Camelia, the Perl 6 bug

IRC log for #cdk, 2008-06-30

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All times shown according to UTC.

Time Nick Message
03:34 CIA-33 jmol: hansonr * r9532 /trunk/Jmol/src/org/jmol/ (5 files in 3 dirs): version=11.5.43_dev # new feature: Ramachandran "r" --- includes third (Z) axis quaternion r difference2 X component equivalent
04:34 CIA-33 jmol: hansonr * r9533 /trunk/Jmol/src/org/jmol/ (export/_PovrayExporter.java viewer/Jmol.properties):
04:34 CIA-33 jmol: 11.5.43 VERSION
04:34 CIA-33 jmol: bug fix POV-RAY output of quadrilaterals.
05:04 CIA-33 jmol: hansonr * r9534 /trunk/Jmol/src/org/jmol/ (util/Quaternion.java viewer/Eval.java viewer/Jmol.properties): (log message trimmed)
05:04 CIA-33 jmol: version=11.5.43 quaternion, POV-RAY, more.
05:04 CIA-33 jmol: # new feature: quaterion % point4f --- "thetaDirected" --
05:04 CIA-33 jmol: # point4f is {x, y, z, w} (w ignored), where {x y z} is a
05:04 CIA-33 jmol: # preferred direction.
05:04 CIA-33 jmol: # Returns a point4f angle-Axis equivalent with x, y, z the normal for the quaternion
05:04 CIA-33 jmol: # rotation and w = theta for the rotation, where the normal and theta are chosen
05:10 CIA-33 jmol: hansonr * r9535 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: (log message trimmed)
05:10 CIA-33 jmol: version=11.5.43 quaternion, POV-RAY, more.
05:10 CIA-33 jmol: # new feature: quaterion % point4f --- "thetaDirected" --
05:10 CIA-33 jmol: # point4f is {x, y, z, w} (w ignored), where {x y z} is a
05:10 CIA-33 jmol: # preferred direction.
05:10 CIA-33 jmol: # Returns a point4f angle-Axis equivalent with x, y, z the normal for the quaternion
05:10 CIA-33 jmol: # rotation and w = theta for the rotation, where the normal and theta are chosen
07:51 thomas_ku moin
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08:32 egonw moin
08:35 jpansanel moin
08:35 egonw hi jpansanel
08:40 jpansanel egonw :  I'v updated my addressbook !
08:41 egonw jpansanel: thanx :)
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14:33 egonw thomas_ku: ping
14:36 thomas_ku hi
14:36 thomas_ku egonw: yes
14:36 egonw looked at C-T coe
14:36 egonw looked at C-T code
14:36 egonw but not sure how to add a new iterative reader
14:37 egonw you are not using teh IteratingMDLReader, are you?
14:38 thomas_ku I think i am using it mom
14:42 thomas_ku oh egon I just remember
14:43 thomas_ku I do not use the cdk iterating reader
14:44 thomas_ku but I can't remember why
14:44 thomas_ku I implemented a reader therefore
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14:46 thomas_ku egonw: my nx server crashed
14:46 egonw no worries
14:46 egonw had not replied yet...
14:46 thomas_ku ok
14:46 egonw when you remember the 'why'... please let me know...
14:49 thomas_ku ah I remember
14:50 thomas_ku the reason was that I used this iterative worker to store the each molecule from the sd file into the postgres database
14:50 thomas_ku and the postgres database gets as input a mol file
14:51 thomas_ku and not a cdk molecule
14:51 egonw mmm...
14:51 egonw that won't work for PubChem XML
14:51 thomas_ku but that should no be no problem
14:51 thomas_ku if you have an iterative reader
14:51 thomas_ku you can build the cdk-taverna worker therefore easily
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14:53 egonw thomas_ku: do you have a template?
14:57 thomas_ku for the worker or the reader?
14:58 egonw the worker
14:58 egonw the PubChem Compounds XML reader is in CDK SVN
14:59 thomas_ku no template but you can use the existing worker therefore
15:00 thomas_ku which are the
15:00 thomas_ku org.openscience.cdk.applications.tave​rna.io.iterative.IteratingFileReader
15:00 thomas_ku org.openscience.cdk.applications.taverna.i​o.iterative.IteratingFileReaderGetContent
15:00 thomas_ku org.openscience.cdk.applications.taverna​.io.iterative.IteratingFileReaderHasNext
15:01 thomas_ku the iterating file reader initialize the reader and stores it in a registry
15:02 thomas_ku the get content gets the id of the reader from the iteratingFileReader and pulls out the content
15:02 thomas_ku and the has next worker gets the id too and pulls out true or flase
15:03 egonw can you please send me an example workflow that uses this reader?
15:03 egonw then I should be able to understand what is happening :)
15:03 thomas_ku will be away now for an hour or two
15:04 egonw ack
15:04 thomas_ku would it be ok if I email you than?
15:04 egonw sure
15:04 thomas_ku or do you need it now
15:04 thomas_ku because I do not have it on this machine...
15:04 egonw no, later is fine
15:05 thomas_ku ok than cu
15:06 shk3 egonw: in a pseudoatom, is the label the right thing to use instead of symbol?
15:06 egonw yes
15:06 shk3 in the atomeditor, if the user enters X as text, it should go to label, right?
15:06 egonw because the symbol for IPseudoAtom is always 'R'
15:06 shk3 no symbol?
15:06 egonw right
15:06 shk3 ok, thanks
15:25 shk3 egonw: another question
15:26 shk3 I am just looking at a cdk bug about cml roundtripping
15:26 shk3 writing cml with properties set produces things like <scalar title="customAtomProperty"...>
15:26 shk3 Do you know where customAtomProperty comes from?
15:26 egonw would have to look that up
15:26 shk3 I am wondering how to do it in the reader
15:27 shk3 hardcode?
15:27 shk3 It's jumbo writing, isn't it?
15:29 shk3 hm, no, it's Convertor
15:30 shk3 perhaps I find somtehing in there
15:47 egonw Jumbo is used for writing, indeed, via Convertor
15:47 egonw (someone entered my room)
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16:19 thomas_ku egonw: Just sent you an email to your gmail account
16:19 egonw received, thanx!
16:20 shk3 egonw: never mind my question about the custom properties
16:20 shk3 was me being stupid
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18:45 CIA-33 cdk: shk3 * r11473 /cdk/trunk/src/test/org/openscience/c​dk/io/cml/CMLCustomPropertyTest.java: added the test given in bug #1930029. The solution is not yet finished.
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21:45 CIA-33 jmol: nicove * r9538 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
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