Perl 6 - the future is here, just unevenly distributed

IRC log for #cdk, 2014-01-19

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
06:26 jbrefort joined #cdk
07:26 Conrad joined #cdk
08:30 egonw__ joined #cdk
09:32 konditorn joined #cdk
09:35 commitbot joined #cdk
09:35 commitbot [cdk] egonw pushed 4 new commits to master: http://git.io/1YdzsQ
09:35 commitbot cdk/master 330982a John May: Don't fail when matching empty structures - this defaults such that an empty structure never matches....
09:35 commitbot cdk/master e19a126 John May: API changed required to correct VF implementation (non public class)...
09:35 commitbot cdk/master 41bbe13 John May: Correct VF target vertex selection - if the query vertex is in the terminal set then the target must also be. This will now correctly match disconnected queries....
09:35 commitbot left #cdk
10:05 commitbot joined #cdk
10:05 commitbot [cdk] egonw pushed 5 new commits to master: http://git.io/XGxVKA
10:05 commitbot cdk/master e3d07bf John May: Convenience method for inverting the label of tetrahedral stereochemistry....
10:05 commitbot cdk/master f79a4c0 John May: Use permutation parity instead of projecting the ligands and then checking for duplicates. Not only is this faster but it extends more naturally to E/Z labelling....
10:05 commitbot cdk/master bfda348 John May: CIP labels for double-bond - one small adjustment (next commit)....
10:05 commitbot left #cdk
10:13 commitbot joined #cdk
10:13 commitbot [cdk] egonw pushed 2 new commits to master: http://git.io/azgU0w
10:13 commitbot cdk/master 0b091e5 John May: Maintain rank stability when ranking invariants (CANON). Previously unique classes were labelled as lowest - now the lowest ranks keep the lowest label. Not only is this less operations (and faster) but it is also required for some procedures (e.g. canonical tautomer generation). These changes alter the canonical SMILES order - example 'NC(O)O' is now 'OC(O)N'. Notice how the oxygen labels are now lower (even though the ni
10:13 commitbot cdk/master 2ae866a John May: Changes to unique SMILES output order - note the tests were also updated to be easier to fix in future....
10:13 commitbot left #cdk
10:25 commitbot joined #cdk
10:26 commitbot [cdk] egonw pushed 2 new commits to master: http://git.io/sX8smA
10:26 commitbot cdk/master 5b6ab05 John May: Pass the Stereocenters instance to the element creation allowing it make a decision about questionable hatch/down bonds....
10:26 commitbot cdk/master 420b4c8 John May: Implementing a procedure to interpret the inverse style down (hatch) bonds when it is unambiguous. This follows IUPAC guidelines on structure depiction that the stereo-center may be at the fat-end of a hatch bond if the configuration is unambiguous....
10:26 commitbot left #cdk
10:32 egonw slyrus: ping?
10:33 slyrus hey egonw
10:33 egonw hi
10:33 zarah saluton egonw
10:33 slyrus it's a bit late here, but I'm still awake
10:33 slyrus ish
10:33 egonw :)
10:33 egonw just wanted to let you know I still have a number of important deadlines...
10:34 egonw and trying to work on them, but stress is involved, which I try to address with reviewing some of John's CDK patches...
10:34 egonw but have not looked at all at teh IUPAC code...
10:34 slyrus ok, i haven't had any time for it in the last week either
10:34 egonw I have teaching time, and a EU project kicking off soon, so rather stressed up
10:34 egonw ok...
10:34 egonw I cannot promise anything, but if there is anything please email...
10:35 egonw if not taking a lot of time, I might get to it
10:47 slyrus ok, thanks. I probably won't have time to dig into the code again until sometime later in the week
10:48 commitbot joined #cdk
10:48 commitbot [cdk] egonw pushed 8 new commits to master: http://git.io/3hz46g
10:48 commitbot cdk/master fba130e John May: We will use a single test class for test multiple predicates....
10:48 commitbot cdk/master 2fb07f5 John May: Filter sub-structure matches for those with unique bond mapping....
10:48 commitbot cdk/master b152a4a John May: A fluent interface to structure search matches....
10:48 commitbot left #cdk
10:56 commitbot joined #cdk
10:56 commitbot [cdk] egonw pushed 5 new commits to master: http://git.io/w2-V1w
10:56 commitbot cdk/master 375bff4 John May: More efficient suppression of hydrogen atoms. We use a different name as not break the existing behaviour (of cloning) but that method will also be updated....
10:56 commitbot cdk/master 6539f00 John May: Updates existing methods to call the new copyAndSuppressHydrogens method. There will likely be a few regressions as the method complains about unset hydrogen counts....
10:56 commitbot cdk/master 8e72767 John May: null != 0 - consider this a methane where one hydrogen is explicit, removing that hydrogen could set the h count to 1 when it should have been 4....
10:56 commitbot left #cdk
11:05 commitbot joined #cdk
11:05 commitbot [cdk] egonw pushed 2 new commits to master: http://git.io/ynL3rA
11:05 commitbot cdk/master 192dc4f John May: Test if an atom is present in a stereo element....
11:05 commitbot cdk/master 1a2dc9f John May: When removing attempting to remove an atom and all connected parts - we now also update the IStereoElements. This linear search is inefficient but matches the style of what was already done and is available in the AtomContainer....
11:05 commitbot left #cdk
11:13 commitbot joined #cdk
11:13 commitbot [cdk] egonw pushed 1 new commit to master: http://git.io/LEbipw
11:13 commitbot cdk/master 0d66616 John May: Fix potential problem with stereo-matching - the end points of the target double bond must be in the same stereo element....
11:13 commitbot left #cdk
15:13 Conrad joined #cdk
15:56 slyrus joined #cdk
17:20 egonw joined #cdk
19:46 Mr_Electronico joined #cdk
20:35 konditorn joined #cdk
21:36 egonw joined #cdk
21:47 Conrad joined #cdk

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary