Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-06-02

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All times shown according to UTC.

Time Nick Message
01:25 rojasm joined #bioclipse
06:29 Gpox joined #bioclipse
07:47 jonalv joined #bioclipse
08:09 shk3 joined #bioclipse
08:16 maclean joined #bioclipse
08:18 egonw joined #bioclipse
08:18 maclean hi egonw
08:22 egonw hi maclean
08:23 * egonw is exhausted from the house move
08:23 maclean but finished?
08:24 egonw Gpox: ping
08:24 Gpox egonw: pong
08:28 maclean maybe he's fallen asleep from exhaustion...
08:30 egonw ubuntu 64 suck big time
08:30 egonw +s
08:30 egonw most unstable ubuntu I ever used
08:30 egonw almost on par with MS products
08:31 egonw (that I used)
08:31 shk3 hi jonalv
08:34 sneumann Can't confirm Ubuntu Problems.
08:34 sneumann WHich problem ?
08:35 egonw 64bit... random kernal lock ups (not frequent, some 5-10 so far in a few weeks)
08:35 egonw java just become horribly sluggish
08:35 sneumann Which Ubuntu ?
08:36 egonw no clue what that is about yet
08:36 egonw jaunty
08:36 sneumann Laptop ?
08:36 egonw plasma crashes ones a day
08:36 egonw due to memory misallocation
08:36 sneumann Hm, gnome here
08:36 egonw yes, that latter is a kubuntu bug, strickly speaking
08:37 egonw but the java thingy and kernel lock up not
08:38 sneumann We had sluggish java here as well,
08:38 sneumann IIRC java-15 helped
08:38 sneumann or the other way around ...
08:39 egonw weird thing is... this started only after the weekend...
08:42 stain my Ubuntu 9.04 x64 has been stable
08:42 stain but there's something weird with the mouse pointer - under load it stops moving
08:42 egonw stain: it's very difficult to decide/determine what is the problem...
08:42 egonw maybe my Dell laptop has crappy chips...
08:42 stain I've not seen that since before they started with 'Windows accelerator' display cards in the early 90s
08:42 stain egonw: laptop.. could it be some power save problem?
08:43 egonw perhaps...
08:43 egonw it seems to work generally well...
08:43 egonw and did fine on 32 bit ubuntu earlier
08:43 stain or do you have some weird ndis-wrapper-driver for your network card?
08:43 egonw (expect that 1900x1200 screen resolution is not recognized after a Suspend session
08:43 olass joined #bioclipse
08:43 stain unless you have >3 GB ram I guess you could just go for 32-bit
08:43 egonw no, regular driver there, AFAIK
08:44 stain Linux and hardware.. a constant battle
08:44 egonw that's one of the reasons :)
08:44 egonw I have 4
08:44 egonw 32 actually uses 3.5 of them
08:44 egonw so pretty OK
08:44 stain I'm thinking of ordering some Sony VAIO, but I should check how it is with Linux
08:44 egonw and I can recompile my kernel to have the 32 bit support 4GB
08:44 egonw no clue why that is not default yet
08:45 shk3 do you feel the vibrations through irc?
08:45 maclean :)
08:46 * maclean turns up the music....
08:46 egonw shk3: no
08:46 egonw earth quake?
08:46 shk3 artifical earthquake, yes
08:47 maclean they're building a car-park next door.
08:47 * olass thought it was the sound of a kernel recompiling
08:48 olass stain: have you considered buying a Mac?
08:48 stain olass: I have one.. a macbook pro
08:48 olass stain: way to go
08:48 olass why switching to something worse?
08:49 stain it's 3 years old.. but now I want something smaller - and it's just a bit disappointing that in 3 years the small laptops like the MacBook Air has worse specs than my 3y old machine
08:49 stain I might go for an iMac instead
08:49 CIA-40 bioclipse: ospjuth * r10909 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (3 files in 2 dirs): Updated decorator for jubs not run.
08:49 stain but I thought it would be more fun with some non-mac-laptop and go back to some linux/windows7 cursing
08:50 stain Apple keeps screwing us up - no Java 6 for my machine for instance
08:51 maclean indeed. no java 6 is annoying.
08:51 maclean "...some linux/windows7 cursing.."  : using the curses library, or swearing?
08:52 egonw what library is that? swearing?
08:53 maclean libcurses is an ancient drawing library. I guess he probably wasn't referring to that :)
08:53 egonw yes, I what cursus is...
08:53 egonw but that other one ?!?
08:54 maclean swearing? as in actually cursing.
