Camelia, the Perl 6 bug

IRC log for #cdk, 2007-11-15

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Time Nick Message
07:08 rojasm joined #cdk
08:04 jpansanel many snow is the vinicy of Grenoble
08:04 jpansanel moin
08:22 egonw joined #cdk
09:12 egonw moin
09:14 rojasm moin egonw
09:15 egonw hi rojasm
09:20 rojasm can you see what I wrote?
09:20 egonw no
09:20 rojasm I think I have problems with privat chat
09:21 rojasm ok
09:21 rojasm you mean cdk.mass as a new directory for mass spectromety things
09:23 rojasm about you proposal of IIsotope. Now I thought that it should be better that IMolecularFormula.add(IAtom)
09:23 rojasm so it can contain the information of the atom and we don't loss it
09:28 rojasm what do you thing, egonw?
09:29 egonw what property of IAtom that is not inherited from IIsotope did you have in mind?
09:30 rojasm nothing. You mean then IMolecularFormula.add(IIsotope)
09:30 egonw right
09:30 rojasm what is the difference then?
09:30 egonw so we don't have the baggage of extra IAtom fields... like Point2D/3D etc
09:31 rojasm I mean computational or chemist
09:31 rojasm ok
09:31 rojasm I see
09:31 rojasm I will change it to IIsotope
09:32 egonw what about the MF itself?
09:32 egonw did you have a look at the classes I emailed?
09:33 rojasm Sorry I didn't find it
09:34 rojasm where is it exactly?
09:37 rojasm should it be in cdk.interfaces.IAdductMormula...
09:42 egonw sorry...
09:43 egonw was away for a sec
09:43 rojasm not problem
09:43 egonw no...
09:43 egonw it's in your email box
09:49 rojasm sorry but the only email from you that I have is from 11-09 about the proposal to use IISotope and the IAdductFormula..
09:49 rojasm but I don't have any file added there
09:50 rojasm could you sent me again please?
09:51 egonw no
09:51 egonw got them on my laptop at home :(
09:51 rojasm oo
09:51 egonw so, not until tonight
09:51 rojasm so let leave for other day
09:52 egonw oh wait...
09:52 egonw maybe I used gmail... mom
09:52 egonw what about my email about valency?
09:52 egonw on Nov 12?
09:52 egonw did you receive that email?
09:52 egonw toMiguel Rojas Cherto <m.rojas@lacdr.leidenuniv.nl>,
09:52 egonw if not...
09:52 egonw ... you have a serious email black hole
09:53 egonw or gmail email is blacklisted or so...
09:53 rojasm not. But may be was a problem of me. Because my kmail has from 1 week always broking with I tried to check the mail and may be it is loss
09:54 egonw shall I put the four classes in SVN?
09:54 egonw because I found them in my Sent box
09:54 rojasm ok, perfect
10:02 egonw hang ong
10:02 egonw -g
10:08 rojasm egonw: hang on means that you committed?
10:08 egonw that I am working on it... :)
10:08 rojasm ach so
10:08 rojasm sorry
10:08 egonw did not have a check out of /mf yet...
10:08 egonw not on this machine anyway
10:09 egonw any news on when MB@UL will visit MB@WUR ?
10:10 rojasm not yet. But I will comment in lunch. What do you think should be the best day
10:10 egonw a friday...
10:10 rojasm for you too
10:10 egonw 7 or 14
10:11 egonw 21 is too late...
10:11 rojasm ok
10:11 egonw too short before xmas
10:11 rojasm I will say in my case the 7
10:12 CIA-16 cdk: egonw * r9432 /branches/miguelrojasch/mf/s​rc/org/openscience/cdk/mass/ (5 files): Added suggested data classes
10:12 rojasm :)
10:12 egonw only IMolecularFormula set is missing...
10:12 rojasm I say you after lunch
10:12 egonw ok, good
10:12 egonw I am not happy about IAdductFormula yet...
10:13 rojasm I have a look
10:13 egonw with IMolecularFormulaSet in mind... IAdductFormula should extend IMolecularFormula
10:13 egonw I will revise that interface...
10:14 egonw having it extend IMolecularFormula
10:14 egonw ... allows us to use IMolecularFormulaSet of adducts too
10:14 egonw does that sound OK?
10:14 rojasm ok
10:15 rojasm More of the functionality of the aduct I put in MolecularFormulaManipulator
10:15 rojasm IAdductFormula
10:17 rojasm but the directory of mass for MolecularFormula is now provisionally, right?
10:18 rojasm because I don't think there is a relation mass== MolecularFormula
10:18 rojasm there is not, sorry
10:18 CIA-16 cdk: egonw * r9433 /branches/miguelrojasch/mf/.project: Better project name for multi branch development in Eclipse
10:18 egonw rojasm: good point...
