16 cdk: rajarshi * r9303 /trunk/cdk/src/org/openscience/cdk/test​/smiles/smarts/parser/ParserTest.java: removed some debugging code
22:33 CIA-16 cdk: rajarshi * r9304 /trunk/cdk/src/org/openscience/cdk/test/aromat​icity/CDKHueckelAromaticityDetectorTest.java: Added test for a substituted pyrrole
22:44 CIA-16 cdk: rajarshi * r9305 /trunk/cdk/src/org/openscience/c​dk/math/RandomNumbersTool.java: Removed exponentialFloat since float does not provide accuracy to satisfy a reasonable (2 decimal places) test. Use the double version if required
22:45 CIA-16 cdk: rajarshi * r9306 /trunk/cdk/src/org/openscience/cdk/t​est/math/RandomNumbersToolTest.java: Updated error messages
22:49 CIA-16 cdk: rajarshi * r9307 /trunk/cdk/src/org/openscience/cdk/test​/smiles/smarts/parser/ParserTest.java: Added a test for a N substituted pyrrole
23:00 CIA-16 cdk: rajarshi * r9308 /trunk/cdk/src/org/openscience/cdk/test/​smiles/smarts/SMARTSQueryToolTest.java: Updated to the new aromaticity detector

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