08:54 egonw ooohhhh :)
08:55 stain cursing, swearing, banning.. kjaert barn har mange navn
08:55 egonw (I thought... let's just play along)
09:00 CIA-40 bioclipse: goglepox * r10910 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui​.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (2 files in 2 dirs):
09:00 CIA-40 bioclipse: Added method named parse() to IPropertyCalculator
09:00 CIA-40 bioclipse: This method is for parsing SDfile properties to property
09:00 CIA-40 bioclipse: without having to calculate it again.
09:00 CIA-40 bioclipse: goglepox * r10911 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui​.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (4 files in 2 dirs):
09:00 CIA-40 bioclipse: Added method to molTable to parseProperties form
09:00 CIA-40 bioclipse: a file.
09:00 CIA-40 bioclipse: goglepox * r10912 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/MoleculesEditor.java:
09:00 CIA-40 bioclipse: Added parsing of calcuated properties when a file is loaded
09:00 CIA-40 bioclipse: The parsing is run in a separate job
09:24 maclean heh. what are these 'xxxxxxxxxx' on startup of eclipse?
09:24 maclean "xxxxxxxxxxxxxxxxINFO - Bioclipse manager: seneca added to Javascript environment."
09:26 maclean oh, never mind. it's in the predictiontool in seneca.
09:27 shk3 yes
09:27 shk3 will look at these
09:42 maclean olass : hmm. I made a diagram, but its a bit cartoony : http://gilleain.tumblr.com/post/116723953
09:42 zarah maclean's link is also http://tinyurl.com/kt3hcr
09:42 olass maclean: I like it!
09:42 maclean I'll put it on the wiki, then?
09:42 olass can you add it to the architecture wiki page?
09:42 olass :)
09:43 olass please write a small caption about it as well
09:43 olass to put it in context
09:43 maclean ok, will do.
09:43 olass thanks a lot
09:43 olass that page is now getting quite good
09:44 olass maclean: I like this highlighting: http://gilleain.tumblr.com/post/80100724
09:44 zarah olass's link is also http://tinyurl.com/mozoqq
09:45 olass is this available in jcp?
09:45 * olass heads for lunch
09:46 maclean not as such, but it was an example of a custom generator, so it could be...
09:46 maclean like the center-of-mass generator.
10:47 CIA-40 bioclipse: jonalv * r10913 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src​/net/bioclipse/seneca/business/SenecaManager.java: layout changes to 80 cols (I don't like scrolling in two directions...)
10:47 CIA-40 bioclipse: jonalv * r10914 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Don't swallow the cause for the BioclipseException but give git it as the casue parmater
10:48 CIA-40 bioclipse: jonalv * r10915 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src​/net/bioclipse/seneca/business/SenecaManager.java: Rewrote SenecaManager.executeJob to use an IReturner and being void so that it can be run as a job followed by a uiJob
10:50 maclean joined #bioclipse
10:55 masak joined #bioclipse
10:58 shk3 Gpox: does an error message relating to P/Virtual and L/Virtual not matching tell you something?
10:59 shk3 do you know what pathes prefixed with L/ or P/ mean in Eclipse?
11:00 Gpox P=project, L=linked maybe
11:03 shk3 hm, ok
11:06 CIA-40 bioclipse: egonw * r10916 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business/src/net/bioclipse/cdk/ (3 files in 2 dirs):
11:06 CIA-40 bioclipse: Added cdk.newMolecule() (implementes #1138). Also updated CDKMolecule.toString() to deal with molecules
11:06 CIA-40 bioclipse: with zero atoms.
11:07 CIA-40 bioclipse: jonalv * r10917 /bioclipse2/trunk/plugins/net.bioclipse.core​/src/net/bioclipse/core/util/LogUtils.java: wrapped pop dialog code in asyncExec so it can be called from any thread
11:10 CIA-40 bioclipse: ospjuth * r10918 /bioclipse2/trunk/plugins/net.bioclipse.ds.d​blookup/src/net/bioclipse/ds/dblookup/impl/ (DBExactMatchTest.java ExternalMoleculeMatch.java): Partial implementation for DBExactMatch. Still requires calculator for inchi and inchikey.
11:35 CIA-40 bioclipse: egonw * r10919 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: Fixed spelling and now uses spaces not tabs
11:39 * egonw wonders if we should use myExperiment instead of Gist in some distant future
11:40 egonw since their definition of workflow is pretty fuzzy nowadays (intentionally)
11:41 egonw in a wild strategic move
11:42 olass RC1 will be tomorrow
11:43 olass please have all commits for this done in the early afternoon tomorrow, ~15 swedish time
11:43 CIA-40 bioclipse: ospjuth * r10920 /bioclipse2/trunk/ (37 files in 37 dirs): Set version to 2.0.0.RC1 for release candidate 1.