10:18 egonw need to think about a better name...
10:19 egonw cdk.formula?
10:19 rojasm sound better
10:19 rojasm for me at least
10:20 egonw ok, will rename it ... hang on
10:20 CIA-16 cdk: egonw * r9434 /branches/miguelrojasch/mf​/src/org/openscience/cdk/ (formula/ mass/): Renamed package cdk.mass to cdk.formula
10:23 rojasm the package path is still cdk.mass I change them
10:24 rojasm or did you do it already
10:24 egonw ah, in the source...
10:24 egonw no forgot that...
10:24 egonw please change
10:24 CIA-16 cdk: miguelrojasch * r9435 /branches/miguelrojasch/mf/src​/org/openscience/cdk/formula/ (4 files): package path not correct
10:25 rojasm sorry what I don't understand really is the AdductFormula
10:26 egonw I think we will need some functionality to say some mass X := [M+Na]+
10:26 rojasm AdductFormula == MolecularFormulaSet
10:26 egonw MFS is not for a set of possible solutions?
10:26 rojasm ok, they have a relation
10:26 rojasm ok
10:26 rojasm I see
10:27 rojasm Perfect
10:27 rojasm Other question: the interface will be in cdk.interface or in this cdk.formula directory?
10:30 egonw cdk.formula for now
10:30 rojasm ok
10:37 CIA-16 cdk: egonw * r9436 /branches/miguelrojasch/mf/src​/org/openscience/cdk/formula/ (AdductFormula.java MolecularFormula.java): Removed @Override clauses, which gave errors here because there is no super class with method to override.
10:39 rojasm make sense to put also molecularFormulaSet
10:39 egonw yes
10:40 rojasm but then it should have to method get(IMolecularFormulaSet) and get(IAdductFormula)
10:40 rojasm right?
10:40 egonw thinking about that...
10:40 rojasm or IAdductFormula will be a extension of IMoleculaF.. as you commented
10:41 egonw yeah, want to move that way...
10:41 egonw OK, what would you want to do with a IMF?
10:42 egonw disregard how to create/modify one...
10:42 egonw 1. get the mass
10:42 egonw 2. overall charge
10:42 rojasm I suggest get the mass for manipulator
10:42 egonw 3. iterate over the IIsotopes
10:42 egonw right,so these three...
10:43 egonw actually 1. is a application of 3
10:43 egonw so, really just these:
10:43 egonw 1. a) iterate over isotopes, b) get count per isotope
10:43 rojasm yes, and the stoff of remove
10:43 egonw 2. get overall charge
10:43 rojasm contians
10:43 rojasm contains
10:44 egonw that a convenience method, but OK
10:44 egonw Good
10:44 egonw next step...
10:44 egonw what would we call something like [M+H]+ ... adduct is fine?
10:44 egonw and [M]+ ?
10:45 rojasm uff
10:45 rojasm I don't know
10:45 egonw :)
10:45 rojasm and a coma
10:45 egonw coma?
10:45 rojasm between [M,H]
10:45 egonw comma?
10:45 egonw why?
10:45 egonw I though the convention was M+H
10:46 egonw OK, going to update the interfaces... and add IMolecularFormulaSet
10:46 rojasm but commented I don't remenber bad. the formula with charge sould be [blabla+]
10:47 rojasm and means that for adduct will be chaos I think [M+H+]
10:54 egonw public Iterator<IMolecularFormula> molecularFormulas();
10:54 egonw
10:54 egonw public void add(IMolecularFormula formula);
10:54 egonw public void add(IMolecularFormulaSet formulaSet);
10:54 egonw public void get(int position);
10:54 egonw public void remove(IMolecularFormula formula);
10:54 egonw public void remove(int position);
10:54 egonw public int size();
10:54 egonw crap
10:54 egonw public interface IAdductFormula extends IMolecularFormula, IMolecularFormulaSet
10:54 egonw that last line...
10:54 egonw does that make sense?
10:54 egonw can we consider [M+H] a set in itself?
10:54 egonw set of size 2
10:54 egonw is that reasonable?
10:55 egonw and extending IMF to provide methods for overall properties, like total charge, total isotope count etc...
10:55 egonw maybe one or two convenience methods, like setMainComponent(IMolecularFormula) ?
11:00 jbrefort joined #cdk
11:00 rojasm I think make sense
11:02 rojasm remark add(IMolecularFormulaSet)
11:02 rojasm add(IMolecularFormula)
11:02 rojasm addMolecularFormula(IMolecularFormula) doesn't it clear
11:02 rojasm to difference both
11:06 egonw you prefer addMF(IMF) and addMFS(IMFSet) ?
