| Time |
S |
Nick |
Message |
| 00:29 |
|
CIA-33 |
cdk: rajarshi * r11605 /cdk/branches/rguha_vdw_removal/: Removed the VdW branch since the changes have been merged into trunk |
| 00:36 |
|
CIA-33 |
cdk: rajarshi * r11606 /cdk/branches/rajarshi-descnames/: |
| 00:36 |
|
CIA-33 |
cdk: Created a new branch in which the descriptor interface will be refactored to |
| 00:36 |
|
CIA-33 |
cdk: allow retrieval of names without calculation and to make sure that no descriptor |
| 00:36 |
|
CIA-33 |
cdk: throws an exception. Rather exceptions will be returned in the DescriptorValue |
| 00:36 |
|
CIA-33 |
cdk: object |
| 01:32 |
|
CIA-33 |
cdk: rajarshi * r11607 /cdk/branches/rajarshi-descnames/src/ (2 files in 2 dirs): |
| 01:32 |
|
CIA-33 |
cdk: Updated DescriptorValue to have a field to hold an exception object. We |
| 01:32 |
|
CIA-33 |
cdk: specifically hold only one exception object since anytime a descriptor throws an |
| 01:32 |
|
CIA-33 |
cdk: exception we will be returning, so only that ezception need be stored |
| 01:36 |
|
CIA-33 |
cdk: rajarshi * r11608 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/IDescriptor.java: |
| 01:36 |
|
CIA-33 |
cdk: Updated to provide a method to get descriptor names. This is useful, since it |
| 01:36 |
|
CIA-33 |
cdk: will allow retrieval of names without a priori calculation. Obviously, the |
| 01:36 |
|
CIA-33 |
cdk: number of names will depend on the parameter settings (if any). So if this is an |
| 01:36 |
|
CIA-33 |
cdk: issue, make sure to set parameters and then call the method. Otherwise the names |
| 01:36 |
|
CIA-33 |
cdk: are constructed from default parameters (if necessary) |
| 01:42 |
|
CIA-33 |
cdk: rajarshi * r11609 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/IMolecularDescriptor.java: Modifed the definition of calculate() so that it does not throw an exception. All exceptions will be caught and returned via a DescriptorValue object |
| 02:20 |
|
CIA-33 |
cdk: rajarshi * r11610 /cdk/branches/rajarshi-descnames/src/ (10 files in 2 dirs): Updated descriptors starting with A to conform to the new policy on not throwing exceptions and providing descriptor names without calculation |
| 02:33 |
|
CIA-33 |
cdk: rajarshi * r11611 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/molecular/ (3 files): Updated descriptors starting with B to conform to the new policy on not throwing exceptions and providing descriptor names without calculation |
| 03:13 |
|
CIA-33 |
cdk: rajarshi * r11612 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/molecular/ (6 files): Updated descriptors starting with C to conform to the new policy on not throwing exceptions and providing descriptor names without calculation |
| 03:22 |
|
CIA-33 |
cdk: rajarshi * r11613 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/molecular/ (3 files): Updated descriptors starting with E, F and G to conform to the new policy on not throwing exceptions and providing descriptor names without calculation |
| 03:31 |
|
CIA-33 |
cdk: rajarshi * r11614 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/molecular/ (2 files): Updated descriptors starting with H to conform to the new policy on not throwing exceptions and providing descriptor names without calculation |
| 03:36 |
|
CIA-33 |
cdk: rajarshi * r11615 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/molecular/ (2 files): Updated descriptors starting with I and K to conform to the new policy on not throwing exceptions and providing descriptor names without calculation |
| 03:58 |
|
CIA-33 |
cdk: rajarshi * r11616 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/molecular/ (4 files): Updated descriptors starting with L to conform to the new policy on not throwing exceptions and providing descriptor names without calculation |
| 04:05 |
|
CIA-33 |
cdk: rajarshi * r11617 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/molecular/ (4 files): Updated descriptors starting with M and P to conform to the new policy on not throwing exceptions and providing descriptor names without calculation |
| 04:12 |
|
|
egonw joined #cdk |
| 04:17 |
|
CIA-33 |