11:44 CIA-40 bioclipse: ospjuth * r10921 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): Set version to 2.0.0.RC1 for release candidate 1.
11:44 egonw shk3, rojasm: are you done with cdk10 ?
11:46 olass egonw: do we need to update ID for the CDK plugins?
11:46 egonw for net.bioclipse.cdk yes
11:46 olass yes, done that
11:46 olass but not for the org.opensc.cdk, right?
11:46 CIA-40 bioclipse: ospjuth * r10922 /bioclipse2/trunk/plugins/ (27 files in 19 dirs): Set version to 2.0.0.RC1 for release candidate 1.
11:46 egonw correct
11:46 olass ok
11:47 egonw Gpox: or have you been making commits to .render and .control post beta5?
11:48 Gpox 2009-05-29 last commit
11:49 Gpox r14599
11:49 egonw Gpox: did you update the plugin version number by appending a new data?
11:49 Gpox no
11:49 egonw ok, mom
11:51 egonw olass: there are a few patches since beta5
11:52 egonw isn't the cheminfo feature not part of the main download?
11:52 olass yes
11:52 egonw so, those two patches don't hurt
11:52 olass oh no
11:52 olass but please increment versions
11:52 olass I had problems before if they weren't touched
11:52 olass but it might work out now anyway
11:53 edrin joined #bioclipse
11:53 edrin olass: your services are down again!
11:53 olass oh no
11:53 olass starting them up
11:53 olass ok, started
11:54 olass edrin: this is not good
11:54 olass why do they go down?
11:54 olass egonw: where was that cron job you set up for autostarting xmpp services?
11:54 edrin olass: it's frequent that tcp/ip connections that last for days break
11:54 egonw in the wiki
11:55 olass xmpp wiki?
11:55 olass ok
11:55 egonw or bioclipse wiki
11:55 olass ?
11:55 olass why?
11:55 egonw @pz crontab
11:55 zarah egonw: Zarro boogs found.
11:55 egonw @pz xmpp
11:55 zarah [1017] XMPP commands to list services... http://tinyurl.com/ncqmz7
11:55 zarah [425] js console throws strange excpe... http://tinyurl.com/deomud
11:55 zarah [842] XMPP service that generates 3D ... http://tinyurl.com/mttfnm
11:55 zarah Entire list at http://tinyurl.com/m48a6q
11:55 egonw olass: as in... I don't remember
11:56 olass egonw: I can't find it on xmpp wiki
11:56 olass it should really be there
11:56 egonw http://wiki.bioclipse.net/ind​ex.php?title=XmppWebServices
11:56 zarah egonw's link is also http://tinyurl.com/5sjy3e
11:56 egonw http://wiki.bioclipse.net/index.php?title=​XmppWebServices#Crontab_to_reboot_services
11:56 zarah egonw's link is also http://tinyurl.com/5sjy3e
11:56 olass egonw: could you please move that info to xmpp wiki?
11:57 edrin olass, egonw: although the components connect via tcp it has a risk to run them from remote. best would be localhost, then such tcp errors wont occur ...
11:57 egonw yes
11:57 olass thanks for the URL
11:57 edrin if not one should run them with a crontab...
11:57 olass edrin: we need to move services to ws1
11:57 olass lack of time...
11:58 edrin xmpp is good because it can handle such tcp disconnects since the analysis logic is not depending on it in contrast to http soap (without polling)
11:59 edrin but at least we should use the feature of xmpp to reconnect
11:59 maclean joined #bioclipse
11:59 olass ehat do you mean now?
11:59 egonw olass: http://pele.farmbio.uu.se/xmp​p-services/index.php/Crontab
11:59 zarah egonw's link is also http://tinyurl.com/ma2n6d
12:01 olass egonw++
12:03 maclean ugh! I may have mentioned it before, but pages from that wiki look horrible in safari.
12:03 maclean (I know : "don't use safari, then!" :))
12:03 masak maclean: yes, what were you thinking? :)
12:04 maclean I was thinking "middle-click to open links in a new tab - how convenient!"