11:07 rojasm for IMolecularFormulaSet is not necessary I think. I am thinking how IAtomContainer is doing
11:08 rojasm so there is not disagrees
11:11 egonw OK, will submit some changes now...
11:11 rojasm perfect
11:11 egonw that will break AdductFormula and MOlecularFormula...
11:12 egonw but then we can decide on the API first...
11:12 rojasm ja
11:12 CIA-16 cdk: egonw * r9437 /branches/miguelrojasch/mf/src​/org/openscience/cdk/formula/ (3 files): Next iteration of API design.
11:16 rojasm we go to lunch, after that we have a seminar. We speak later then
11:17 egonw ok, good
11:48 jonalv joined #cdk
12:19 steinbeck joined #cdk
12:19 egonw hi steinbeck
12:19 steinbeck Cheerio
12:19 * steinbeck is in his new office and DSL is working !!!
12:19 steinbeck yeah
12:20 egonw ha cool!
12:20 steinbeck Fast internet every day
12:20 steinbeck hehe
12:20 egonw how was CIC?
12:20 steinbeck very nice
12:20 steinbeck thank you
12:20 steinbeck lot's of positive feedback
12:20 steinbeck hope to see you again next year
12:20 egonw yeah, hope so too
12:21 steinbeck egonw: the compilation problem is solved
12:21 steinbeck ant clean dist-all
12:21 steinbeck did the job
12:21 steinbeck but refreshing 1000 times didn't :-)
12:22 egonw mmm... annoying...
12:22 * egonw makes a mental note
12:22 steinbeck well, this seems to be state-dependent, in a way.
12:22 steinbeck State of your personal Eclipse installation, that is
12:25 egonw steinbeck: I'm quite happy with the branching setup...
12:25 egonw lots of commits...
12:25 egonw more ease of coding...
12:25 egonw easier commenting and trying things...
12:25 egonw I can do several changes at the same time now...
12:26 egonw each branch uncovered problems in trunk/ too...
12:26 egonw so, I fix trunk/, backport that to the branch, and continue hacking in the branch...
12:26 steinbeck egonw: very good. I still have to setup branching for me. I'm planning to work on a deterministic generator from scratch, so that will be a perfect test.
12:27 egonw oh, cool
12:27 egonw very useful
12:27 * egonw has planned to compare the current version with one just after Junfeng's last commit
12:29 * egonw got to go now for a meeting...
12:29 egonw bbl
13:42 dleidert joined #cdk
13:58 CIA-16 jmol: hansonr * r8623 /trunk/Jmol/src/org/jmol/ (6 files in 2 dirs):
13:59 CIA-16 jmol: version=11.3.45_dev {atomset}.boundbox
13:59 CIA-16 jmol: # new feature: Jmol math {atomset}.boundbox returns list of center, vector, corner0, corner1 for this set of atoms
13:59 CIA-16 jmol: # code: ModelSet.BoxInfo abstraction/refactoring
14:00 CIA-16 jmol: hansonr * r8624 /trunk/Jmol/src/org/jmol/mod​elset/ModelCollection.java:
14:00 CIA-16 jmol: version=11.3.45_dev {atomset}.boundbox
14:00 CIA-16 jmol: # new feature: Jmol math {atomset}.boundbox returns list of center, vector, corner0, corner1 for this set of atoms
14:00 CIA-16 jmol: # code: ModelSet.BoxInfo abstraction/refactoring
14:29 CIA-16 cdk: egonw * r9438 /branches/miguelrojasch/mf/src/org/opensc​ience/cdk/formula/MolecularFormula.java: Matches new interface now.
14:31 rojasm egonw: yesterday was here Satoh for a symposium she focused her work in prediction reaction!
14:31 rojasm and tools for chemoinformatic
14:31 egonw ah, sounds nice
14:31 egonw who is satoh?
14:31 rojasm as chemojum
14:32 rojasm I search the web
14:32 egonw satoh T. ?
14:33 rojasm http://research.nii.ac.jp/~hsatoh/index-e.html
14:33 rojasm and nmr chemical shift predictions
14:35 rojasm she is doing in few years a lot of things
14:36 rojasm did you know about her?
14:36 egonw no
14:36 rojasm I have to take a look how is really doing the prediction of reactions
14:37 egonw I'm not impressed with the graphics...