cdk: rajarshi * r11618 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/molecular/ (4 files): Updated descriptors starting with R, T and V to conform to the new policy on not throwing exceptions and providing descriptor names without calculation |
| 04:37 |
|
CIA-33 |
cdk: rajarshi * r11619 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/molecular/ (6 files): Updated remaining descriptors to conform to the new policy on not throwing exceptions and providing descriptor names without calculation |
| 04:46 |
|
|
rguha joined #cdk |
| 04:46 |
|
egonw |
hi rguha |
| 04:46 |
|
rguha |
hi |
| 04:46 |
|
rguha |
how're things going? |
| 04:47 |
|
egonw |
in general, or something in particular? |
| 04:47 |
|
* egonw |
hates 'how are you' questions... |
| 04:47 |
|
egonw |
never get them properly |
| 04:47 |
|
rguha |
ha ha |
| 04:47 |
|
rguha |
just generally |
| 04:47 |
|
rguha |
btw when are you moving to Uppsala? |
| 04:47 |
|
egonw |
september |
| 04:48 |
|
rguha |
JArl's group? |
| 04:48 |
|
egonw |
yes |
| 04:48 |
|
rguha |
nice |
| 04:48 |
|
egonw |
so, working hard now gettings things finished in Wageningen |
| 04:48 |
|
rguha |
aah |
| 04:49 |
|
egonw |
who are, btw, looking for a qualified bio/chemoinformatician |
| 04:49 |
|
egonw |
seen the ad in my blog? |
| 04:49 |
|
rguha |
yes, saw that |
| 04:49 |
|
egonw |
you were looking in USA, but wanted to mentioned it nevertheless |
| 04:49 |
|
rguha |
your replacemnent :) |
| 04:49 |
|
egonw |
and of Mark Fiers |
| 04:49 |
|
egonw |
our workflow dude |
| 04:49 |
|
rguha |
thanks, but I'll ahve to stay here |
| 04:49 |
|
rguha |
aah |
| 04:49 |
|
egonw |
he wrote, singlehanded, a workflow tool, Cyrille2 |
| 04:49 |
|
egonw |
web based |
| 04:50 |
|
egonw |
looks quite nice |
| 04:50 |
|
egonw |
but no community like Taverna |
| 04:50 |
|
egonw |
and very performant |
| 04:50 |
|
egonw |
they use it for large scale sequence annotation and sorts |
| 04:50 |
|
egonw |
see BMC BioInf |
| 04:50 |
|
egonw |
[06:49] <rguha> thanks, but I'll ahve to stay here |
| 04:50 |
|
egonw |
at Indiana? |
| 04:50 |
|
rguha |
the US |
| 04:51 |
|
egonw |
did they manage an extension, fixed position, or so? |
| 04:51 |
|
rguha |
impressive! |
| 04:51 |
|
egonw |
ah, ok |
| 04:51 |
|
rguha |
things wll get settled by the end of August |
| 04:51 |
|
egonw |
ok, will ask then :) |
| 04:51 |
|
rguha |
:) |
| 04:51 |
|
rguha |
btw, did you se the mail wrt names for non-molecular descriptors? |
| 04:52 |
|
egonw |
anyway... if you happen to know someone, post-doc range, who might be interested, and who knows his way around in workflows... |
| 04:52 |
|
egonw |
please let me know |
| 04:52 |
|
egonw |
I hope at least Thomas will apply... (hint hint ;) |
| 04:52 |
|
rguha |
sure |
| 04:54 |
|
egonw |
will file the RFE now |
| 04:54 |
|
egonw |
on that performance issue |
| 04:55 |
|
rguha |
thanks |
| 04:55 |
|
CIA-33 |
cdk: rajarshi * r11620 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java: Updated descriptor to conform to the new policy on not throwing exceptions and providing descriptor names without calculation |
| 04:55 |
|
egonw |
ok, got to go and catch a train |
| 04:55 |
|
|
jbrefort joined #cdk |
| 04:56 |
|
rguha |
bye |
| 04:56 |
|
egonw |
bbl |
| 04:56 |
|
egonw |
bye |
| 04:58 |
|
CIA-33 |
cdk: rajarshi * r11621 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/IAtomicDescriptor.java: Updated interface to emove exceptions on calculate() |
| 05:03 |
|
|
bag joined #cdk |
| 05:10 |
|
CIA-33 |
jmol: hansonr * r9605 /trunk/Jmol/src/org/jmol/ (shapespecial/Draw.java util/Quaternion.java): new Quaternion algorithm uses double precision |
| 05:11 |
|
CIA-33 |
jmol: hansonr * r9606 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: new Quaternion algorithm uses double precision |
| 05:15 |
|
CIA-33 |
cdk: rajarshi * r11622 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/atomic/ (4 files): Updated atom descriptors starting with A, to not throw eceptions and to return names outside of calculate() |
| 06:08 |
|
|
rojasm joined #cdk |
| 06:15 |
|
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rojasm joined #cdk |
| 06:36 |
|
|
egonw joined #cdk |
| 06:39 |
|
|
masak joined #cdk |
| 06:55 |
|
thomas_ku |
moin |
| 07:01 |
|
|
rojasm joined #cdk |
| 07:05 |
|
egonw |
hi rojasm, thomas_ku |