12:04 maclean although, since safari-4 beta, I've been thinking "ugh! tabs on the top :((("
12:11 egonw olass: bumped version number, but will commit later
12:11 olass egonw: ok
12:16 CIA-40 bioclipse: goglepox * r10923 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Added support for the use field in choice generator
12:16 CIA-40 bioclipse: goglepox * r10924 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui​.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (4 files in 3 dirs):
12:16 CIA-40 bioclipse: Fixed molTable.parseProperties()
12:16 CIA-40 bioclipse: Added toString(value) to IPropertyCalculator interface
12:17 CIA-40 bioclipse: goglepox * r10925 /bioclipse2/trunk/plugins/ (6 files in 3 dirs):
12:17 CIA-40 bioclipse: Added getProperty(String,IMolecule.Property) to ICDKMolecule
12:17 CIA-40 bioclipse: Implemented this method on CDKMolecule
12:17 CIA-40 bioclipse: with a Map<String,Object>
12:17 CIA-40 bioclipse: fixes bug #647
12:17 zarah bug #647 | http://tinyurl.com/nkg9au
12:25 CIA-40 bioclipse: jonalv * r10926 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): removed IProgressMonitor.unknown from BioclipseJobs and added some stuff that for some reason (don't ask me I have no idea) was neeeded to get progressmonitoring in seneca manager
12:40 CIA-40 bioclipse: ospjuth * r10927 /bioclipse2/trunk/features/ (10 files in 10 dirs): Set version to 2.0.0.RC1 for release candidate 1.
12:52 CIA-40 bioclipse: shk3 * r10928 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src​/net/bioclipse/seneca/editor/SenecaJobEditor.java: avoids this P/Virtual and L/Virtual not matching problem by giving path as string - not great, but works.
12:53 egonw shk3: under what conditions will it not work? what makes it not great?
12:54 maclean it's 'not great' in the sense of being a hack...
12:54 egonw sure
12:54 egonw what makes it a hack instead of a proper fix?
12:54 maclean is that not obvious?
12:55 maclean well, obviously it is not obvious, but it seems so to me.
12:55 egonw no, it's not obvious to me why using the path as string is suboptimal
12:55 egonw that's why I ask
12:56 shk3 using IFile if we have got it seems better than
12:56 shk3 IFile.getPath().toOSString()
12:56 shk3 I believe
12:56 egonw sounds logical...
12:56 egonw so why is this not great then?
12:57 maclean did you look at the diff?
12:58 shk3 was:
12:58 shk3 .saveSDFile(sdfile, mols);
12:58 shk3 is:
12:58 shk3 .saveSDFile(sdfile.getFullPath().toOSString(), mols);
12:58 egonw maclean: no, not yet... I cannot look at all patches, so scan them first by commit message (which is why they exist, not?)
12:58 maclean uhhh.
12:58 egonw maclean:
12:58 maclean not this again.
12:59 maclean yeesss.
12:59 egonw and no, the diff does not explain me why the new solution is better, but not great
12:59 maclean really?
12:59 egonw please enlighten me
12:59 egonw I seem to be stupid here
12:59 shk3 it's better because it works
13:00 shk3 it's not great because it should not be needed
13:00 egonw ic
13:00 egonw so the underlying problem is that
13:00 egonw saveSDFFile(IFIle) it not working?
13:00 maclean suppose so.
13:00 shk3 in that particular situation, yes
13:00 egonw which makes this hack needed
13:00 shk3 it seems to be related to threading or so
13:01 egonw maclean: it really would have been helpful if the commit would include the reason why this hack was needed
13:01 egonw maclean: yes, that again
13:01 maclean it wasn't my commit!
13:01 egonw maclean: and I wasn't asking you for an explanation
13:02 shk3 ok, my fault
13:02 egonw oh no
13:02 egonw no fault assignments please
13:02 shk3 don't beat each other up, please
13:02 egonw I was just trying to understand the patch
13:02 CIA-40 bioclipse: shk3 * r10929 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (3 files in 2 dirs): monitor is now initialised with proper number of steps and is counting them
13:02 shk3 that's as verbose as it gets, I believe
13:24 CIA-40 bioclipse: shk3 * r10930 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (3 files in 2 dirs): better handling of steps
13:38 CIA-40 bioclipse: jonalv * r10931 /bioclipse2/trunk/plugins/net.bioclipse.​core/src/net/bioclipse/managers/business​/AbstractManagerMethodDispatcher.java: pick the returnvalues also from comple returns when runnign JavaScript.
13:39 CIA-40 bioclipse: shk3 * r10932 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src​/net/bioclipse/seneca/business/SenecaManager.java: removed usage of subprogressmonitor in executejob, since it is not needed and makes things more complicated
13:46 CIA-40 bioclipse: shk3 * r10933 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src​/net/bioclipse/seneca/editor/SenecaJobEditor.java: empty result (=cancelled) properly handled
13:53 CIA-40 bioclipse: shk3 * r10934 /bioclipse2/trunk/plugins/net.biocli​pse.data.seneca/data/hko3/hko3.sjs: proper sjs file for example
14:06 olass shk3: is SaveSDF broken?
