| Time |
S |
Nick |
Message |
| 06:25 |
|
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sneumann joined #bioclipse |
| 07:45 |
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annzi joined #bioclipse |
| 07:46 |
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Gpox joined #bioclipse |
| 07:47 |
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Gpoks joined #bioclipse |
| 07:56 |
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sneumann joined #bioclipse |
| 08:46 |
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egonw joined #bioclipse |
| 08:46 |
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egonw |
moin |
| 08:46 |
|
zarah |
oh hai egonw |
| 08:46 |
|
jpansanel |
moin |
| 08:46 |
|
zarah |
oh hai jpansanel |
| 08:47 |
|
egonw |
jpansanel: any luck on bioclipse.net ? |
| 08:47 |
|
jpansanel |
works agin |
| 08:47 |
|
egonw |
good |
| 08:48 |
|
jpansanel |
egonw: Do you known if Bioclipse is usable for SAR studies ? |
| 08:50 |
|
egonw |
yes it is very much |
| 08:51 |
|
jpansanel |
good |
| 08:51 |
|
egonw |
check my blog post of yesterday |
| 08:51 |
|
jpansanel |
I've written a short article (in french) about FOSS for molecular screening |
| 08:51 |
|
egonw |
it has some relevant links |
| 08:51 |
|
jpansanel |
thx |
| 08:51 |
|
egonw |
ah, cool |
| 08:52 |
|
egonw |
there are three relevant bioclipse features: QSAR, MetaPrint2D, and DS (decision support) |
| 08:52 |
|
egonw |
make sure you check the matching wiki.bioclipse.net pages |
| 08:52 |
|
jpansanel |
very nice |
| 08:52 |
|
egonw |
jpansanel: btw, to what extend are you still working on MyChem? |
| 08:52 |
|
egonw |
actively? |
| 08:52 |
|
jpansanel |
porting to mysql 5.1 |
| 08:52 |
|
egonw |
I think jonalv is exploring making a Bioclipse frontend to it... |
| 08:52 |
|
egonw |
as part of his StructureDB project |
| 08:52 |
|
jpansanel |
mysql 5.1 has a new plugin structure |
| 08:53 |
|
jpansanel |
and many security lock |
| 08:53 |
|
jpansanel |
it is hard to write a big plugin like mychem with the new security framework :( |
| 08:53 |
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annzi joined #bioclipse |
| 09:03 |
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annzi1 joined #bioclipse |
| 09:21 |
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jonalv joined #bioclipse |
| 10:02 |
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masak joined #bioclipse |
| 10:18 |
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annzi joined #bioclipse |
| 10:24 |
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egonw joined #bioclipse |
| 10:26 |
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egonw |
Gpox: ping |
| 10:26 |
|
Gpox |
egonw: pong |
| 10:26 |
|
egonw |
throw new IllegalArgumentException("modle must have a resource."); |
| 10:26 |
|
egonw |
patch 3f432b2b118aafa671f10255c080b7e606e7eabf |
| 10:26 |
|
egonw |
1. Model |
| 10:27 |
|
egonw |
2. perhaps be a bit more descriptive so that developers getting that Exception get a clue how to fix the problem |
| 10:28 |
|
egonw |
about patch 3103b312562957a41a7f5567a9aa58e3e6a1d887 |
| 10:28 |
|
egonw |
calculateCoordianates -> please fix typo |
| 10:29 |
|
egonw |
/FIXME work-around for bug 613 -> please file a new bug ticket for that indicating that that needs to be fixed when 613 is fixed, and mention that new ticket in the source code please |
| 10:29 |
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annzi joined #bioclipse |
| 10:29 |
|
CIA-60 |
bioclipse.cheminformatics: Arvid Berg master * rca436f3 / plugins/net.bioclipse.cdk.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/editor/MoleculeTableContentProvider.java : Increased cache size to 50 - http://bit.ly/driwyN |
