Camelia, the Perl 6 bug

IRC log for #cdk, 2008-09-01

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All times shown according to UTC.

Time Nick Message
00:24 CIA-14 cdk: egonw * r6 /tags/ (3 files in 2 dirs): Proper tagging
00:26 CIA-14 cdk: egonw * r7 /trunk/linkDOI.js: Putting up a Ubiquity script, to see if I can get the MIME application/x-javascript working
00:32 CIA-14 cdk: egonw * r8 /trunk/linkDOI.js: Next attempt: getting the 'this'...
00:35 CIA-14 cdk: egonw * r9 /trunk/linkDOI.js: Next attempt...
00:42 CIA-14 cdk: egonw * r10 /trunk/linkDOI.js: Next attempt...
00:46 CIA-14 cdk: egonw * r11 /trunk/linkDOI.js: OK, let make it change the content now...
00:48 CIA-14 cdk: egonw * r12 /trunk/linkDOI.js: Fixed execute parameter...
00:59 CIA-14 cdk: egonw * r13 /trunk/linkDOI.js: Does it work in rich environments now?
01:01 CIA-14 cdk: egonw * r14 /trunk/linkDOI.js: Does it work in rich environments now, maybe?
01:07 CIA-14 cdk: egonw * r15 /trunk/linkDOI.js: Typo...
01:15 CIA-14 cdk: egonw * r16 /trunk/linkDOI.js: Mmmm... really would it to work in blogger editing...
01:19 CIA-14 cdk: egonw * r17 /trunk/linkDOI.js: Mmmm... really would it to work in blogger editing...
01:29 CIA-14 cdk: egonw * r18 /trunk/linkDOI.js: Split up into add-doi and resolve-doi; the former for blogger.com, the latter for inline HTML
01:34 CIA-14 cdk: egonw * r19 /trunk/ (addDOI.js resolveDOI.js): OK, together in one file does not seem to work :(
02:01 CIA-14 cdk: egonw * r20 /trunk/linkDOI.js: Obsolete: replaces by addDOI and resolveDOI
02:01 CIA-14 cdk: egonw * r21 /trunk/addDOI.js: Removed the foo/bar bits
02:17 CIA-14 cdk: egonw * r22 /trunk/sechemticInChI.js: Added a script for semantic markup for chemistry
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09:27 egonw rojasm1: received your email
09:43 rojasm1 Hi egonw
09:43 rojasm1 perfect
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10:00 thomas_ku moin
10:00 zarah hi thomas_ku
10:58 s_wolf joined #cdk
10:59 s_wolf hi there
11:10 egonw hi s_wolf
11:10 s_wolf Iterator<IAtom> atoms = molecule.atoms();
11:10 s_wolf while (atoms.hasNext()) {
11:10 s_wolf IAtom atom = atoms.next();
11:10 s_wolf IAtomType type = matcher.findMatchingAtomType(molecule, atom);
11:10 s_wolf AtomTypeManipulator.configure(atom, type);
11:10 s_wolf }
11:10 s_wolf i have a problem with this code
11:11 s_wolf i try to type the atoms but when it hits a S it throws an error
11:11 s_wolf I just want to add hydrogens to a molecule
11:12 s_wolf the error is: Exception in thread "main" java.lang.IllegalArgumentException: The IAtomType was null.
11:12 s_wolf at org.openscience.cdk.tools.manipulator.AtomTypeMa‚Äčnipulator.configure(AtomTypeManipulator.java:61)
11:12 s_wolf at test.test.main(test.java:34)
11:13 s_wolf the molecule is the following: http://www.genome.jp/dbget-bin/www_bget?cpd:C03392
11:17 s_wolf i read in the mol file with cdk. Did I do something wrong?
11:33 jpansanel moin
11:33 zarah hi jpansanel
11:33 jpansanel specs.net integrates InChI for searching compounds
11:33 jpansanel cool
11:46 egonw s_wolf: no, this just means that the sulphur does not match any of the atom types defined in the CDK (or, also possible, you've hit a big in the atom typer..)
11:46 egonw s_wolf: I'll investigate
11:46 s_wolf thanks alot
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