| Time |
S |
Nick |
Message |
| 05:20 |
|
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jbrefort joined #cdk |
| 06:05 |
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egonw joined #cdk |
| 07:15 |
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egonw joined #cdk |
| 07:29 |
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Gpox joined #cdk |
| 07:32 |
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carsten joined #cdk |
| 08:37 |
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masak joined #cdk |
| 08:37 |
|
masak |
egonw: rednael, right? |
| 08:37 |
|
egonw |
it's rednael |
| 08:37 |
|
egonw |
masak: you know Zarah Leander, right? |
| 08:37 |
|
egonw |
that's the link to zarah :) |
| 08:37 |
|
masak |
egonw: yes. ah, I see. |
| 08:37 |
|
masak |
an homage of sorts. |
| 08:38 |
|
egonw |
leander nick was already registered |
| 08:38 |
|
masak |
bet it was. |
| 08:44 |
|
masak |
egonw: a good move, in case you haven't done so already, is to commit the bot to the cdk repo. |
| 09:10 |
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bag joined #cdk |
| 09:12 |
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shk3 joined #cdk |
| 09:19 |
|
egonw |
shk3: http://pele.farmbio.uu.se/nmrs[…]b/?moleculeId=234 |
| 09:19 |
|
zarah |
egonw's link is also http://tinyurl.com/c4x36y |
| 09:19 |
|
masak |
pele++ |
| 09:27 |
|
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jbrefort joined #cdk |
| 09:31 |
|
shk3 |
egonw: any particular purpose of that? |
| 09:31 |
|
shk3 |
sorry for asking stupid questions |
| 09:36 |
|
jpansanel |
moin |
| 09:36 |
|
zarah |
ni hao jpansanel |
| 09:50 |
|
egonw |
shk3: yes, Linked Open Drug Data |
| 10:05 |
|
jpansanel |
egonw : what is Open Drug Data ? |
| 10:05 |
|
egonw |
a group of people who want to make a RDF network of drug related data |
| 10:06 |
|
jpansanel |
good idea |
| 10:06 |
|
jpansanel |
it's about approved drugs, new drugs or both ? |
| 10:07 |
|
egonw |
I think just about anything remotely relevant |
| 10:08 |
|
egonw |
they are even linking potions... |
| 10:08 |
|
egonw |
chinese medicine, that is |
| 10:08 |
|
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jbrefort joined #cdk |
| 10:08 |
|
jpansanel |
ok |
| 11:12 |
|
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maclean joined #cdk |
| 11:13 |
|
egonw |
shk3: http://chem-bla-ics.blogspot.c[…]moleculesnet.html |
| 11:13 |
|
zarah |
egonw's link is also http://tinyurl.com/ddprcx |
| 11:13 |
|
egonw |
shk3: that provides some context |
| 11:17 |
|
shk3 |
egonw++ |
| 11:22 |
|
maclean |
egonw : around? |
| 11:24 |
|
egonw |
yes |
| 11:25 |
|
egonw |
well... in 10 minutes, OK? |
| 11:25 |
|
maclean |
ok |
| 11:33 |
|
egonw |
back |
| 11:33 |
|
maclean |
ah, right |
| 11:33 |
|
maclean |
it's about cloning of IAtomContainers |
| 11:34 |
|
maclean |
I reused (copy/pasted) the code from the clone method of cdk.AtomContainer |
| 11:34 |
|
maclean |
and it wasn't working |
| 11:34 |
|
maclean |
so, I altered the line that looked like |
| 11:34 |
|
maclean |
newAtoms[j] = clone.getAtom(getAtomNumber(bond.getAtom(j))); |
| 11:35 |
|
maclean |
to lookup using a unique ID rather than '==' |
| 11:35 |
|
maclean |
and that worked |
| 11:36 |
|
egonw |
define unique ID |
| 11:36 |
|
maclean |
I have a gist of this |
| 11:36 |
|
egonw |
and what's not working? |
| 11:36 |
|
egonw |
ok |
| 11:36 |
|
maclean |
http://gist.github.com/81069 |
| 11:37 |
|
maclean |
unique ID is a stringified number - each atom is given a sequential numerical ID |
| 11:37 |
|
egonw |
I guess that works if you have IDs |
| 11:37 |
|
egonw |
which is not generally the case... |
| 11:37 |
|
maclean |
I know |
| 11:37 |
|
egonw |
but what exactly was not working? |
| 11:38 |
|
maclean |
the atom references returned by getAtomByEquals were not right |
| 11:38 |
|
maclean |
which I could tell by the string ids when I printed them out. |
| 11:39 |
|
egonw |