| 07:05 |
|
egonw |
and masak |
| 07:05 |
|
masak |
egonw: hiya |
| 07:05 |
|
egonw |
rojasm: please check the discussion on the QSAR API... and the commits from Rajarshi in the branch |
| 07:30 |
|
|
egonw joined #cdk |
| 08:35 |
|
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zarah joined #cdk |
| 09:03 |
|
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shk3 joined #cdk |
| 09:59 |
|
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malick joined #cdk |
| 10:57 |
|
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zarah joined #cdk |
| 10:59 |
|
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zarah joined #cdk |
| 11:00 |
|
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zarah joined #cdk |
| 12:22 |
|
|
steinbeck joined #cdk |
| 12:22 |
|
steinbeck |
shk3: around? |
| 12:33 |
|
egonw |
he was just at #bioclipse |
| 12:33 |
|
shk3 |
we already met |
| 12:45 |
|
egonw |
ack |
| 13:03 |
|
thomas_ku |
hi steinbeck |
| 13:13 |
|
steinbeck |
Hi thomas_ku |
| 13:45 |
|
egonw |
steinbeck: no, that did not help |
| 13:45 |
|
egonw |
same error on cdknews.org |
| 13:46 |
|
steinbeck |
Same error but with different number? |
| 13:46 |
|
egonw |
no, don't think so |
| 13:46 |
|
steinbeck |
hm - mom |
| 13:47 |
|
egonw |
I don't seem able to make steinbeck an admin |
| 13:47 |
|
egonw |
ah, wait, I think I can |
| 13:47 |
|
egonw |
that does not solve the missing admin pwd though :) |
| 13:48 |
|
egonw |
ok, the steinbeck account should now be journal manager too |
| 13:48 |
|
steinbeck |
well, the username should be enough. Is it "admin" |
| 13:48 |
|
egonw |
well, 'steinbeck' is journal manager now too |
| 13:48 |
|
egonw |
which should allow you to reproduce the problem with #31 |
| 13:49 |
|
steinbeck |
what was the url again? Just deleted your mail :-) |
| 13:49 |
|
egonw |
http://www.steinbeck-molecular[…]tor/submission/31 |
| 13:49 |
|
zarah |
egonw's link is also http://tinyurl.com/6x33x6 |
| 13:49 |
|
steinbeck |
thought I had solved it :-) |
| 13:51 |
|
steinbeck |
I can open this sdf |
| 13:51 |
|
egonw |
pdf, you mean? |
| 13:51 |
|
egonw |
I still can't even see the details... |
| 13:52 |
|
egonw |
Fatal error: Allowed memory size of 8388608 bytes exhausted (tried to allocate 58368 bytes) in /var/www/cdknews/lib/smarty/Smarty_Compiler.class.php on line 1380 |
| 13:52 |
|
steinbeck |
yes, pdf |
| 13:52 |
|
steinbeck |
have you tried it again? |
| 13:53 |
|
egonw |
yes |
| 13:53 |
|
steinbeck |
weird. works for me |
| 13:54 |
|
egonw |
really, weird... |
| 13:54 |
|
egonw |
and rather annoying |
| 13:54 |
|
steinbeck |
I now adjusted all php.ini in question |
| 13:54 |
|
steinbeck |
maybe a session problem? |
| 13:54 |
|
egonw |
I just tried logging out, and relogin |
| 13:54 |
|
egonw |
did not help |
| 14:00 |
|
steinbeck |
anyone here ever had to do the "Laptop Drive of Shame"? :-) |
| 14:00 |
|
steinbeck |
http://www.networkworld.com/community/node/29791 |
| 14:00 |
|
zarah |
steinbeck's link is also http://tinyurl.com/55v6el |
| 14:00 |
|
egonw |
that's the advantage of having a separate desktop machine :) |
| 14:01 |
|
egonw |
umm.. now also tried with a different browser |
| 14:01 |
|
egonw |
same problem |
| 14:08 |
|
* steinbeck |
is going for a run |
| 14:08 |
|
|
steinbeck left #cdk |
| 14:21 |
|
egonw |
outcome SF SVN upgrade info: http://sourceforge.net/communi[…]plies=1#post-6659 |
| 14:21 |
|
zarah |
egonw's link is also http://tinyurl.com/5m9d5s |
| 14:21 |
|
CIA-33 |
jmol: hansonr * r9607 /trunk/Jmol/src/org/jmol/ (5 files in 4 dirs): |
| 14:21 |
|
CIA-33 |
jmol: version=11.5.48_dev sheetsmoothing, messageCallback |
| 14:21 |
|
CIA-33 |
jmol: # bug fix: sheetsmoothing not consistent among structures in multi-chain systems |
| 14:21 |
|
CIA-33 |
jmol: # bug fix: messages not sent to messageCallback |
| 15:07 |
|
CIA-33 |
jmol: hansonr * r9608 /trunk/Jmol/src/org/jmol/viewer/ (Jmol.properties ScriptManager.java Viewer.java): version=11.5.48_dev # bug fix: queue thread termination when applets are off screen |
| 15:24 |
|
|
malick joined #cdk |
| 17:00 |
|
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rojasm joined #cdk |
| 17:24 |
|
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bag joined #cdk |
