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| 07:07 |
maclean |
morning |
| 07:09 |
maclean |
Ah bug reports which are actually (possibly) feature requests.... |
| 07:09 |
maclean |
"am creating a database so i would like to incorporate Jmol into the database but for that i have to write a script which would should each molecule when clicked upon it." |
| 07:21 |
egonw |
hej maclean |
| 07:21 |
maclean |
hej |
| 07:21 |
egonw |
yeah, actually sounds like a support request to me :) |
| 07:22 |
maclean |
It also has a "accidentally the whole thing" error (IE : a missing word). |
| 07:25 |
* egonw |
is install the eclipse maven2 plugin (again) |
| 07:26 |
egonw |
but now in a separate eclipse install |
| 07:26 |
egonw |
as I hate that extension... |
| 07:26 |
egonw |
(which could change...) |
| 07:26 |
maclean |
why, what does it do that's so bad? |
| 07:26 |
egonw |
it starts at random time downloading huge amounts of data... |
| 07:26 |
maclean |
Ohhh. Yes, this is a maven feature. |
| 07:26 |
egonw |
and that is not useful when I am hacking on Bioclipse or CDK that do not really use maven |
| 07:27 |
egonw |
yes |
| 07:27 |
maclean |
Any use of maven is likely to trigger huge downloads. |
| 07:27 |
maclean |
I think that there is a way to turn this off... |
| 07:27 |
maclean |
Like in global settings. |
| 07:27 |
egonw |
possibly... |
| 07:27 |
egonw |
I might look that up... |
| 07:28 |
egonw |
OK, there it goes... |
| 07:30 |
maclean |
" I agree, it is not pretty. Ideally we could allow to to have "update |
| 07:30 |
maclean |
on startup" flag (or "update at such intervals") per repository, but I |
| 07:30 |
maclean |
was hesitating to add setting like this in an attempt to keep |
| 07:30 |
maclean |
configuration UI simple." |
| 07:30 |
egonw |
:) |
| 07:31 |
maclean |
Yes, 'ideally' you could add that obvious and necessary feature. But basically you don't want to... |
| 07:31 |
egonw |
yeah, it's always good software engeering practice to think what you like best is what the customer wants ... |
| 07:31 |
* egonw |
is guilty as charged (wrt to the CDK) |
| 07:31 |
* maclean |
too |
| 07:31 |
egonw |
who wants scientific accuracy... we want those damn aromatic SMILES |
| 07:31 |
egonw |
who wants scientific accuracy, or specification conformance... we want those damn aromatic SMILES |
| 07:32 |
* egonw |
wonders of _ilbot2 filters out cursing ... |
| 07:32 |
egonw |
zarah: do you do RTs ? |
| 07:32 |
zarah |
egonw: are you talking to *me*? |
| 07:33 |
egonw |
zarah: would be cool if you could have a command @rt |
| 07:33 |
zarah |
egonw: eh... wha'? |
| 07:33 |
egonw |
@tell masak can I haz @rt ? |
| 07:33 |
zarah |
Consider it noted. |
| 07:33 |
maclean |
retweet? |
| 07:33 |
maclean |
oh nonono. |
| 07:33 |
egonw |
:) |
| 07:33 |
egonw |
yeah, it might scare away people |
| 07:34 |
egonw |
with these logs... no one knows that anything they say here is public anyway |
| 07:34 |
egonw |
who cares about reading channel topics... |
| 07:34 |
maclean |
ah. channel topic. that actually answers a question I had. |
| 07:42 |
slyrus_ |
can i haz decent 2d rendering? :) |
| 07:42 |
maclean |
>:| |
| 07:43 |
maclean |
Writing unit tests and javadocs is hard... |
| 07:43 |
maclean |
But yes, I think many of us (including me) want decent 2d rendering. |
| 07:43 |
egonw |
slyrus_: we are working on it... |
| 07:43 |
slyrus_ |
yay! |
| 07:43 |
egonw |
but, say, 65k euro would help a lot |
| 07:43 |
egonw |
allowing us to put someone on it full time |
| 07:45 |
maclean |
that's like 56K in real mo...er in pounds ! |
| 07:45 |
maclean |
Quite a bit. |
| 07:47 |
maclean |
Also, I like the range of google queries that end "65,000 ..." such a "65,000 a year amount per month" :) |
| 07:49 |
egonw |
that's with overhead etc... |
| 07:49 |
egonw |
not what a person would earn... |
| 07:54 |
slyrus_ |
is there an academic paper to be had from a more fully-functioning 2d renderer or is that "solved"? |
| 07:54 |
egonw |
yeah, there is some related literature |
| 07:54 |
egonw |
the JChemPaint paper from 2000 |
| 07:54 |
egonw |
this year a paper by Ertl |
| 07:55 |
egonw |
2-3 years ago a paper on MCDL |
| 07:55 |
egonw |
but not so much really... |
| 07:55 |
slyrus_ |
so, no, in other words? :) |
| 07:55 |
egonw |
it is believed a solved problem |
| 07:55 |
slyrus_ |
oh, great, since it's solved I'll just wait for the answer then :) |
| 07:55 |
egonw |
but for many it's also core business, and thus closed source |
