Camelia, the Perl 6 bug

IRC log for #cdk, 2007-10-05

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All times shown according to UTC.

Time Nick Message
04:49 egonw joined #cdk
05:16 carsten joined #cdk
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07:38 jpansanel moin
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08:15 thomas_ku joined #cdk
08:16 thomas_ku moin
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11:47 CIA-31 jmol: hansonr * r8355 /trunk/Jmol/src/org/jmol/ (modelset/ModelSet.java viewer/Eval.java): 11.3.29 code clean up -- VERSION
12:28 carsten joined #cdk
13:02 test joined #cdk
13:02 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 3597 test, 43 fails + 68 errors (3.09%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk
13:02 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 3597 test, 43 fails + 68 errors (3.09%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk
13:03 jpansanel hi carsten
13:03 carsten moin
13:04 jpansanel look at oxidane.cml for water
13:04 jpansanel (water directory)
13:04 carsten yes, but that is just one molecule
13:04 carsten I need more, correctly aligned
13:04 carsten a ice-crystal basically
13:08 jpansanel ok
13:09 jpansanel it's more complicated
13:09 jpansanel as you've more than one type of crystral for water
13:10 carsten well, I need one :-)
13:10 carsten doesn't matter, it is school, not university
13:17 jpansanel ok
13:35 CIA-31 jmol: nicove * r8356 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
14:05 rojasm left #cdk
15:06 CIA-31 bioclipse: carl_masak * r3928 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java:
15:06 CIA-31 bioclipse: [MatrixGridEditor.java]
15:06 CIA-31 bioclipse: * added 'Copy' menu alternative
15:54 CIA-31 bioclipse: carl_masak * r3929 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java:
15:54 CIA-31 bioclipse: [MatrixGridEditor.java]
15:54 CIA-31 bioclipse: * fixed ArrayIndexOutOfBoundsException bug
16:05 CIA-31 bioclipse: carl_masak * r3930 /trunk/plugins/net.bioclipse.statistics/sr​c/net/bioclipse/model/MatrixResource.java:
16:05 CIA-31 bioclipse: [MatrixResource.java]
16:05 CIA-31 bioclipse: * different regular expression to recognize several whitespace characters in a row
16:14 CIA-31 bioclipse: carl_masak * r3931 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java:
16:14 CIA-31 bioclipse: [MatrixGridEditor.java]
16:14 CIA-31 bioclipse: * undo of last commit
16:17 CIA-31 cdk: rajarshi * r9016 /trunk/cdk/src/data/smiles/drugs.smi: Added a collection of SMILES representing drugs and is useful for test for multiple SMARTS matches and SMILES parsing
16:32 CIA-31 cdk: rajarshi * r9017 /trunk/cdk/src/org/openscience/cdk/test/​smiles/smarts/parser/RecursiveTest.java: Added a test to go through a set of smiles looking for matches
16:50 carsten joined #cdk
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17:13 CIA-31 jmol: hansonr * r8357 /trunk/Jmol/src/org/jmol/ (modelset/ModelSet.java viewer/Jmol.properties): version=11.3.30_dev # new feature: adds Nitrogen logic to aromatic bond assignments
17:23 carsten jpansanel: man, thanks forf the mail!
17:31 CIA-31 jmol: hansonr * r8358 /trunk/Jmol/src/org/jmol/ (3 files in 2 dirs): version=11.3.30_dev # bug fix: menu for UNITCELL
17:50 CIA-31 jmol: hansonr * r8359 /trunk/Jmol/src/org/jmol/ (modelset/ModelSet.java viewer/Jmol.properties): 11.3.30_dev adding Oxgyen, Sulfur logic to aromatic bonding
18:32 CIA-31 cdk: rajarshi * r9018 /trunk/cdk/src/data/smiles/drugs.smi: Updted drug smiles list