your code is not working because you ask at what position the cloned atom is in the original molecule |
| 11:39 |
|
maclean |
the atoms are in the same order |
| 11:39 |
|
egonw |
yes |
| 11:39 |
|
maclean |
this is how the code in AtomContainer.clone works |
| 11:40 |
|
egonw |
but the getAtomByEquals() method is passed a cloned atom |
| 11:40 |
|
egonw |
which will never be part of the source IAtomCotnainer |
| 11:40 |
|
egonw |
I sure hope the AtomContainer.clone() is not doing that... |
| 11:40 |
|
maclean |
no it isn't |
| 11:40 |
|
egonw |
sure? |
| 11:40 |
|
maclean |
for (IBond bond : source.bonds()) { |
| 11:40 |
|
maclean |
'bond' is from source |
| 11:41 |
|
egonw |
ah, indeed |
| 11:41 |
|
egonw |
sorry |
| 11:41 |
|
maclean |
it's weird - the code in AtomContainer /should/ work |
| 11:42 |
|
maclean |
it uses '==' to check for referential equality |
| 11:42 |
|
egonw |
yes, indeed |
| 11:42 |
|
maclean |
So I assume that I have done something wrong, but I can't see how. |
| 11:42 |
|
maclean |
I'm trying to make a test case for it, so that I can check this |
| 11:42 |
|
egonw |
ok |
| 11:43 |
|
maclean |
Maybe I should get back to you when I know more :) |
| 11:43 |
|
egonw |
please do |
| 11:43 |
|
maclean |
tack |
| 11:57 |
|
shk3 |
egonw: how do I get the code of the 1.2 branch from git? |
| 11:57 |
|
shk3 |
would be great if you can just tell me the command or so |
| 11:58 |
|
egonw |
git clone git://cdk.git.sourceforge.net/gitroot/cdk |
| 11:58 |
|
egonw |
git checkout -b local-cdk-1.2.x cdk-1.2.x |
| 12:00 |
|
shk3 |
sorry |
| 12:00 |
|
shk3 |
first one works |
| 12:01 |
|
shk3 |
second doesn't |
| 12:01 |
|
egonw |
try: |
| 12:01 |
|
egonw |
git branch -a |
| 12:01 |
|
shk3 |
do I need to be in the new directory |
| 12:01 |
|
shk3 |
? |
| 12:01 |
|
egonw |
the last may be something like: |
| 12:01 |
|
egonw |
git checkout -b local-cdk-1.2.x origin/cdk-1.2.x |
| 12:01 |
|
shk3 |
yes |
| 12:01 |
|
egonw |
no, no new directory |
| 12:01 |
|
shk3 |
* master |
| 12:01 |
|
shk3 |
origin/HEAD |
| 12:01 |
|
shk3 |
origin/cdk-1.2.x |
| 12:01 |
|
shk3 |
origin/master |
| 12:01 |
|
egonw |
shk3: you can though |
| 12:01 |
|
egonw |
if you really want |
| 12:01 |
|
egonw |
cd .. |
| 12:02 |
|
shk3 |
Branch local-cdk-1.2.x set up to track remote branch refs/remotes/origin/cdk-1.2.x. |
| 12:02 |
|
shk3 |
Switched to a new branch "local-cdk-1.2.x" |
| 12:02 |
|
shk3 |
does that mean it was done? |
| 12:02 |
|
egonw |
git clone cdk <secondFolder> |
| 12:02 |
|
shk3 |
ah yes |
| 12:02 |
|
egonw |
then: cdk <secondFolder> and do the branch swtich there |
| 12:02 |
|
egonw |
shk3: yes |
| 12:02 |
|
shk3 |
git log gives me your new changes |
| 12:02 |
|
egonw |
good :) |
| 12:03 |
|
shk3 |
now I need to import to eclipse |
| 12:05 |
|
maclean |
shk3 : that google also turned up this site: |
| 12:05 |
|
maclean |
http://www-cs-students.stanfor[…]tmagic/index.html |
| 12:05 |
|
zarah |
maclean's link is also http://tinyurl.com/64gy5z |
| 12:07 |
|
maclean |
heh, including a chapter on "Git shortcomings" - I thought they didn't exist :p |
| 12:07 |
|
egonw |
sure, it doesn't cure cancer yet |
| 12:08 |
|
maclean |
what!? Bah. I'm moving to Hg, then. |
| 12:08 |
|
egonw |
no, no... |
| 12:08 |
|
egonw |
you do not understand... |
| 12:08 |
|
egonw |
Hg causes cancer |
| 12:08 |
|
maclean |
Ohhh. |
| 12:08 |
|
maclean |
:) |
| 12:08 |
|
egonw |
hahahah |
| 12:08 |
|
maclean |
Cures syphillis, though *cough*. |
| 12:09 |
|
egonw |
http://cheat.errtheblog.com/s/gitsvn/ |
| 12:09 |
|
zarah |
egonw's link is also http://tinyurl.com/4rnmh3 |
| 12:09 |
|
egonw |
oh... wrong one... |
| 12:09 |
|
egonw |
oops |
| 12:09 |
|
egonw |
http://cheat.errtheblog.com/s/git/ |
| 12:09 |
|
zarah |
egonw's link is also http://tinyurl.com/28naxk |
| 12:10 |
|
egonw |
oh no... |
| 12:19 |
|
maclean |
wow, that's an impressive surname : "Cihan Kamil Öğüt" |
| 12:19 |
|
maclean |
near-maximal diacritic density |
| 12:37 |
|
maclean |
