Camelia, the Perl 6 bug

IRC log for #cdk, 2009-02-17

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All times shown according to UTC.

Time Nick Message
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08:56 thomas_ku moin
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09:31 egonw hi dr Thomas Kuhn!
09:31 egonw I presume?
09:39 thomas_ku you are right
09:39 egonw congrats!
09:39 thomas_ku thanks
09:40 thomas_ku i am really happy
09:41 egonw sure
09:41 egonw can I get a copy of your final thesis (electronic)?
09:41 jonalv joined #cdk
09:41 egonw (or did I already?)
09:41 thomas_ku yes of course
09:42 thomas_ku (not sure if I send already a version to you... )
09:42 thomas_ku but will send you a version tomorrow
09:42 egonw thanx
09:43 thomas_ku I hope I will not forget it. (Please remind me if I do so...)
09:43 maclean congratulations dr!
09:43 thomas_ku thanks
09:49 egonw thomas_ku: can you please send a copy to sneumann too...
09:49 thomas_ku of course
09:50 thomas_ku can you sent me a mail with the email adress?
09:50 sneumann sneumann at ipb-halle dot de
09:50 egonw sneumann: tack :)
09:50 thomas_ku thanks
10:54 jpansanel moin
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10:56 egonw hi julio, rojasm, jpansanel
11:05 rojasm hi
11:05 julio hi
11:07 jpansanel hi
11:07 zarah hi
11:09 sneumann hi
11:12 shk3 joined #cdk
11:12 egonw hi shk3
11:12 shk3 hi egonw
11:13 shk3 going to check the molecular weight stuff
11:15 maclean shk3 : could you take bioclipse bug #506 ?
11:15 maclean @pele 506
11:15 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=506
11:15 maclean (undo/redo)
11:16 shk3 sure
11:16 shk3 I would like to hear your opinions on my suggestion, though
11:16 maclean I thought we already talked it through
11:16 egonw shk3: I won't have time to think about that soon...
11:17 maclean mom, just re-reading the mail
11:17 egonw that is... the time to study how Eclipse does undo/redo
11:17 shk3 so I will go ahead
11:18 shk3 and do things
11:18 shk3 in such a way that they can be reused
11:18 maclean ok, cool
11:19 maclean the idea from the mailing list conversation was that there would be a base set of abstract classes
11:19 maclean extended in either jcp or bioclipse-jcp
11:19 shk3 sounds still reasonable for me
11:20 maclean me too
11:20 egonw Gpox: can you please comment on #518
11:20 egonw same here
11:20 egonw preferably, actions are revertable...
11:20 egonw which requires methods in the hub need the invert equivalents...
11:21 * egonw is getting lunch first now
11:21 maclean hmmm. cleanp might be a bit difficult to undo
11:27 egonw not that bad actually
11:27 egonw just a list of coordinate changes
11:28 maclean I thought you were getting lunch - get lunch! :)
11:29 egonw I got my lunch
11:29 egonw it's standing in front of me
11:29 maclean ohh, the lasagne
11:30 maclean I don't understand bug 515
11:30 maclean @pele 515
11:30 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=515
11:30 maclean (Properties View should list Coordinate Space for chemical files)
11:34 maclean oh, wait, I've been reading 508, now I understand n/m
11:44 shk3 egonw: can you spend a minute on discussing the mass stuff?
11:45 egonw yes
11:45 shk3 ok
11:45 shk3 1.
11:46 shk3 there is getTotalExactMass and getNaturalExacMass
11:46 shk3 in ACManipulator and MFManipulator
11:46 shk3 Am I right that getNatural is using natural abundance of isotopes
11:47 shk3 whereas the other mathod uses actual isotopes?
11:49 shk3 The naming isn't too clear
11:50 egonw mom, let me check
11:55 egonw shk3: still checking
11:55 egonw had to boot eclipse, change git branch
11:56 shk3 sorry
11:56 egonw yes, the last one uses the natural masses for the actually given masses...
11:57 egonw it's used to calculate for a particular molecule
11:57 egonw instance...
11:57 egonw thingy...
11:57 egonw you know...
11:57 egonw [13]CH4 versus methane
11:57 shk3 ok+
11:57 egonw [13C]H4 versus methane
11:58 shk3 since atoms in jcp are not configured by default, no isotope is found
11:58 shk3 so I would either
11:58 shk3 need to configure them to major isotope by default
11:58 shk3 or have a method assuming major isotope if none is given
11:58 shk3 what would you think?
11:58 egonw there is helper code for that
11:59 shk3 for what?
11:59 egonw getMajorIsotopeMolecularFormula
11:59 shk3 in?
11:59 egonw MFMan
12:01 shk3 ok
12:02 shk3 hm
12:02 shk3 this seems to assume major isotope in any case
12:02 shk3 I think if an isotope is configured in jcp, it should be used
12:03 egonw ah, yes, indeed...
12:03 egonw for (IIsotope isotope : formula.isotopes()) {
12:03 egonw IIsotope major = factory.getMajorIsotope(isotope.getSymbol());
12:03 egonw mass += major.getExactMass() * formula.getIsotopeCount(isotope);
12:03 egonw }
12:03 egonw replace the for loop with:
12:04 egonw IAtom atom : atomcontainer.atoms()
12:04 egonw etc...
12:04 egonw anyway...
12:04 egonw well...
12:04 egonw like this:
12:04 shk3 it can be done
12:04 shk3 sure
12:04 egonw for (IAtom atom : container.atoms()) {
12:04 shk3 should I add this as a new method?
12:04 egonw no
12:05 egonw it's just a few lines...
12:05 egonw rojasm: or should he?
12:05 shk3 might be the old method is also used sometimes
12:05 shk3 in its own right
12:12 shk3 well, I will do it
12:12 egonw so what?
12:13 egonw ummm .... do what?
12:13 egonw typo
12:14 shk3 make a new method
12:17 egonw in the jcp code?
12:17 egonw please send it as patch to Miguel
12:18 egonw , too
12:27 shk3 isotope.getExactMass() for Carbon
12:27 shk3 gives 12
12:27 shk3 I expected 12.0107
12:27 shk3 is that intended?
12:28 egonw 12.0107 is the natural mass for carbon
12:28 egonw not the mass of 12C
12:28 egonw which is 12.0 by definition
12:29 shk3 ah hm
12:29 shk3 mom
12:29 shk3 ok, we are going for lunch
12:29 shk3 I will come back to you on this
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13:36 steinbeck Hi everyone
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21:05 CIA-62 cdk: gilleain * r14191 /cdk/branches/jchempaint-primary/src/main/o​rg/openscience/cdk/renderer/Renderer.java: Synchronised with the bioclipse jcp, then some minor tidying; some methods made static.
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