Camelia, the Perl 6 bug

IRC log for #cdk, 2012-04-12

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All times shown according to UTC.

Time Nick Message
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11:09 konditorn egonw: do you want me to mail my latest patch to the CDK-mailing list for a patch review?
11:27 konditorn egonw: ping
11:30 egonw let's see...
11:31 egonw so, we read the information now from SMILES
11:31 egonw from MDL molfiles too?
11:31 egonw let
11:31 egonw let's add that first, and then submit
11:31 konditorn oki, is it only in MDLV2000Reader.java?
11:32 egonw that would be the best place to start, yes
11:34 konditorn is mdlStereo == 4 the same as that the molecule has bond order 4 (on row 678?
11:41 egonw no, that should be different
11:41 egonw btw, quick SMILES question...
11:41 egonw your patch does not set SINGLE_OR_DOUBLE for ':' yet, does it?
11:41 egonw that should be added
11:41 egonw (and tested too)
11:42 konditorn oki
11:44 egonw another thought... does it support the '$' bond?
11:47 konditorn what kind of bond is that?
11:47 egonw QUADRUPLE
11:48 egonw btw, you know this site: http://opensmiles.org/spec/open-smiles.html ?
11:48 egonw nope, the CDK parser does not support $ yet :)
11:48 egonw http://apps.ideaconsult.net:8080/ambit2/depict/cdk​?search=%5BRh-%5D%28Cl%29%28Cl%29%28Cl%29%28Cl%29%​24%5BRh-%5D%28Cl%29%28Cl%29%28Cl%29Cl&smarts=a
11:48 zarah egonw's link is also http://tinyurl.com/6spea6y
11:49 egonw neither do any of the other tools...
12:01 konditorn mm, do we want to raise the SINGLE_OR_DOUBLE-flag every time the flag ISAROMATIC is true and the bond is in a ring?
12:05 CIA-121 cdk: Egon Willighagen cdk-1.4.x * r117377e / src/main/org/openscience/cdk/smil​es/smarts/parser/SMARTSParser.jjt :
12:05 CIA-121 cdk: Updates with the SMARTS specs, among others to fix 'Sc' parsing (patch by Dazhi Jiao; fixes #2786624)
12:05 CIA-121 cdk: Change-Id: I34ad117aef815c89978223f7625c5b6558e2d62d
12:05 CIA-121 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://git.io/kIG8ZA
12:05 CIA-121 cdk: Egon Willighagen cdk-1.4.x * r92604d8 / src/main/org/openscience/cdk/smiles/smart​s/parser/visitor/SmartsQueryVisitor.java :
12:05 CIA-121 cdk: Fixes recursion errors (patch by Dazhi Jiao)
12:05 CIA-121 cdk: Change-Id: I65f2afcbc85aa72041f3af8ed75819d644090a8a
12:05 CIA-121 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://git.io/1dtlAA
12:05 CIA-121 cdk: Egon Willighagen cdk-1.4.x * r0aa84d7 / src/test/org/openscience/cdk/smiles/​smarts/parser/SMARTSSearchTest.java :
12:05 CIA-121 cdk: Fixed the tests to have the right match counts (patch by Dazhi Jiao)
12:05 CIA-121 cdk: Change-Id: Ib8e6b9f11aeee2623abe76a6ad616a8250b3af44
12:05 CIA-121 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://git.io/AxUOxg
12:16 konditorn egonw: should I only consider the use of a ':' if it's in a ring, or shall I leave that up to the user, i.e. if the ':' is used the bond always get the SINGLE_OR_DOUBLE-flag?
12:16 egonw I think ':' always is SINGLE_OR_DOUBLE
12:16 konditorn ok
13:18 konditorn egonw: now I have fixed the usage of ':' in the Smile parser and made the MDL V200 reader raise the SINGLE_OR_DOUBLE-flag if the bond-order is 4...
13:18 egonw cool
13:18 egonw konditorn++
13:19 konditorn =)
13:19 konditorn I've tested the parser, but not the reader….
13:22 konditorn so do you want to see patches of it?
13:23 egonw sure!
13:23 egonw I have a presentation in about 30 minutes
13:23 egonw and slides to finish
13:23 egonw so, cannot look at it before I go home
13:23 egonw but can then check on the train
13:23 konditorn it's ok for me?
13:23 egonw so, please send
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13:24 egonw hi slyrus
13:25 slyrus morning egonw
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