14:37 rojasm Toshi, our post-doc was there and said the presentation and results was very nice
14:38 rojasm that is true
14:38 rojasm but I think the 3D they used for the reactions and then they thought, may be, they could create a graphic
14:41 egonw they cite the CDK, but *not* the article :(
14:41 rojasm :(
14:41 rojasm not good
14:42 egonw the article from 2006 is not good
14:45 * egonw is now checking the 13C prediction articles in Tetrahedron
14:46 steinbeck joined #cdk
14:50 CIA-16 bioclipse: ospjuth * r4246 /branches/bioclipse2/core/plugins/ (net.bioclipse.core.ui/ net.bioclipse.ui/):
14:50 CIA-16 bioclipse: ospjuth * r4247 /branches/bioclipse2/core/plugins/ (net.bioclipse.core.ui.tests/ net.bioclipse.ui.tests/):
14:52 CIA-16 bioclipse: ospjuth * r4248 /branches/bioclipse2/core/plugin​s/net.bioclipse.logging.tests/: Initial import of test plugin for logging.
14:52 CIA-16 bioclipse: ospjuth * r4249 /branches/bioclipse2/core/plugi​ns/net.bioclipse.logging.tests/ (11 files in 7 dirs): Initial import of test plugin for logging.
14:54 egonw steinbeck: do you know the 13C prediction work of Satoh?
14:54 egonw rojasm: did you read the paper in Tetrahedron 59?
14:54 egonw where they use CAST as extension of sort of HOSE code for prediction...
14:54 rojasm I am looking for it still
14:54 rojasm now I have
14:54 egonw doi:10.1016/S0040-4020(03)00662-8
14:55 egonw ah, ok
14:55 egonw it's much like HOSE code lookup
14:55 egonw but with some stereo added...
14:55 egonw now, there first examples really just indicates that that is not useful at all...
14:55 egonw check atom 18
14:55 rojasm And I think this new code is which they are using to predict reactions
14:55 egonw in figure 2 and 4
14:56 egonw the look up database has 3 shifts for that metyl
14:56 egonw they say stereo is important but
14:56 egonw looking at the differences I get:
14:56 egonw stereo up: 27.8 (table 2)
14:57 egonw stereo down: 28.1 + 25.5 /2
14:57 egonw or, stereo does *not* matter for the carbon shift
14:57 egonw am I missing something here ... ?
14:58 * egonw checks their highlighted example... atom 11
14:59 egonw of test 2
15:00 egonw OK, there they do see an effect...
15:00 egonw nice... cherry picking...
15:00 * egonw goes off to nmrshiftdb.org to find a counter example :)
15:04 egonw argh...
15:04 egonw no molecules with a sterane skeleton??
15:04 CIA-16 bioclipse: ospjuth * r4250 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (13 files in 6 dirs): Renamed packages and ID
15:04 CIA-16 bioclipse: ospjuth * r4251 /branches/bioclipse2/core/plu​gins/net.bioclipse.ui.tests/ (8 files in 6 dirs): Renamed packages and ID
15:09 CIA-16 bioclipse: ospjuth * r4252 /branches/bioclipse2/core/plugins/ (net.bioclipse.ui/.project net.bioclipse.ui.tests/.project): Updated project names
15:16 egonw giving up...
15:23 egonw found another way to find related molecules in the nmrshiftdb
15:23 egonw the annoying thing is...
15:23 egonw it seems to work quite well for that particular atom :(
15:25 CIA-16 blueobelisk: cjames53 * r161 /smiles-spec/trunk/ (ChangeLog open-smiles-3-input.html): Fixed cis/trans example.
15:39 CIA-16 cdk: egonw * r9439 /branches/miguelrojasch/mf/src/org/open​science/cdk/formula/AdductFormula.java: Updated for latest API changes.
16:38 rojasm left #cdk
16:59 steinbeck Cheers
16:59 steinbeck left #cdk
17:45 rguha joined #cdk
18:00 CIA-16 cdk: rajarshi * r9440 /trunk/cdk/src/org/openscience/cdk​/renderer/progz/TestRenderer.java: Added code to test out arbitrary smiles
19:48 CIA-16 jmol: hansonr * r8625 /trunk/Jmol/src/org/jmol/sh​apespecial/Polyhedra.java: nuisance message
19:54 CIA-16 cdk: rajarshi * r9441 /trunk/cdk/src/org/openscience/​cdk/qsar/DescriptorEngine.java: Added type info to the containers
21:19 jbrefort joined #cdk
21:59 Conrad joined #cdk
21:59 cpyang joined #cdk
21:59 CIA-16 joined #cdk
21:59 LaserJock joined #cdk
21:59 jpansanel joined #cdk
22:56 edrin joined #cdk
23:18 CIA-16 jmol: hansonr * r8626 /trunk/Jmol/src/org/jmol/ (10 files in 6 dirs):
23:18 CIA-16 jmol: version=11.3.45_dev
23:18 CIA-16 jmol: # bug fix: state not saved for coloring elements
23:18 CIA-16 jmol: # bug fix: state not properly representing deleted bonds
23:18 CIA-16 jmol: # bug fix: setColix not clearing shading in certain cases

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