| 10:41 |
|
CIA-60 |
bioclipse.rdf: annzi master * r15a4328 / (3 files in 2 dirs): Added convenient methods to the chembl plug-in - http://bit.ly/bmuDky |
| 10:47 |
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annzi1 joined #bioclipse |
| 10:47 |
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Gpox joined #bioclipse |
| 10:53 |
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annzi joined #bioclipse |
| 11:01 |
|
Gpox |
egonw: fixed |
| 11:02 |
|
* egonw |
is pulling |
| 11:02 |
|
egonw |
fetching, really .) |
| 11:02 |
|
egonw |
:) |
| 11:03 |
|
egonw |
Gpox: almost fixed :) |
| 11:03 |
|
egonw |
model.getResource().getLocationURI()+"dose not exist "); |
| 11:03 |
|
egonw |
missing space + dOEs :) |
| 11:04 |
|
CIA-60 |
bioclipse.cheminformatics: Arvid Berg master * rd368371 / (2 files in 2 dirs): Put 2D-coordiante generation in moltable lookup code instead of in the renderer. - http://bit.ly/9KBmV1 |
| 11:04 |
|
egonw |
(you forgot the same typo fix in the commit message I now notice) |
| 11:07 |
|
CIA-60 |
bioclipse.cheminformatics: Arvid Berg master * rc6d2d2b / plugins/net.bioclipse.cdk.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/editor/MoleculeTableContentProvider.java : Cancel task when item is removed from cache. - http://bit.ly/dchSKS |
| 11:24 |
|
Gpox |
egonw: fixed the ' does' too |
| 11:25 |
|
CIA-60 |
bioclipse.cheminformatics: Arvid Berg master * rf662f87 / plugins/net.bioclipse.cdk.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/business/MoleculeTableManager.java : |
| 11:25 |
|
CIA-60 |
bioclipse.cheminformatics: Added check that file exsists before parsing properties. |
| 11:25 |
|
CIA-60 |
bioclipse.cheminformatics: Solves bug #1612 - http://bit.ly/9o8J1a |
| 11:25 |
|
egonw |
thanx! |
| 11:26 |
|
zarah |
bug #1612 | http://tinyurl.com/y9dn3wy |
| 12:03 |
|
egonw |
jonalv: ping |
| 12:03 |
|
egonw |
jonalv: d'you got a sec? |
| 12:03 |
|
egonw |
if so, can you drop by? |
| 12:27 |
|
CIA-60 |
bioclipse.cheminformatics: Egon Willighagen master * r5c6745b / (2 files in 2 dirs): Fixed copying of properties (fixes #613) - http://bit.ly/c5Cs8x |
| 12:27 |
|
zarah |
bug #0613 | http://tinyurl.com/cm84ht |
| 12:37 |
|
CIA-60 |
bioclipse.cheminformatics: Egon Willighagen master * r40a1f40 / plugins/net.bioclipse.cdk.business.test/src/net/bioclipse/cdk/business/test/AbstractCDKManagerPluginTest.java : Updated test; SMILES are not unique or canonical. Instead test for a substring that always be present - http://bit.ly/9TYJH0 |
| 12:57 |
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olass joined #bioclipse |
| 13:21 |
|
egonw |
jonalv: ping |
| 13:21 |
|
egonw |
jonalv: another question |
| 13:21 |
|
jonalv |
egonw: shoot |
| 13:21 |
|
egonw |
did the proxy start wrapping bioclipse excepotions in runtime exception? |
| 13:22 |
|
jonalv |
egonw: hm exceptions is a bit of a mess... |
| 13:22 |
|
jonalv |
I think the asnwer is that it depends |
| 13:22 |
|
jonalv |
if you are running as a job then exception handling is done by the proxy yes |
| 13:23 |
|
jonalv |
if not then I have a feeling that there was a special case which hasn\t been fully explored and solved yet |
| 13:27 |
|
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samuell joined #bioclipse |
| 13:30 |
|
jpansanel |
hi jonalv |
| 13:30 |
|
egonw |
jpansanel: he's a away for fika (:= coffee + cake) |
| 13:46 |
|
jpansanel |
ok |
| 13:51 |
|
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edrin joined #bioclipse |
| 13:51 |
|
edrin |
hi again |
| 13:56 |
|
edrin |
I will be in Stockholm next week, maybe someone of you will have time for a meeting :) ? |
| 14:08 |
|
egonw |