14:06 olass if so, is there a bug?
14:06 shk3 for jonalv
14:06 olass good
14:06 shk3 but works for me
14:06 olass hmm
14:06 olass ok
14:07 shk3 I am updating for testing
14:07 olass as long as there is a bug for 2.0 I'm happy
14:07 * olass is trying to make sense for the release
14:07 olass mek sense out of quite some bugs..
14:07 olass blah
14:07 * olass is relocating to jonalv for some discussions
14:10 shk3 do you do the rc today?
14:11 CIA-40 bioclipse: gilleain * r10935 /bioclipse2/trunk/plugins/net.bioclipse​.seneca/src/net/bioclipse/seneca/job/St​ochasticStructureElucidationJob.java: Inner class MonitorWrapper now extends the ProgressMonitorWrapper instead of implementing IProgressMonitor
14:12 CIA-40 bioclipse: shk3 * r10936 /bioclipse2/trunk/plugins/net.bioclipse.bibtex/ (. .settings/): added stuff to svn ignore
14:15 CIA-40 bioclipse: gilleain * r10937 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/​anneal/AdaptiveAnnealingEngine.java: Cleaned up if/else construct for code clarity purposes.
14:17 jonalv @pz 816
14:17 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=816
14:29 masak joined #bioclipse
14:34 Gpox joined #bioclipse
14:38 Gpoks joined #bioclipse
14:46 CIA-40 bioclipse: goglepox * r10938 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (2 files in 2 dirs): Implemented InChI property calculator
14:48 CIA-40 bioclipse: goglepox * r10939 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/MoleculeTableManager.java: Only save properties that are cached.
15:16 CIA-40 bioclipse: carl_masak * r10940 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
15:16 CIA-40 bioclipse: [JsConsoleView] whitespace therapy
15:16 CIA-40 bioclipse: Also fixed one instance of s/"\\n"/NEWLINE/
15:29 CIA-40 bioclipse: miguelrojasch * r10941 /bioclipse2/trunk/plugins/net.bioclipse.reaction/ (12 files in 7 dirs): Added new view-page to visualize reaction and structure from the Reaction editor instance of to have the viewer in the editor.
15:29 edrin hi
15:29 zarah ni hao edrin
15:30 edrin anyone has access to the following article: http://www.ncbi.nlm.nih.gov/pubmed/18374​183?ordinalpos=11&amp;itool=EntrezSystem​2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pub​med_DefaultReportPanel.Pubmed_RVDocSum
15:30 edrin PMID: 18374183
15:30 zarah edrin's link is also http://tinyurl.com/nkkfq4
15:30 edrin ?
15:30 egonw joined #bioclipse
15:31 olass edrin: I'm looking
15:31 edrin cool :)
15:31 olass yes
15:31 olass will send you pdf
15:32 olass edrin: sent
15:34 edrin thank you :)
15:51 olass egonw: please file a bug for Gpox to define datatype in the Calculators extension point using XML schema datatypes
15:51 olass (so you can verify it upon finished)
15:53 shk3 jonalv++
15:59 * jonalv gives up for today
15:59 Gpox joined #bioclipse
15:59 Gpoks joined #bioclipse
16:03 CIA-40 bioclipse: goglepox * r10942 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (3 files in 3 dirs): Added InChI calculator to extension
16:04 CIA-40 bioclipse: shk3 * r10943 /bioclipse2/trunk/plugins/net.bioclipse​.seneca/src/net/bioclipse/seneca/job/St​ochasticStructureElucidationJob.java: the cancel in java now works
16:04 edrin left #bioclipse
16:06 CIA-40 bioclipse: shk3 * r10944 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src​/net/bioclipse/seneca/editor/SenecaJobEditor.java: after a cancel, no sdf editor is opened
16:41 CIA-40 bioclipse: ospjuth * r10945 /bioclipse2/trunk/plugins/ (7 files in 7 dirs): Set version to 2.0.0.RC1 for release candidate 1.
17:37 sneumann_ joined #bioclipse
17:59 sneumann__ joined #bioclipse
18:11 CIA-40 bioclipse: miguelrojasch * r10946 /bioclipse2/trunk/plugins/net.bioclips​e.reaction/src/net/bioclipse/reaction/ (2 files in 2 dirs): Added a context menu provider for the boxes
21:29 CIA-40 bioclipse: miguelrojasch * r10947 /bioclipse2/trunk/plugins/net.bioclipse.r​eaction/src/net/bioclipse/reaction/model/ (CompoundObjectModel.java ReactionObjectModel.java): Initiate a IAtomContainer or IReaction when an AbstractObjectModel is generated

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