Camelia, the Perl 6 bug

IRC log for #cdk, 2011-02-15

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All times shown according to UTC.

Time Nick Message
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13:36 maclean hi
13:36 zarah oh hai maclean
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13:50 egonw hi maclean
13:50 egonw hi jbrefort
13:50 egonw hi all
13:50 zarah saluton egonw
13:50 jbrefort hi all
13:50 zarah saluton jbrefort
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14:58 maclean hmmm. CDK-Taverna 2-point -zero. Cool : but what is 'reaction enumeration'?
14:59 maclean heh. *goes to friendfeed, finds that egon has anticipated and answered my question*
15:00 maclean "Variabel" - hmmm. spalcek!
15:02 egonw :)
15:02 egonw it's open source?
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15:23 CIA-48 cdk: Egon Willighagen 13-unsorted-patches * rd163bb2 / (2 files): Proper initialization at the primary renderer too. (renderextra). (+220 more commits...) - http://bit.ly/ehRx7S
15:24 egonw crap.. wrong repos
15:25 egonw or not?
15:25 egonw now I am confused...
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15:30 CIA-48 org.openscience.cdk: Egon Willighagen bioclipse2.6 * r7a3a431 / (2 files): Proper initialization at the primary renderer too. Commited upstream as: https://github.com/egonw/cdk/commit/d1​63bb2d36aeb31830813e1cf66facf16d787435 - http://bit.ly/hwBtSb
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15:52 maclean back
15:52 maclean egonw : "it's open source?" - do you mean "go look"?
15:53 egonw nah... like, everyone can fix typos
15:54 egonw btw, can you review these six lines of bug fixing for cdkjcp? https://github.com/egonw/cdk/commit/d1​63bb2d36aeb31830813e1cf66facf16d787435
15:58 maclean Sure.
15:59 maclean Typos in images are a little harder though...
16:00 egonw ah, indeed
16:04 maclean uh oh. egonw : duplication in ReactionRenderer - it is registering the generators twice I think.
16:04 maclean https://github.com/egonw/cdk/blob/d163bb2d36a​eb31830813e1cf66facf16d787435/src/main/org/op​enscience/cdk/renderer/ReactionRenderer.java
16:05 maclean line 121-126.
16:06 egonw omg
16:06 egonw thanx
16:07 maclean further, it should have been in the other constructor, which doesnt register the atomcontainer generators.
16:07 maclean line 136ish
16:08 egonw quite so...
16:08 egonw damn virusses
16:09 egonw wondering if I did it right in bioclipse...
16:09 egonw ah...
16:09 maclean ah?
16:10 egonw [2011-02-15 16:31] <CIA-48> org.openscience.cdk: Egon Willighagen bioclipse2.6 * r7a3a431 / (2 files): Proper initialization at the primary renderer too. Commited upstream as: https://github.com/egonw/cdk/commit/d1​63bb2d36aeb31830813e1cf66facf16d787435 - http://bit.ly/hwBtSb
16:10 egonw follow the bitly link
16:10 egonw I did it right there...
16:10 egonw but copy/pasted into the wrong class
16:10 egonw bugger...
16:11 maclean reactionSETrenderer eh?
16:11 maclean hmmm
16:12 maclean right, right, it just passes the list on to the contained reactionrenderer
16:16 egonw I think they should just share the renderer model, but that's anohter thing :)
16:24 maclean Ah, I see. The AbstractRenderer has a ref to a model. Hmmm tricky.
16:26 egonw yeah, that dates back before the hierarchical renderer design...
16:26 egonw would be afair point for a referee
16:26 maclean Well, luckily you can't do "ReactionSetRenderer rsr = new ReactionSetRenderer(new ReactionRenderer());"
16:27 maclean otherwise, you could get one ref to the RR.model and one ref to the RSR.model, and changing one would not result in changes in the other.
16:27 maclean Hierarchical classes are an effing nightmare.
16:30 maclean I think I would suggest that only the atom_container_renderer makes renderer_models, and the containing types (ReactionR, RSR, etc) all get refs to this from contained types.
16:31 maclean So, if you pass in a contained type (eg: ReactionR to RSR), it sets the ref in its parent, which it got from its child mol_set_renderer, and so on.
16:32 egonw yes, sounds like a good idea
16:33 egonw AtomContainerRenderer should be about the most basic thing
16:33 maclean Yes, I thought about an AtomRenderer for a little while before quickly rejecting the idea :)
16:35 maclean Probably no-one wants to render all sulphurs in Arial-22-bold and all oxygens in Helvetica-12-italic.
16:36 egonw actually...
16:36 egonw you'd be surprised what they want
16:36 maclean Well, you know my rule : "the customer is never right".
16:37 egonw :)
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16:55 maclean heheh. smiles produced using the canonical labelling from a signature.
16:57 maclean g2g & get food.
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17:40 egonw @tell maclean I have updated the patch, thanx for the reviewing!
17:40 zarah Consider it noted.
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19:11 maclean hi
19:11 zarah hi maclean
19:11 zarah maclean: You have new messages. Write '/msg zarah @messages' to read them.
19:11 maclean zarah: Just tell me...
19:11 zarah maclean: are you making fun of me?
19:11 maclean damn. I thought that worked.
19:14 egonw yeah, it should be something like that
19:19 maclean egonw : no-problem, anyway. thanks for the comments on the N3 triples. I see there is a cdk-taverna workflow (in the paper) on checking atomtypes. Could have used that...
19:21 egonw not sure if the first CDK-Taverna has a PDB reader...
19:22 maclean Well I had to write my own CIF reader (IteratingCIFReader, in fact) so that would have been worse. I don't know how to make taverna workers.
19:22 egonw indeed
19:22 egonw ah... yes, you mentioned that...
19:22 egonw itereting CIF reader ... cool
19:22 egonw did not know those could be concatenated too
19:23 maclean CIF is a horrible, horrible format. It's like XML with none of the convenience.
19:24 maclean so reading that in was only marginely less painful than writing RDF...
19:25 egonw :)
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19:41 maclean haha. " Git is a saw with no guard that makes it easy to cut your own arm off. But it also comes with an easy arm reattachment kit, and you can even attach the arm to your knee if you want."
19:46 egonw yes, nice
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