Camelia, the Perl 6 bug

IRC log for #cdk, 2009-04-15

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All times shown according to UTC.

Time Nick Message
05:10 egonw joined #cdk
06:20 rednael [master] Merge branch 'cdk-1.2.x'  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=4c816​ee20749a5ec777a8fe46342a4f8c8bb9f50
06:20 zarah rednael's link is also http://tinyurl.com/cswzfc
06:20 rednael [master] Partially fixed SMARTS matching for R0. Updated target molecule initialization to...   http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=c1a3e​36596c5d673396c75fc67d333358b508f26
06:20 zarah rednael's link is also http://tinyurl.com/d6jnxo
06:31 Gpox joined #cdk
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07:13 egonw joined #cdk
07:21 rednael [cdk-1.2.x] Made class public, to unbreak adding it to the build/*.javafiles  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=e62c8​e3b68af0e5aa1f4c261f95c18a67a7e876b
07:21 rednael [cdk-1.2.x] Partially fixed SMARTS matching for R0. Updated target molecule initialization to...   http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=c1a3e​36596c5d673396c75fc67d333358b508f26
07:21 zarah rednael's link is also http://tinyurl.com/dlwk2t
07:21 rednael [cdk-1.2.x] Fixed dubious equality test. A private method was checking Double objects via reference.  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=90627​6de3a62bbab051b33cc4baa45eaf6d0b405
07:21 rednael [cdk-1.2.x] Added test method annotation. Completes coverage for data module  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=575ed​a71ffb21ed2a91679bc3a0332a7ae86c8f5
07:21 zarah rednael's link is also http://tinyurl.com/d6jnxo
07:21 zarah rednael's link is also http://tinyurl.com/dg2rha
07:21 zarah rednael's link is also http://tinyurl.com/c9odcf
07:22 egonw rednael++
07:48 rednael [master] Merge branch 'cdk-1.2.x'  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=bdf67​bb5f65235fd738d194eda832518dc1cf20a
07:48 rednael [master] Made class public, to unbreak adding it to the build/*.javafiles  http://cdk.git.sourceforge.net/git/g​itweb.cgi?p=cdk;a=commitdiff;h=e62c8​e3b68af0e5aa1f4c261f95c18a67a7e876b
07:48 zarah rednael's link is also http://tinyurl.com/dx8h69
07:48 zarah rednael's link is also http://tinyurl.com/dlwk2t
08:10 maclean joined #cdk
08:34 CIA-58 cdk: goglepox * r14550 /cdk/branches/jchempaint-primary/src/main/org​/openscience/cdk/controller/MoveModule.java: Workaround to so move actions dirties the editor in bioclispe
08:34 CIA-58 cdk: goglepox * r14551 /cdk/branches/jchempaint-primary/src/​main/org/openscience/cdk/controller/ (ControllerHub.java IChemModelRelay.java): Added fireStrucureChangedEvent
09:25 maclean joined #cdk
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10:47 maclean so, I'm looking at improving the behaviour of the PDBREader
10:47 maclean er, Reader.
10:47 egonw huh PDBeater?
10:47 maclean And it seems that it does not really handle ligands. Especially not their typing.
10:48 maclean But I may be over-thinking the problem.
10:48 egonw there is a patch about PDBReader improves
10:48 egonw which needs reviewing
10:48 maclean Oh?
10:48 egonw can you take that along
10:48 maclean Sure.
10:48 egonw mom...
10:50 egonw info on patch forwarded
10:50 egonw was on cdk-devel last Oct
10:51 maclean Tack. It might be that I can just collect the ligand atoms in to their own container and type them.
10:52 egonw why not type everything?
10:52 maclean Well, the reader types the protein residues quite well
10:53 maclean but ligands cannot be done the same way.
10:53 egonw true
10:53 maclean Because it is easy to say "ALA.CA" == "Carbon.
10:53 maclean But not "DIQ.P1" == "Phosphorous".
10:54 maclean Whatever 'DIQ' is - I just mean for any of the many, many ligand residue names.
10:54 maclean But, maybe I can just use the normal mechanism for ligands, no?
10:55 egonw DIQ.P1 I have never seen before
10:56 maclean Well, I sortof made that up, but the point is the same.
10:58 maclean http://www.ebi.ac.uk/thornton-srv/databa​ses/cgi-bin/vctr/hetgroups.pl?name=index
10:58 zarah maclean's link is also http://tinyurl.com/c7gpeb
10:59 egonw :)
10:59 egonw anyway, really interesting...
10:59 egonw will ping you shortly
10:59 maclean oki
11:02 * maclean goes to hunt down a fresh desk lunch
11:06 egonw poor duch lunch
11:06 egonw poor duck lunch
11:12 maclean duck lunch? I wish
13:03 CIA-58 cdk: shk3 * r14552 /cdk/branches/jchempaint-primar​y/src/main/org/openscience/cdk/ (controller/ControllerHub.java geometry/GeometryTools.java): unified the layout at cleanup and loading of molecules
13:05 CIA-58 cdk: shk3 * r14553 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (3 files in 3 dirs): unified the layout at cleanup and loading of molecules
15:51 maclean egonw : am I right in thinking that jmol doesn't used the CDK?
15:51 maclean s/used/use/
15:51 egonw it did use CDK
15:51 egonw versions 6-9
15:52 egonw or so
15:52 maclean but then...it stopped doing so?
15:53 egonw yes
15:53 egonw because it was too slow
15:53 maclean We seem to have a Bspt class (made by M.Howard), and jmol has a Bspt class (made by M.Howard)
15:53 egonw did not scale
15:53 maclean ohhhh.
15:53 egonw yes, same origin
15:53 maclean :(:(
15:53 egonw I ported that to the CDK
15:54 maclean and jmol now has more stuff on molecular orbitals than the cdk does! (I think)
15:54 maclean it's weird.
15:55 maclean not to mention the situation of BioPolymer (CDK), BioPolymer (Jmol), and Protein (Biojava)...
15:57 maclean aargh! and org.jmol.smiles package.
15:57 maclean grrrrr.
15:58 egonw yes
15:58 egonw well the jmol SMILES package only does a minor subset
15:59 maclean $Author : one egon 'w'
16:00 egonw maclean: anyway... Jmol is LGPL too, so we can easily grab things
16:00 egonw like the UFF force field
16:00 maclean true.
16:00 egonw and maybe the PDB reader...
16:01 egonw but the data model is not a 1:1 match, I think
16:01 egonw but that can change now master is open to core API changes
16:01 maclean Well, the jmol model classes have a lot of stuff necessary for rendering efficiently in 3D.
16:02 maclean But I guess that they could implement the cdk interfaces.
16:03 maclean My megalomaniacal dream is to synchronise CDK, Jmol, and (structural) Biojava.
16:03 egonw :)
16:03 maclean I'm sure it wouldn't be very much work...
16:03 egonw maclean: I think you got yourself a grant application topic
16:03 maclean heh.
16:03 egonw OK, gone for dinner
16:03 maclean Good eating.
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