Camelia, the Perl 6 bug

IRC log for #cdk, 2010-02-05

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All times shown according to UTC.

Time Nick Message
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08:58 * egonw found a CDK patch in his inbox from a new contributor ... I always like that :)
08:58 egonw ummm... he
10:03 olass joined #cdk
10:21 PeterOdeus olass: have a look at https://sourceforge.net/tracker/?func=detail&amp​;aid=2944080&group_id=20024&atid=120024# to determine whether getSubgraphAtomsMap(...) or getOverlaps(...) should be used when finding MCSS matches in ReactionSmartsQueryTool.
10:22 olass PeterOdeus: yes
10:22 olass looking at this
10:22 olass will submit a unit test to cdk about this
10:22 olass we want to map atom-atom
10:25 egonw PeterOdeus: I saw the comment...
10:25 egonw PeterOdeus: I need to fix a ChEMBL RDF server first today
10:26 egonw but will look at it directly after... taking into account what olas has gotten to by then
10:26 PeterOdeus olass: Is there a reason why getOverlaps is not sufficient to map reactant atoms to product atoms? Otherwise I can see a path forward using getOverlaps(...).
10:26 olass PeterOdeus: if you can map atom to atom then I am satisfied
10:27 olass that is what I need
10:27 olass please try your solution
10:27 PeterOdeus Great. I'm on it.
10:27 olass I will submit a unit test to CDK anyway
10:27 olass I suspect a bug
10:27 PeterOdeus ok
10:27 olass which should be ruled out anyways :)
10:29 PeterOdeus I'm still curious about the semantic difference between the two, if any.
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10:36 egonw PeterOdeus, olass: BTW, I am working together with Asad to get his SMSD stuff into the CDK...
10:36 egonw PeterOdeus, olass: that's pretty relevant to MCSS
10:36 egonw PeterOdeus: have you seen/read that paper?
10:36 PeterOdeus nope.
10:37 egonw http://www.ebi.ac.uk/thornton-srv/software/SMSD/
10:37 zarah egonw's link is also http://tinyurl.com/dcn3dt
10:37 egonw paper:
10:37 egonw http://www.jcheminf.com/content/1/1/12
10:37 zarah egonw's link is also http://tinyurl.com/lomcgu
10:37 PeterOdeus appreciate it.
10:39 egonw PeterOdeus: I am not using the SMSD patch in Bioclipse yet, but hope to do that before summer
10:39 egonw I'm sure with some help from others, it could be pushed into 2.4
10:39 egonw PeterOdeus: please let me know if you and Lars think it will contribute to your work
10:40 egonw PeterOdeus: I know too little about what you're doing to judge that right now
10:41 olass egonw: we could discuss this on monday...
10:42 egonw yeah, sounds like a plan
10:47 PeterOdeus I'm sure a specialised MCS lib is the way to go as requirements go beyond what UniversalIsomorphismTester is designed to handle :-)
10:51 olass egonw: can I attach the patch to LC69's bug report?
10:52 olass and if so, how? (SF is so non-intuitive...)
10:52 egonw scroll down
10:52 egonw you must be logged in
10:53 olass I am loged in
10:53 olass and I have scrolled down
10:53 olass but it should be possible, right?
10:54 olass it says "No Files Currently Attached" but no option to attach an new file...
10:54 olass I can add a comment though
10:54 olass egonw: do I lack privileges?
10:55 egonw is the URL you are on https:// ?
10:55 olass yes
10:55 olass SF--
10:55 olass will send by email to you
10:55 olass SF--
11:08 egonw received
13:39 CIA-50 cdk: mark_rynbeek * r15376 /jchempaint/trunk/build.xml: restored a signjar line (got lost in comment)
14:19 CIA-50 cdk: Brian Gilman master * r8eacbfc / src/main/org/openscience/cdk/io/​pubchemxml/PubChemXMLHelper.java :
14:19 CIA-50 cdk: Updated to include the float and binary information found in PubChem
14:19 CIA-50 cdk: Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net> - http://bit.ly/d82Z9g
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22:57 CIA-50 cdk: aherraez * r15377 /jchempaint/trunk/po/es.po: Spanish

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