Camelia, the Perl 6 bug

IRC log for #cdk, 2007-08-14

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All times shown according to UTC.

Time Nick Message
00:02 CIA-1 jmol: hansonr * r8068 /trunk/Jmol/src/org/ (6 files in 4 dirs): 11.3.10 preliminary webExport for application
01:31 CIA-1 jmol: hansonr * r8069 /trunk/Jmol/src/org/ (17 files in 4 dirs): 11.3.10 preliminary webExport for application
05:51 egonw joined #cdk
05:52 CIA-1 jmol: hansonr * r8070 /trunk/Jmol/src/org/ (12 files in 2 dirs):
05:52 CIA-1 jmol: 11.3.10
05:52 CIA-1 jmol: # new feature: application option for web page export (preliminary)
06:57 jbrefort joined #cdk
07:33 jpansanel moin
07:42 steinbeck joined #cdk
07:42 steinbeck moin
07:53 egonw steinbeck: will be around for short questions, but pretty tied up a writing a grant proposal today...
07:54 egonw and not at the keyboard full time...
07:54 egonw like now, getting coffee :)
07:54 steinbeck ack
07:58 jpansanel coffee is a good idea
07:58 * jpansanel is also getting a coffee
08:00 * steinbeck is already hypercaffeinated
08:15 thomas_ku joined #cdk
08:16 thomas_ku moin
08:16 jpansanel moin
08:23 Nielsout moin
08:23 CIA-1 cdk: steinbeck * r8684 /trunk/cdk/src/org/openscienc​e/cdk/layout/AtomPlacer.java: Commented out a line which affects SO2 group layout. The new version looks better.
08:23 steinbeck moin thomas_ku
08:24 thomas_ku hi steinbeck
08:25 jonalv joined #cdk
08:25 thomas_ku could you please sent me your adress to would like so sent you an invitation
08:25 thomas_ku -to +I
08:30 steinbeck thomas_ku: who? Me?
08:30 shk3 joined #cdk
08:30 steinbeck Hi shk3
08:31 shk3 hi
08:39 CIA-1 cdk: steinbeck * r8685 /trunk/cdk/src/org/openscienc​e/cdk/layout/AtomPlacer.java:
08:39 CIA-1 cdk: Removed lines which used HydrogenAdder to add Hydrogens during layout.
08:39 CIA-1 cdk: This adds an additional unneccessary dependency and also is bad design.
08:39 CIA-1 cdk: SDG should layout what it gets and not add and remove things during layout.
08:53 carsten joined #cdk
09:01 CIA-1 cdk: steinbeck * r8686 /trunk/cdk/src/org/openscience/c​dk/geometry/GeometryTools.java: Updated author information
09:24 jpansanel moin carsten
09:24 jpansanel carsten : I'm working on the integration of your patch into KOpenBabel
09:24 jpansanel the code modification is done
09:25 jpansanel but I need to update my KDE4 installation before compiling
09:25 carsten jpansanel: ok, as I said you cannot take all changes
09:25 carsten because I need to modify it a bit for kalzium.
09:25 jpansanel carsten : I've take all change, and added somes
09:25 carsten but that is mostly the buttons
09:25 carsten as I am using a KDialog as the mainclass and you a kmainwindow
09:25 jpansanel I'll send you a mail when updated
09:31 jpansanel qt takes a lot of time to compile
09:37 carsten indeed :)
09:37 carsten But finally 4.3.1 is out
09:41 steinbeck left #cdk
10:50 CIA-1 cdk: fichte01 * r477 /trunk/protonprediction/Data/ (30 files in 6 dirs):
11:14 steinbeck joined #cdk
11:40 neksa joined #cdk
11:40 egonw hi neksa
11:41 neksa hi everybody!