| 07:55 |
slyrus_ |
ah, right... |
| 07:55 |
egonw |
so, it's both unimportant and important at the same time |
| 07:56 |
slyrus_ |
right. the 2 things I've been wanting are good 2d rendering and molecule -> IUPAC names |
| 07:56 |
slyrus_ |
both of which exist in commercial libraries but not (well enough for 2d drawing anyway) in CDK |
| 07:58 |
egonw |
indeed |
| 07:58 |
egonw |
actually, I don't think many companies to IUPAC names either |
| 07:59 |
slyrus_ |
chemaxon does, I think |
| 08:02 |
maclean |
I think naming is one of those problems that looks easy at the start, then rapidly gets difficult. |
| 08:02 |
slyrus_ |
indeed |
| 08:02 |
slyrus_ |
sort of like 2-d drawing :) |
| 08:03 |
maclean |
Like "Oh well there's alkanes, and alkenes" but then "oh and bridged cycles, and spira-fused rings and..." |
| 08:03 |
maclean |
yes, much like 2d drawing. |
| 08:03 |
egonw |
slyrus_: anyway... CDK has a framework for it... |
| 08:03 |
egonw |
and does IUPAC naming... |
| 08:04 |
egonw |
but only for a small set of molecules... |
| 08:04 |
egonw |
curtosy to Manchester University |
| 08:04 |
egonw |
slyrus_: patches welcome |
| 08:04 |
maclean |
egonw: unfortunately, that's pretty much the same as "CDK doesn't do it". |
| 08:04 |
slyrus_ |
oh? |
| 08:04 |
maclean |
It's like pregnancy - there's no "almost works" for some things. |
| 08:05 |
egonw |
maclean: indeed... the stress should be on 'framework' |
| 08:05 |
maclean |
true. |
| 08:05 |
slyrus_ |
where is that? |
| 08:05 |
egonw |
slyrus_: looking up details, hang on... |
| 08:06 |
slyrus_ |
there's the IUPAC name -> molecule framework, but I haven't found the opposite direction |
| 08:06 |
slyrus_ |
not that it's not there... |
| 08:06 |
egonw |
oh, bugger... |
| 08:06 |
egonw |
indeed... |
| 08:07 |
egonw |
Manchester did the *parser*... |
| 08:07 |
egonw |
ah, then that generator framework was mine... |
| 08:07 |
egonw |
and even less functional... |
| 08:07 |
slyrus_ |
oh, cool |
| 08:07 |
egonw |
and hence pulled... |
| 08:07 |
slyrus_ |
not cool :) |
| 08:07 |
egonw |
should be somewhere in the archives... |
| 08:07 |
egonw |
would be a nice student project |
| 08:07 |
egonw |
but it is so complex... |
| 08:07 |
egonw |
the rules contradict |
| 08:08 |
egonw |
so, prioritization is important |
| 08:08 |
egonw |
the framework did all that... |
| 08:08 |
egonw |
but I never had time to persue it further |
| 08:08 |
* egonw |
install egit |
| 08:08 |
slyrus_ |
anyway, time for some sleep. talk to y'all another night. |
| 08:09 |
maclean |
night |
| 08:09 |
* maclean |
should get to work |
| 08:10 |
egonw |
slyrus_: ack... |
| 08:11 |
egonw |
slyrus_: please do ask on blueobelisk.shapado.com about an OS IUPAC name generator... |
| 08:11 |
egonw |
slyrus_: perhaps there is critical mass to bootstrap some project |
| 08:16 |
maclean |
later. |
| 08:16 |
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| 09:12 |
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| 09:13 |
caligula |
need help with standard dev |
| 09:13 |
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| 09:17 |
egonw |
huh? |
| 09:42 |
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| 10:04 |
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| 11:46 |
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| 12:59 |
CIA-98 |
cdk: Egon Willighagen master * r714c51e / pom.xml : Updated version and confirmed inception year - http://bit.ly/agWAhl |
| 13:02 |
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| 13:04 |
maclean |
egonw : I just wiped out the molecule layout code :((( |
| 13:05 |
maclean |
Oh no! Wait. |
| 13:06 |
egonw |
deleted the branch |
| 13:06 |
egonw |
? |
| 13:07 |
egonw |
or the whole git folder? |
| 13:07 |
maclean |
Actually, git did the right thing for once. |
| 13:08 |
maclean |
I cloned a project into the same directory that was already there. |
| 13:08 |
maclean |
And...it's preserved the branch I had. |
| 13:09 |
maclean |
But git (or eclipse?) has put the other checkout I had into a sub-directory. |
| 13:09 |
maclean |
Weird. |
| 13:10 |
maclean |
Anyway : false alarm. The moral of the story is... don't try to work in coffee shops. |
| 13:12 |
egonw |
no, joints are not good for concentration :) |
| 13:14 |
maclean |
Oh. Not a Dutch coffee shop, no :) |
| 13:14 |
egonw |
:) |
| 13:15 |
maclean |
Oh, and with regard to Taverna-CDK, I think the problem was that the CDK plugin doesn't work with the latest Taverna, not a CDK problem. |