18:56 CIA-31 cdk: rajarshi * r9019 /trunk/cdk/src/data/smiles/drugs.smi: Updated the drug smiles list to have molecules with no basic amines
18:58 CIA-31 cdk: rajarshi * r9020 /trunk/cdk/src/org/openscience/cdk/test/​smiles/smarts/parser/RecursiveTest.java: Added a comprehensive test for basic amines
19:16 CIA-31 cdk: rajarshi * r9021 /trunk/cdk/src/org/openscience/cdk/pha​rmacophore/PharmacophoreMatcher.java: Added logging code
19:54 CIA-31 cdk: rajarshi * r9022 /trunk/cdk/src/org/openscience/cdk/pha​rmacophore/PharmacophoreMatcher.java: Added logging code
20:29 CIA-31 cdk: rajarshi * r9023 /trunk/cdk/src/org/openscience/cdk/phar​macophore/PharmacophoreQueryBond.java: Fixed some javadocs
21:34 CIA-31 cdk: rajarshi * r9024 /trunk/cdk/src/org/openscience/cdk/test/​smiles/smarts/parser/RecursiveTest.java: Added another test case for the basic amine
21:39 CIA-31 jmol: hansonr * r8360 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs): 11.3.30 Povray Exporter
21:46 CIA-31 cdk: rajarshi * r9025 /trunk/cdk/src/data/mdl/cnssmarts.sdf: added an sdf for smarts testing
21:50 CIA-31 cdk: rajarshi * r9026 /trunk/cdk/src/org/openscience/cdk/test/sm​iles/smarts/parser/SMARTSSearchTest.java: Updted to include amino acid tests which now all work
22:10 CIA-31 cdk: rajarshi * r9027 /trunk/cdk/src/org/openscience/cdk/test/sm​iles/smarts/parser/SMARTSSearchTest.java: Added a test case to search for a smarts in an SDF molecule
22:23 CIA-31 jmol: hansonr * r8361 /trunk/Jmol/src/org/jmol/viewer/Eval.java: 11.3.30 Povray Exporter -- preliminary for Pim
22:34 CIA-31 cdk: rajarshi * r9028 /trunk/cdk/src/org/openscience/cdk/isomorphi​sm/matchers/smarts/TotalConnectionAtom.java: removed boxing
22:35 CIA-31 jmol: hansonr * r8362 /trunk/Jmol/src/org/jmol/modelset/ModelSet.java: 11.3.30 aromatic logic for N,O,S includes formal charge on O,S
22:36 CIA-31 jmol: hansonr * r8363 /trunk/Jmol/src/org/jmol/e​xport/PovrayExporter.java: 11.3.30 Povray Exporter -- preliminary for Pim -- more
22:49 CIA-31 cdk: rajarshi * r9029 /trunk/cdk/src/org/openscience/cdk/test/sm​iles/smarts/parser/SMARTSSearchTest.java: Updated test for reading from SDF
22:57 CIA-31 cdk: rajarshi * r9030 /trunk/cdk/src/org/openscience/cdk/isomorphism​/matchers/smarts/ExplicitConnectionAtom.java: Updated to take into account the fact that getHydrogenCount() might return null (UNSET) in which we case assume it's 0
22:59 CIA-31 cdk: rajarshi * r9031 /trunk/cdk/src/org/openscience/cdk/test/sm​iles/smarts/parser/SMARTSSearchTest.java: Added another example
23:00 CIA-31 cdk: rajarshi * r9032 /trunk/cdk/src/org/openscience/cdk/​smiles/smarts/SMARTSQueryTool.java:
23:00 CIA-31 cdk: Updated initialization code for the total connections of an atom. The old code
23:00 CIA-31 cdk: would subtract the count of explicit H;'s from the total number of connections.
23:00 CIA-31 cdk: But Daylight indicates that Xn means that an atom should have n bonds (including
23:00 CIA-31 cdk: implicit H's) and does not say that explicit H's should be ignored
23:12 CIA-31 cdk: rajarshi * r9033 /trunk/cdk/src/org/openscience/cdk/test/ph​armacophore/PharmacophoreMatcherTest.java: Added a test case for the CNS pharmacophore
23:13 CIA-31 cdk: rajarshi * r9034 /trunk/cdk/src/org/openscience/cdk/pha​rmacophore/PharmacophoreMatcher.java: Added logging code at various points. Also fixed a bug which would return non-unique smarts matches when creating pharmacophore atoms
23:22 CIA-31 cdk: rajarshi * r9035 /trunk/cdk/src/org/openscience/cdk/test/​smiles/smarts/parser/RecursiveTest.java: Minor change to an exampel to make it more robust

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