egonw : false alarm on that cloning thing - it was my fault :( sorry |
| 12:37 |
|
* maclean |
mutters bloody structure generation... |
| 12:54 |
|
egonw |
yeah, structgen is not simple material |
| 12:58 |
|
maclean |
I was fusing two atom containers, so it wasn't surprising that using the count wasn't working :) |
| 13:00 |
|
egonw |
ok :) |
| 13:00 |
|
egonw |
yeah, writing unit tests is quite useful |
| 13:00 |
|
egonw |
helps you understand in detail what is going on |
| 13:18 |
|
maclean |
lol egonw you have a feature request here: |
| 13:18 |
|
maclean |
http://sourceforge.net/tracker[…]20024&atid=370024 |
| 13:18 |
|
zarah |
maclean's link is also http://tinyurl.com/dzkgda |
| 13:18 |
|
maclean |
about a SMARTs visual editor |
| 13:18 |
|
maclean |
where you say " I've got |
| 13:18 |
|
maclean |
this planned for early May." |
| 13:18 |
|
egonw |
hahaha |
| 13:19 |
|
egonw |
well, that gives a bit of time :) |
| 13:19 |
|
maclean |
submit date :2004-04-01 15:43 |
| 13:19 |
|
egonw |
doesn't say which May, does it :) |
| 13:19 |
|
maclean |
true |
| 13:19 |
|
egonw |
seriously... this shows how long the JCP design was overdue |
| 13:19 |
|
maclean |
this is so |
| 14:55 |
|
egonw |
shk3: ping |
| 14:55 |
|
egonw |
shk3: do spectra also have unique URLs in NMRShiftDB, like molecules have: |
| 14:56 |
|
egonw |
http://nmrshiftdb.ice.mpg.de/p[…]/molNumber/NUMBER |
| 14:56 |
|
zarah |
egonw's link is also http://tinyurl.com/deuts8 |
| 14:59 |
|
shk3 |
no |
| 14:59 |
|
shk3 |
only via molecule |
| 14:59 |
|
egonw |
ack |
| 14:59 |
|
shk3 |
would not be a problem to add |
| 15:03 |
|
egonw |
would be nice |
| 15:03 |
|
egonw |
it would give spectra their own URLs |
| 15:03 |
|
egonw |
but not crucial |
| 15:08 |
|
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rajarshi joined #cdk |
| 15:18 |
|
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goomba`` joined #cdk |
| 15:22 |
|
rednael |
[cdk-1.2.x] Applied patch #2675819 (Stefan Kuhn): Patch to add a removeReaction to reactionSet http://cdk.git.sourceforge.net[…]54da4118f2fe50f0b |
| 15:23 |
|
egonw |
rednael++ |
| 15:24 |
|
maclean |
type(rednael) == bot? |
| 15:24 |
|
egonw |
bot rdf:type bot |
| 15:24 |
|
egonw |
umm |
| 15:24 |
|
maclean |
:) |
| 15:24 |
|
egonw |
rednael rdf:type bot |
| 15:24 |
|
egonw |
rednael is a hack up to monitor the Git RSS feed |
| 15:24 |
|
egonw |
to get commit messages here |
| 15:25 |
|
maclean |
ahh |
| 15:25 |
|
maclean |
careful you don't create a feedback loop somewhere : irc->blog->svn->bot->irc |
| 15:25 |
|
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CIA-62 joined #cdk |
| 15:46 |
|
masak |
maclean: how would a blog commit to SVN? |
| 15:46 |
|
maclean |
you never know... |
| 15:46 |
|
maclean |
*waves hands* javascript! |
| 15:46 |
|
sneumann |
where is zarah today ? |
| 15:47 |
|
sneumann |
Day off ? |
| 15:47 |
|
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jonalv joined #cdk |
| 15:47 |
|
jonalv |
oh hai |
| 15:47 |
|
maclean |
ohai |
| 15:47 |
|
maclean |
(tm) |
| 15:48 |
|
sneumann |
;-) |
| 15:48 |
|
jonalv |
isn't zarah here? |
| 15:49 |
|
egonw |
no, she left at some point |
| 15:49 |
|
masak |
that's odd. |
| 15:51 |
|
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zarah joined #cdk |
| 15:51 |
|
jonalv |
zarah: hi |
| 15:51 |
|
zarah |
hello jonalv :) |
| 15:51 |
|
masak |
zarah: you're welcome. |
| 15:51 |
|
zarah |
masak: that was not so easy for a little bot to understand |
| 15:52 |
|
egonw |
hi zarah |
| 15:52 |
|
masak |
she doesn't reply to that. |
| 15:52 |
|
masak |
zarah: you're the quiet one! |
| 15:52 |
|
zarah |
masak: no, YOU'RE the quiet one! |
| 16:03 |
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carsten joined #cdk |
| 17:10 |
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jbrefort joined #cdk |
| 18:24 |
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steinbeck joined #cdk |
| 22:04 |
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bag joined #cdk |