12:12 CIA-1 cdk: steinbeck * r8687 /trunk/cdk/src/org/openscience/cdk/la​yout/StructureDiagramGenerator.java: Support for setting the orientation of the first bond to be laid out is now back in again. Had somehow disappeared from the code
12:25 CIA-1 cdk: thomaskuhn * r8688 /trunk/paper/: Create a folder for paper
12:26 CIA-1 cdk: thomaskuhn * r8689 /trunk/paper/cdk-taverna/: Folder for paper from the cdk-taverna project
12:27 thomas_ku joined #cdk
12:31 carsten joined #cdk
12:31 jpansanel hi carsten
12:37 carsten moin
12:55 jpansanel I've some issues with KDE compilation
12:59 carsten more details :)
13:04 jpansanel /var/opt/src/KDE/kdelibs/kjs/regexp.cpp: In constructor ‘KJS::RegExp::RegExp(con
13:04 jpansanel st KJS::UString&, char)’:
13:04 jpansanel /var/opt/src/KDE/kdelibs/kjs/regexp.cpp:149: error: ‘PCRE_NO_UTF8_CHECK’ was not declared in this scope
13:06 carsten wtf
13:06 carsten well, "outdated kdelibs" is the answer I always give :)
13:06 jpansanel I have updated  two minutes ago
13:08 carsten Qt 4.3.1 I guess.
13:08 carsten but that shouldn't be important....
13:08 carsten today is not monday so compilation should be fine
13:10 jpansanel I've got today the last copye of qt-copy
13:11 carsten [15:10] <SaroEngels> I finished build now
13:11 carsten jpansanel: for Saro it works...
13:11 carsten jpansanel: which gcc?
13:12 jpansanel yes
13:13 carsten he's using mingw
13:13 carsten jpansanel: which version? 4.2 is  very picky
13:15 jpansanel 4.1.2
13:16 carsten same here
13:22 jpansanel I have maybe a solution
13:22 jpansanel I've two file pcre.h
13:22 jpansanel on my laptop
13:23 jpansanel the other one is coming with EMBPSS
13:23 jpansanel and doesn't define PCRE_NO_UTF8_CHECK
13:25 carsten those things suck
13:25 jpansanel carsten : I've removed EMBOSS
13:25 jpansanel it works now
13:25 jpansanel I don't know why EMBOSS is coming with a separate pcre version
14:54 CIA-1 blueobelisk: neksa * r82 /ctfr/trunk/png/ (. index.xml valid/ valid/index.xml valid/rosiglitazone.png):
14:54 CIA-1 blueobelisk: added png testfile with molfile entry in tEXt field
14:54 CIA-1 blueobelisk: file taken from Rich's blog
15:12 CIA-1 jmol: hansonr * r8071 /trunk/Jmol/src/org/openscience/jmol/app/ (12 files in 2 dirs):
15:12 CIA-1 jmol: 11.3.10
15:12 CIA-1 jmol: # new feature: application option for web page export (preliminary)
15:14 CIA-1 jmol: hansonr * r8072 /trunk/Jmol/src/org/openscience/jmol/​Properties/Jmol-resources.properties:
15:14 CIA-1 jmol: 11.3.10
15:14 CIA-1 jmol: # new feature: application option for web page export (preliminary)
15:26 shk3 left #cdk
15:34 CIA-1 jmol: hansonr * r8073 /trunk/Jmol/src/org/openscience/jmol/ (4 files in 3 dirs):
15:34 CIA-1 jmol: 11.3.10
15:34 CIA-1 jmol: # new feature: application option for web page export (preliminary)
16:34 CIA-1 jmol: hansonr * r8074 /trunk/Jmol/src/org/jmol/ (3 files in 3 dirs): 11.3.10 dipole fix
16:42 jbrefort joined #cdk
16:42 CIA-1 jmol: hansonr * r8075 /trunk/Jmol/src/org/opensc​ience/jmol/app/webexport/ (pop_in.png script_button.png script_button_instructions.html): 11.3.10 preliminary webExport for application
16:52 CIA-1 jmol: hansonr * r8076 /trunk/Jmol/src/org/openscience/jmol/app/w​ebexport/script_button_instructions.html: 11.3.10 preliminary webExport for application
16:53 CIA-1 jmol: hansonr * r8077 /trunk/Jmol/src/org/opensc​ience/jmol/app/webexport/ (pop_in_instructions.html script_button_instructions.html): 11.3.10 preliminary webExport for application
16:54 CIA-1 jmol: hansonr * r8078 /trunk/Jmol/src/org/openscience/jmol/app​/webexport/script_button_template.html: 11.3.10 preliminary webExport for application
17:07 CIA-1 jmol: hansonr * r8079 /trunk/Jmol/src/org/openscience/j​mol/app/webexport/WebPanel.java: 11.3.10 preliminary webExport for application
18:15 egonw joined #cdk
18:16 egonw moin
19:02 jbrefort hi egonw
19:13 egonw hi jbrefort
19:31 neksa hi  jbrefort
19:31 jbrefort hi neksa
19:32 neksa jbrefort: does gchempaint support writing out images with embedded MOL ?