| 17:28 |
|
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malick joined #cdk |
| 19:16 |
|
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egonw joined #cdk |
| 19:18 |
|
CIA-33 |
jmol: hansonr * r9609 /trunk/Jmol/src/org/jmol/ (4 files in 3 dirs): |
| 19:18 |
|
CIA-33 |
jmol: version=11.5.48_dev quaternion arrows;connect aromatic auto |
| 19:18 |
|
CIA-33 |
jmol: # bug fix: quaternion derivative DRAW arrows placed on residue i+1 instead of residue i |
| 19:18 |
|
CIA-33 |
jmol: # bug fix: connect aromatic auto; select connected([bond type],...) |
| 19:20 |
|
CIA-33 |
cdk: rajarshi * r11623 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/atomic/ (4 files): Updated atom descriptors starting with B,C,D,E, to not throw eceptions and to return names outside of calculate() |
| 19:21 |
|
egonw |
moin |
| 19:36 |
|
CIA-33 |
cdk: egonw * r11624 /cdk/branches/egonw-atowl/src/main/org/openscience/cdk/dict/data/cdk-sybyl-mappings.owl: Added template for CDK2Sybyl atom typing mapping |
| 19:41 |
|
CIA-33 |
cdk: rajarshi * r11625 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/atomic/ (6 files): Updated atom descriptors starting with I, to not throw eceptions and to return names outside of calculate() |
| 20:52 |
|
CIA-33 |
jmol: nicove * r9610 /trunk/Jmol-FAH/projects/p2175.xyz.gz: |
| 20:54 |
|
CIA-33 |
cdk: rajarshi * r11626 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/DescriptorValue.java: removed a deprecated constructor since it has been cleaned up |
| 20:55 |
|
CIA-33 |
cdk: rajarshi * r11627 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/ (2 files in 2 dirs): Updated atom pair descriptors to conform to the new descriptor policy |
| 20:55 |
|
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rguha joined #cdk |
| 20:57 |
|
CIA-33 |
cdk: rajarshi * r11628 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/atomic/ (16 files): Updated remaining atom descriptors according to the new descriptor policy |
| 21:19 |
|
CIA-33 |
cdk: rajarshi * r11629 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/ (7 files in 2 dirs): Updated bond descriptors according to the new descriptor policy |
| 21:19 |
|
CIA-33 |
jmol: nicove * r9611 /trunk/Jmol/ (17 files in 4 dirs): Translation: Russian (ru) |
| 21:23 |
|
CIA-33 |
cdk: rajarshi * r11630 /cdk/branches/rajarshi-descnames/src/test/org/openscience/cdk/qsar/descriptors/DescriptorTest.java: Some minor cleanups |
| 21:28 |
|
CIA-33 |
cdk: rajarshi * r11631 /cdk/branches/rajarshi-descnames/src/test/org/openscience/cdk/qsar/descriptors/DescriptorTest.java: Added a test to check that we can get descriptor names without calculating and that the return array is not null and length >= 1 |
| 21:37 |
|
CIA-33 |
cdk: rajarshi * r11632 /cdk/branches/rajarshi-descnames/src/test/org/openscience/cdk/qsar/descriptors/ (3 files in 3 dirs): Updated test superclasses to ensure that the calculate() method never throws an exception |
| 21:41 |
|
CIA-33 |
cdk: rajarshi * r11633 /cdk/branches/rajarshi-descnames/src/test/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptorTest.java: Updated test since descriptors now shouldn't throw an exception |
| 21:49 |
|
CIA-33 |
cdk: rajarshi * r11634 /cdk/branches/rajarshi-descnames/src/test/org/openscience/cdk/qsar/descriptors/ (3 files in 3 dirs): Added a test to the descriptor test superclasses to check that the names obtained directly from the decsriptor clas matches the names from the decsriptor value object |
| 22:45 |
|
CIA-33 |
cdk: rajarshi * r11635 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/molecular/CPSADescriptor.java: Made descriptor names into static final |
| 23:10 |
|
CIA-33 |
cdk: rajarshi * r11636 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/descriptors/molecular/ (34 files): Made descriptor names into static final String[] where applicable |
| 23:15 |
|
CIA-33 |
cdk: rajarshi * r11637 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/qsar/DescriptorEngine.java: Updated to take into account new descriptr policies |
| 23:26 |
|
CIA-33 |
cdk: rajarshi * r11638 /cdk/branches/rajarshi-descnames/src/main/org/openscience/cdk/io/cml/QSARConvention.java: Updated to take into account new descriptr policies |