| 13:15 |
maclean |
As in, the Taverna API changed, or something, and the CDKplugin wasn't updated. |
| 13:15 |
egonw |
but he was using 1.7.2, right? |
| 13:16 |
egonw |
the code is being ported to 2.2 ... |
| 13:16 |
egonw |
Andreas is working on that, and I believe they will have a workshop soon |
| 13:16 |
egonw |
devel workshop, that is |
| 13:17 |
egonw |
and it worked on other platforms... |
| 13:17 |
egonw |
just not on that vista system |
| 13:17 |
egonw |
I hope he saw the question about him using 32 or 64 vista... |
| 13:19 |
maclean |
Ok, right yes. Am I not awake today, or something? |
| 13:19 |
egonw |
no worries |
| 13:19 |
egonw |
I had that earlier this week |
| 13:20 |
maclean |
What are you working on today? |
| 13:21 |
egonw |
stuff with maven |
| 13:21 |
egonw |
e.g. the CDK pom.xml |
| 13:21 |
egonw |
in master |
| 13:21 |
maclean |
ah cool. |
| 13:21 |
egonw |
upon popural request... |
| 13:22 |
egonw |
unlike some like to believe, I *can* bend backwards... |
| 13:22 |
maclean |
Probably ignore maven when it says it prefers src/main/java and src/test/java. |
| 13:22 |
maclean |
As the CDK has just src/java and src/test. I don't think it matters. |
| 13:23 |
egonw |
yeah, we don't have that extra java/ |
| 13:23 |
egonw |
not sure where the pom.xml is supposed to teach maven that... |
| 13:24 |
maclean |
hmmm. not sure. |
| 13:25 |
maclean |
there's a child element of _build_ called _sourceDirectory_ and _testSourceDirectory_ |
| 13:25 |
maclean |
sorry, there are two children of... |
| 13:26 |
maclean |
I have them just before the plugins element |
| 13:26 |
egonw |
ah, indeed! |
| 13:26 |
egonw |
found it...tack! |
| 13:26 |
maclean |
n/p |
| 13:29 |
maclean |
oh god. It's like a neverending nightmare. The zombie Data/data directory. |
| 13:33 |
maclean |
nothing works. git reset --hard, git clean -f, git checkout -f -b newbranch |
| 13:34 |
egonw |
try on #git |
| 13:36 |
maclean |
It's a known problem - the case-sensitivity thing on macs. |
| 13:36 |
maclean |
The workaround is to set up a filesystem on a partition or some such crazyness. |
| 13:40 |
maclean |
Or, alternatively. Just branch, delete the dir, and forever work on that branch. Sigh.... |
| 13:40 |
egonw |
(OS/X)-- |
| 13:40 |
egonw |
I always thought that BSD was case sensitive... |
| 13:42 |
maclean |
Well it's not quite BSD. Or some parts are, and some are not. |
| 13:42 |
maclean |
I guess the filesystem is not the same. |
| 13:43 |
egonw |
indeed... |
| 13:43 |
egonw |
that's probably more significant |
| 14:01 |
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| 14:05 |
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| 15:32 |
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| 15:33 |
maclean |
haha! the day is looking up, as I fix a bug. |
| 15:33 |
egonw |
maclean++ |
| 15:33 |
* egonw |
is going offline for now |
| 15:33 |
maclean |
ok, cu |
| 15:44 |
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| 15:50 |
slyrus_ |
maclean: you can repartition your hard drive with case-sensitive HFS+ or whatever they call it |
| 15:51 |
maclean |
I probably /can/ (with much cursing, I expect) - but do I really want to? :) |
| 15:51 |
slyrus_ |
heh, well, no |
| 15:52 |
maclean |
It's one of those issues that occurs infrequently enough that by the next time it comes up, I will have forgotten a) why it happens and b) how to fix it. |
| 15:55 |
* maclean |
sometimes wonders if people troll software mailing list with bizarre questions. |
| 15:58 |
maclean |
I mean "I am working on a database where there are several molecules in the drop down menu..." ? |
| 16:16 |
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| 16:22 |
maclean |
egonw : I assigned that signature/aromatic patch to you - do feel free to re-assign it :) |
| 16:23 |
egonw |
ok |
| 16:23 |
egonw |
yeah, will try to review some patches this weekend |
| 16:24 |
egonw |
no promises though |
| 16:25 |
maclean |
anytime. It's only necessary that it exist in the patch list, not that it be reviewed quickly. |
| 16:31 |
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| 16:46 |
maclean |
layout code : |
| 16:46 |
maclean |
http://github.com/gilleain/cdk/commit/57a3d5432faa56783c1353a67898f0cb74681517 |
| 16:46 |
zarah |
maclean's link is also http://tinyurl.com/2wg4tth |
| 16:49 |
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| 17:15 |
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