19:33 jbrefort no, it is possible to embed the InChI at the moment, but it would be easy to add
19:34 neksa jbrefort: how do you embed InChI? point me to the source code, please. i have gchempaint-0.8.2 in hands
19:35 jbrefort it is not in 0.8.2, only in gchemutils HEAD
19:35 egonw neksa: don't think I will be online tomorrow...
19:35 jbrefort it was added as an experimental plugin for wikipedia
19:36 egonw jbrefort: Rich showed that nice idea of being able to open a PNG image in an editor again...
19:36 neksa egonw: ack. I have enough things to do. no planned discussions for tomorrow
19:36 egonw by storing a MDL or CML file, GChemPaint could continue editing the PNG image as if it was not an image at all...
19:36 egonw neksa: OK, good
19:36 jbrefort yes, that's an interesting idea
19:36 egonw neksa: please, please, blog about your schedule for the last week...
19:37 egonw jbrefort: check depth-first.com
19:38 neksa egonw: ack. If I fix that thing with SDF substreams today, I'll be able to make a large commit
19:38 jbrefort egonw, do you now the license?
19:39 egonw neksa: OK
19:39 egonw jbrefort: of what?
19:39 jbrefort of the java pubchem stuff
19:40 egonw ah, Rich has not decided about the license for Firefly yet...
19:40 egonw but I will add it to JChemPaint too...
19:40 egonw but the idea is simple enough...
19:40 egonw if you can add InChI...
19:41 egonw it simply goes in to tEXT to... or what's the name of the container again...
19:41 egonw and than as molfile=<MOLFILE>
19:41 egonw better as text than XML, to preserve newlines...
19:41 egonw got to go now...
19:41 jbrefort of course, any text format would go
19:46 neksa jbrefort: where do you store InChI? in which meta data field?
19:46 jbrefort tEXT I think
19:47 jbrefort keys.push_back (const_cast<char*> ("tEXt::InChI"));
19:47 jbrefort values.push_back (const_cast<char*> (InChI));
19:47 neksa ok InChI keyword.
19:48 neksa jbrefort: could you please send me one valid sample structure (image file) to neksa@neksa.net?
19:49 jbrefort np
19:49 neksa and please tell me the license for this file: GPL/BSD/whatever... I'll put it into test repository
19:49 jbrefort do you have a preference for a molecule?
19:49 jbrefort keys.push_back (const_cast<char*> ("tEXt::Copyright"));
19:49 jbrefort values.push_back (const_cast<char*> ("Public domain"));
19:50 jbrefort is Public domain OK?
19:50 neksa I personally prefer caffeine, but choice is yours ;)
19:50 neksa jbrefort: Public Domain completely OK
19:57 jbrefort arg, gchempaint crashed
20:05 jbrefort neksa, sent
20:06 neksa jbrefort: thanks, got it. could you show me the page with Wikipedia requirements for publishing molecules?
20:07 jbrefort not really there, but a good start: http://en.wikipedia.org/wiki/Wikipedi​a_talk:WikiProject_Chemistry/Structur​e_drawing_workgroup/Archive_Jun_2007
20:08 lambdabot2 http://tinyurl.com/3598p4
20:14 neksa jbrefort: thanks for the cool link
20:25 jbrefort bye
20:31 CIA-1 blueobelisk: neksa * r83 /ctfr/trunk/png/valid/ (caffeine.png index.xml): Added test file caffeine.png which contains InChI identifiers in tEXt.InChI chunk.keyword
22:16 neksa_ joined #cdk
23:48 CIA-1 jmol: hansonr * r8080 /trunk/Jmol/src/org/opensc​ience/jmol/app/webexport/ (8 files): 11.3.10 preliminary webExport for application

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