in stockholm or uppsala? |
| 14:08 |
|
egonw |
around what time? |
| 14:09 |
|
egonw |
btw, still going to the ice hotel? |
| 14:12 |
|
edrin |
egonw: yes |
| 14:12 |
|
jonalv |
edrin: cool |
| 14:12 |
|
jonalv |
:) |
| 14:13 |
|
egonw |
jonalv: jpansanel pinged you earlier |
| 14:13 |
|
jonalv |
egonw: oh. jpansanel: uhm, pong? |
| 14:14 |
|
edrin |
I will fly to Stockholm on Monday and will fly to Kiruna on Thursday |
| 14:14 |
|
edrin |
That means I will be in or around Stockholm on Tuesday and Wednesday |
| 14:14 |
|
olass |
edrin: oh no, I'd love to meet up but I will be in California :( |
| 14:14 |
|
jonalv |
edrin: Kiruna, that\s probably even cooler >( |
| 14:14 |
|
jonalv |
hm wrong layout |
| 14:15 |
|
jonalv |
olass: you going to California next week? |
| 14:15 |
|
edrin |
olass: oh, that's really too bad. |
| 14:15 |
|
olass |
EclipseCon |
| 14:15 |
|
jonalv |
olass: ah right is that already next week. |
| 14:16 |
|
olass |
yes |
| 14:16 |
|
olass |
http://bioclipse.blogspot.com/[…]-for-eclipse.html |
| 14:16 |
|
zarah |
olass's link is also http://tinyurl.com/yldwett |
| 14:16 |
|
olass |
edrin: bad timing :( |
| 14:17 |
|
egonw |
edrin: yeah, can't you ask the move the wedding? |
| 14:17 |
|
egonw |
theY move |
| 14:18 |
|
edrin |
I can try, maybe it's too late... |
| 14:18 |
|
egonw |
:) |
| 14:18 |
|
edrin |
heh |
| 14:18 |
|
egonw |
meeting in Uppsala then? |
| 14:18 |
|
olass |
edrin: are you getting married again? |
| 14:18 |
|
olass |
:) |
| 14:19 |
|
egonw |
olass++ |
| 14:19 |
|
olass |
in the ice hotel |
| 14:19 |
|
edrin |
yes, however I have to arrange this with my wife |
| 14:19 |
|
olass |
cool |
| 14:19 |
|
olass |
very cool |
| 14:19 |
|
edrin |
olass: .. no it's a friend of my wife who is getting married with a Swedish guy |
| 14:19 |
|
edrin |
? |
| 14:19 |
|
olass |
ah |
| 14:20 |
|
olass |
cold I guess.. |
| 14:20 |
|
edrin |
probably |
| 14:20 |
|
olass |
egonw: pingeling |
| 14:20 |
|
egonw |
wassup? |
| 14:20 |
|
edrin |
otherwise it will be very wet |
| 14:21 |
|
edrin |
yes, however I have to arrange this with my wife <- this was directed to egonw, and not to ola |
| 14:21 |
|
egonw |
edrin: ack |
| 14:22 |
|
edrin |
;) |
| 14:23 |
|
samuell |
egonw: JFYI: Have asked on smw-devel now about ARC vs RAP |
| 14:23 |
|
egonw |
ack |
| 14:28 |
|
* egonw |
finds himself writing yet another save method in the CDKManager ... |
| 14:29 |
|
jonalv |
&me guesses he is supposed to ask egonw: 'Why? How is this one different?' |
| 14:29 |
|
jonalv |
hm wrong layout again |
| 14:30 |
|
egonw |
sharing code, fixing bugs |
| 14:36 |
|
olass |
egonw: sorry, was interrupted by 2 phone calls |
| 14:36 |
|
olass |
(at the same time) |
| 14:37 |
|
olass |
egonw: you know that bug about QSAR should accept SMILES as input? |
| 14:37 |
|
egonw |
the DnD one? |
| 14:37 |
|
olass |
well... the Add... did not show smiles files |
| 14:37 |
|
olass |
the dialog |
| 14:37 |
|
egonw |
yes, I remember that one too |
| 14:38 |
|
olass |
well, this dialog is from cheminformatics plugin |
| 14:38 |
|
olass |
and teh ChemoinformaticUtils class |
| 14:38 |
|
olass |
isMolecule(...) |
| 14:38 |
|
* egonw |
has a bad feeling about where this is going |
| 14:38 |
|
olass |
so, in order to solve it I need to add smiles content type there |
| 14:38 |
|
olass |
is that ok? |
| 14:39 |
|
olass |
I could send you a patch |
| 14:39 |
|
olass |
and confirm it works |
| 14:40 |
|
olass |
but wanted to clear things out before sending the patch |
| 14:40 |
|
olass |
egonw: what do you think? |
| 14:40 |
|
egonw |
mom |
| 14:40 |
|
olass |
ok |
| 14:40 |
|
egonw |
ok, extending the SUPPORTED_CONTENT_TYPES list, right? |
| 14:41 |
|
olass |
