Camelia, the Perl 6 bug

IRC log for #cdk, 2012-03-23

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20:17 slyrus egonw: my other gripe, in the same vein as the E/Z thing, is the lack of hashed/wedged bonds for steroechemistry in the SDG -- or is that just my ignorance of how to do it?
20:18 egonw not sure about that
20:20 slyrus now that 1.4.x and master have diverged so much, will there be a forward part of your 13-unsorted-patches branch to master?
20:22 slyrus ah, it could be that the it's the smiles parsers fault: "This parser does not parse stereochemical information, but the following..."
20:23 slyrus although who knows if that comment is still operative
20:26 slyrus egonw: wasn't there an effort to rewrite the SDG?
20:29 egonw I am in the process of cleaning up renderextra enough for cdk-1.4.x
20:29 egonw and note in my email an exception for totally new classes...
20:30 egonw those apply clean enough to both branches...
20:30 egonw it's patches like this that cause trouble:
20:30 CIA-121 cdk: Egon Willighagen master * rdab47fb / (49 files in 14 dirs): (log message trimmed)
20:30 CIA-121 cdk: s/NewDefaultChemOjectBuilder​/DefaultChemObjectBuilder/g (closes #3456420)
20:30 CIA-121 cdk: Conflicts:
20:30 CIA-121 cdk:  src/main/org/openscience/cdk/reaction​/type/AdductionProtonLPReaction.java
20:30 CIA-121 cdk:  src/main/org/openscience/cdk/reaction​/type/AdductionProtonPBReaction.java
20:30 CIA-121 cdk:  src/main/org/openscience/cdk/reaction​/type/AdductionSodiumLPReaction.java
20:30 CIA-121 cdk:  src/main/org/openscience/cdk/reaction/​type/CarbonylEliminationReaction.java
20:30 egonw here lines of code changed in both branches...
20:31 egonw SMILES parses @ and @@ stereochemistry nowadays
20:31 egonw but not / and \
20:32 egonw and, the answer to your 3rd q, I thought Christoph's group was looking into that, but have not heard about that in a long time
20:34 slyrus OK
20:35 slyrus I think it parses @ and @@ but the renderer is looking for bond up/down info and that doesn't get generated from the CW/CCW chirality info (AFAICT).
20:35 egonw correct
20:36 egonw but, you can render them as R, S
20:49 CIA-121 cdk: Egon Willighagen master * rfb9194e / (2 files):
20:49 CIA-121 cdk: Replaced (I)Molecule with (I)AtomContainer
20:49 CIA-121 cdk: Change-Id: I077605ed6ad2a4f62a7925e5b5ccdf0b30f73cf3 (+8 more commits...) - http://git.io/WsZwTw
20:57 slyrus egonw: oh?
20:58 egonw where is that patch... I think in Bioclipse tree...
20:58 egonw mom
20:58 egonw https://github.com/bioclipse/bioclipse.ch​eminformatics/blob/master/plugins/net.bio​clipse.cdk.jchempaint/src/net/bioclipse/c​dk/jchempaint/generators/RSGenerator.java
21:14 slyrus does bioclipse appear enough times in that URL? :)
21:15 CIA-121 cdk: Egon Willighagen master * r6d051a6 / (3 files in 3 dirs):
21:15 CIA-121 cdk: More unit tests. All methods are now at least tested once. (closes #3005889)
21:15 CIA-121 cdk: Change-Id: I305ed297ff335cdd20cd119c84c3968e6e7b13d6 (+7 more commits...) - http://git.io/uyw_Sw
21:19 egonw :)
21:34 CIA-121 cdk: Egon Willighagen master * r07d42e1 / src/test/org/openscience/cdk/cove​rage/CoverageAnnotationTest.java : (log message trimmed)
21:34 CIA-121 cdk: Bridge methods are methods introduced by compilers in relation to methods that use generics. Various renderer related method trigger test methods for just bridge methods, but are never really implemented.
21:34 CIA-121 cdk: For example, the below interface code causes the coverage test before
21:34 CIA-121 cdk: this patch to expect the bridge generate(IChemObject object, RendererModel model)
21:34 CIA-121 cdk: method to be tested:
21:34 CIA-121 cdk: public interface IGenerator<T extends IChemObject> {
21:34 CIA-121 cdk:  public IRenderingElement generate(T object, RendererModel model);
22:02 CIA-121 cdk: Egon Willighagen master * r63dccdf / src/test/org/openscience/cdk/smil​es/DeduceBondSystemToolTest.java :
22:02 CIA-121 cdk: Unit test with the SMILES reported by Kevin Lawson
22:02 CIA-121 cdk: Change-Id: I2a3c6cfec082a82ce48434ab0120ae4ac8fd2bd6
22:02 CIA-121 cdk: Conflicts:
22:02 CIA-121 cdk:  src/test/org/openscience/cdk/smil​es/DeduceBondSystemToolTest.java - http://git.io/Z3Iyug
22:02 CIA-121 cdk: Egon Willighagen master * rc52d676 / src/test/org/openscience/cdk/smil​es/DeduceBondSystemToolTest.java :
22:02 CIA-121 cdk: The Bioclipse test case of failing bond order assignment
22:02 CIA-121 cdk: Change-Id: I86f9bc709bfd3b3e1a3b816914e2dc32bbad6df0
22:02 CIA-121 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://git.io/nkCyjA
22:02 CIA-121 cdk: Egon Willighagen master * re3a726b / AUTHORS :
22:02 CIA-121 cdk: Added Kevin Lawson to the list of AUTHORS
22:02 CIA-121 cdk: Change-Id: I1c9c71514c7f6691b632defc8f7b1b851a9a47d2
22:02 CIA-121 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://git.io/dmeOaA

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