Camelia, the Perl 6 bug

IRC log for #cdk, 2008-12-08

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All times shown according to UTC.

Time Nick Message
00:28 timvdm joined #cdk
01:57 slyrus_ I don't suppose somebody has a nice set of validated canonical smiles examples for checking a canonical smiles generator do they?
05:45 egonw joined #cdk
05:56 CIA-16 cdk: egonw * r13502 /cdk/branches/cdk-1.2.x/build.props: Preparing release 1.1.3
05:57 CIA-16 cdk: egonw * r13503 /cdk/tags/cdk-1.1.3/: Released CDK 1.1.3
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07:21 slyrus_ egonw: yay. finally got my smiles stuff doing reasonably-canonical smiles writing so now I can round trip smiles from strings to objects and back. no geometric isomers or stereochemistry yet, but that's next.
07:38 egonw good to hear that
07:44 slyrus_ it strikes me that this canonicalization isn't really all that hard -- it's just that no on has written a proper spec on how to do it and all the literature out there is contradictory.
07:47 egonw yes, there are many ways to uniquely number atoms...
07:47 egonw and each algorithm results in a different unique SMILES
07:48 slyrus_ sure, but what seems to be out there are a whole bunch of approximations to one poorly specified algorithm.
07:48 slyrus_ seems like one could finish the task of spec'ing out that algorithm and be done with it.
07:48 egonw what specified algorithm?
07:49 egonw really... the canonilization algo for the official unique SMILES has not been published at all
07:49 slyrus_ I was using weinenger 89 as the poorly spec'ed algorithm.
07:50 slyrus_ official unique is useless if not published.
07:50 slyrus_ unfortunately, the opensmiles guys seem to be shying away from the issue :(
07:51 egonw they try to take one step at a time...
07:51 egonw anyway... we have InChI for uniqueness now
07:51 slyrus_ yeah, I guess that's where I'll have to go next.
07:52 egonw I am just upgrading the JNI-InChI bridge...
07:52 egonw so CDK should soon support generating of keys
07:52 egonw so CDK InChI generation should soon support generating of keys
07:52 egonw and work on 64 bit systems, as well as OS/X
07:52 slyrus_ huh. is the inchi library a C library?
07:53 egonw yes
07:53 egonw or C++, not sure about that
07:53 slyrus_ ah. ok. C would be preferable for me. I imagine the JNI stuff works with C++ libraries as well?
07:54 egonw yeah, think so
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10:17 CIA-16 cdk: mark_rynbeek * r13504 /cdk/branches/mark_rynbeek-vflib/s​rc/main/org/openscience/cdk/isomor​phism/VF2SubgraphIsomorphism.java: added copyright header
10:39 CIA-16 cdk: mark_rynbeek * r13505 /cdk/branches/mark_rynbeek-vflib/s​rc/main/org/openscience/cdk/isomor​phism/VF2SubgraphIsomorphism.java: set the SVN keyword substitution on
11:00 CIA-16 cdk: mark_rynbeek * r13506 /cdk/branches/mark_rynbeek-vflib/src/​main/org/openscience/cdk/isomorphism/ (9 files): added copyright headers
11:14 CIA-16 cdk: gilleain * r13507 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/v​isitor/TransformingDrawVisitor.java: Clearer dashed wedge drawing code.
12:52 jbrefort joined #cdk
13:14 egonw jonalv: http://chem-bla-ics.blogspot.com/2008/12/​peer-reviewed-cheminformatics-2-code.html
13:14 zarah egonw's link is also http://tinyurl.com/6kyzse
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15:44 jonalv egonw: nice
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17:16 CIA-16 cdk: gilleain * r13508 /cdk/branches/jchempaint-primary/src​/main/org/openscience/cdk/renderer/ (3 files in 2 dirs): Removed the (bad idea of) hard coding the highlight radius in the generator.
18:09 jbrefort joined #cdk
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21:05 CIA-16 cdk: egonw * r13509 /cdk/branches/cdk-1.2.x/src​/test/org/openscience/cdk/ (6 files in 3 dirs): New setup, using get/setBuilder, to allow extending of IChemObjectTest classes, adding tons of tests
21:06 CIA-16 cdk: egonw * r13510 /cdk/branches/cdk-1.2.x/src​/test/org/openscience/cdk/ (16 files in 3 dirs): The full IAtom family is now properly implementing all tests, using the new get/setBuilder set up
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