yes, adding the smi content types |
| 14:41 |
|
olass |
smi single and smi multi |
| 14:41 |
|
olass |
since we open them in MoleculesEditor it feels accurate |
| 14:41 |
|
egonw |
yeah, sounds good |
| 14:42 |
|
olass |
ok, pul lrequest coming up |
| 14:42 |
|
olass |
sent |
| 14:44 |
|
CIA-60 |
bioclipse.qsar: Ola Spjuth master * r878ff5c / (15 files in 7 dirs): Added has2d and has3d as attributes on StructureType. - http://bit.ly/cchNPH |
| 14:44 |
|
CIA-60 |
bioclipse.qsar: Ola Spjuth master * rb159dad / (3 files in 3 dirs): |
| 14:44 |
|
CIA-60 |
bioclipse.qsar: Override getNo2D. getNo3D, getNoStructures in ResourceTypeImpl. |
| 14:44 |
|
CIA-60 |
bioclipse.qsar: Also, deprecate addCalculatedProps() method. - http://bit.ly/cR2IpD |
| 14:44 |
|
CIA-60 |
bioclipse.qsar: Ola Spjuth master * r27bebcc / (3 files in 3 dirs): Override getNoMols and adap to overridden model methods has2d and has3d and getNoMols. - http://bit.ly/9l7c7G |
| 14:48 |
|
egonw |
who wrote this CDKManager ?!?! |
| 14:50 |
|
jonalv |
egonw: lot's of people... |
| 14:50 |
|
egonw |
each time I look at it I find a mess |
| 14:51 |
|
jonalv |
egonw: I am afraid it's become too big. There was a time when I read through it and looked at things in it. Ihave given that up :) |
| 14:52 |
|
egonw |
just spend two hours fixing failing unit tests, and bugs |
| 14:52 |
|
jonalv |
egonw++ |
| 14:52 |
|
olass |
egonw++ |
| 14:53 |
|
CIA-60 |
bioclipse.cheminformatics: Ola Spjuth master * r4e41b42 / plugins/net.bioclipse.chemoinformatics/src/net/bioclipse/chemoinformatics/util/ChemoinformaticUtils.java : |
| 14:53 |
|
CIA-60 |
bioclipse.cheminformatics: Added smiles extension for QsarEditor Add... dialog |
| 14:53 |
|
CIA-60 |
bioclipse.cheminformatics: (bug 1883). - http://bit.ly/cYg7Dx |
| 14:53 |
|
zarah |
bug #1883 | http://tinyurl.com/yfzbn6y |
| 14:53 |
|
egonw |
I wish people would just run those bloody test suites :( |
| 14:54 |
|
egonw |
yeah, I am looking at you |
| 14:54 |
|
olass |
me? |
| 14:54 |
|
olass |
*gulp* |
| 14:55 |
|
egonw |
:) |
| 14:55 |
|
* jonalv |
whishes we had nightly run of the test suites |
| 14:55 |
|
masak |
*gulp* |
| 14:55 |
|
egonw |
jonalv: the test run for the CDK manager takes less than a minute |
| 14:55 |
|
* jonalv |
looks at that sentence and feels that he can write better english than that |
| 14:55 |
|
jonalv |
egonw: still |
| 14:56 |
|
jonalv |
it's not so much the time though... |
| 14:56 |
|
egonw |
true |
| 14:56 |
|
egonw |
it's mostly Eclipse not wanting to run the tests at all |
| 14:56 |
|
egonw |
I know |
| 14:58 |
|
* egonw |
notes that Gpox's patch make the mol table performance nice again |
| 14:58 |
|
egonw |
Gpox++ (for fixing it) |
| 14:58 |
|
egonw |
Gpox-- (for breaking it in the first place) |
| 14:58 |
|
egonw |
(just to discourage people intentionally breaking things, to fix it then again, and gain free karma) |
| 14:58 |
|
egonw |
yes, I am looking at you |
| 15:01 |
|
olass |
*gulp* |
| 15:01 |
|
* olass |
hides |
| 15:04 |
|
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annzi joined #bioclipse |
| 15:51 |
|
jonalv |
zarah: seen jpansanel ? |
| 15:51 |
|
zarah |
I have not seen jpansanel |
| 15:52 |
|
jonalv |
egonw: didn't you say that jpansanel pinged me? |
| 17:10 |
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samuell joined #bioclipse |
| 17:51 |
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samuell joined #bioclipse |
| 18:45 |
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edrin left #bioclipse |
| 19:11 |
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egonw joined #bioclipse |
| 22:47 |
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zarah joined #bioclipse |
