Camelia, the Perl 6 bug

IRC log for #cdk, 2011-03-24

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All times shown according to UTC.

Time Nick Message
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08:43 egonw__ moin moin
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10:04 jkerssem hi everyone
10:07 egonw hi jkerssem
10:07 jkerssem I decided to fix the PDB_atomtypes.xml typos today
10:08 jkerssem so "be afraid, be very afraid" :-)
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10:12 jkerssem If I recall a scolding once, if I touch any whitespace..
10:12 jkerssem that makes a separate patch, no?
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10:12 egonw jkerssem: yes
10:12 jkerssem Okay
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10:12 jkerssem Since the first thing I noticed when looking at pdb_atomtypes.xml
10:13 jkerssem was that the TYR-block was misaligned to the entire rest of the file
10:14 egonw :)
10:15 jkerssem No, I don't have an alignment-pet-peeve. Why ever did you ask? o:-)
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10:25 egonw sneumann: ah, back at EBI?
10:27 sneumann egonw :-)
10:27 sneumann Metabolomics workshoüp
10:27 sneumann Metabolomics workshop
10:28 egonw ah nice :)
10:28 egonw hosted by Chris?
10:28 egonw maclean, sneumann: you have surely met in person already, right?
10:28 maclean yes, I have
10:33 * maclean is working with asad to merge code
10:40 jkerssem someone knowledgeable in pdb_atomtypes.xml present?
10:40 jkerssem I'm finding some additional inconsitencies
10:40 jkerssem and I'm not sure they're supposed to be different, or errors
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10:43 jkerssem Does anyone know where the info in pdb_atomtypes.xml comes from?
10:44 egonw try git log -- src/path/to/pdb_atomtypes.xml
10:44 egonw and git blame src/path/to/pdb_atomtypes.xml
10:44 maclean "Merge made by octopus." :/
10:46 jkerssem "octopus"? as in the animal?
10:46 jkerssem that sure beats 3-way merging :)
10:46 jkerssem egonw, git-log shows only my work of today, and your original commit:
10:46 jkerssem Merged the branch egonw/maintest: sets up src/main and src/test for splitting main library from unit tests
10:47 jkerssem and the blame for every line is egonw, except the ones I touched today :-P
10:47 jkerssem Anyway, I meant: "on what external sources is pdb_atomtypes.xml" based?
10:48 egonw jkerssem: mom... let me look up the blog post about that
10:48 jkerssem oki
10:48 jkerssem I'm noticing some more vdwradii inconsistencies
10:49 jkerssem and I want to look them up in the original source
10:49 egonw ok, search engine fail...
10:49 egonw here goes:
10:50 egonw that last commit is when we moved src/*.java to src/main*.java
10:50 egonw do, you need to do:
10:50 egonw git log 7c5c872c6be0e6a24a519eb227e7ed0b76ac37d6^1 -- ./src/org/openscience/cdk/co​nfig/data/pdb_atomtypes.xml
10:51 egonw 7c5c872c6be0e6a24a519eb227e7ed0b76ac37d6 is the commit with the moev
10:51 egonw ^1 indicates the last commit *before* that commit
10:51 egonw also note that I updated the path from:
10:51 egonw ./src/main/org/openscience/cdk​/config/data/pdb_atomtypes.xml
10:51 egonw to
10:51 egonw ./src/org/openscience/cdk/co​nfig/data/pdb_atomtypes.xml
10:52 egonw in principle, git can follow files when moved, but I tried that before, and that never worked for this commit
10:52 egonw ok, using that hash I found the blog post :)
10:52 egonw http://chem-bla-ics.blogspot.com/search?q​=7c5c872c6be0e6a24a519eb227e7ed0b76ac37d6
10:52 zarah egonw's link is also http://tinyurl.com/6butsjy
10:55 jkerssem thanks
10:55 jkerssem The log-command you suggested points at you again (unsurprisingly ;-)
10:56 jkerssem either you, or someone named "choppe"
10:56 egonw christian hoppe
10:56 jkerssem egonw: "Atom type list for PDB atom codes (closes RFE #1062516)"
10:56 egonw http://sourceforge.net/tracker/?func=detail&amp​;aid=1062516&group_id=20024&atid=370024
10:56 zarah egonw's link is also http://tinyurl.com/6fd57mo
10:57 egonw a shame that I did not record how I got a CML2 format... :(
10:58 egonw it seems from EMBOSS
10:58 egonw damn, have I been sloppy
10:58 jkerssem egonw, that was 6 years ago...
10:59 jkerssem we live and learn...
10:59 jkerssem thanks for the tracker-link btw
10:59 jkerssem of course, the rcsb changed all URLs since :)
10:59 jkerssem lemme check
11:00 jkerssem on another note: the emboss-prefix in the xml file does not resolve anymore
11:00 jkerssem ---> xmlns:emboss="http://cdk.sf.net/dict/emboss/"
11:00 jkerssem but that url gives a 404
11:00 jkerssem is that bad?
11:01 egonw no, it's just a namespace
11:03 jkerssem oki, at least the schema's resolve
11:03 egonw hahaha
11:04 jkerssem though I'm not sure "org.openscience.cdk.io.cml.data.cml25b1.xsd" in the package-hierarchy is a good location...
11:04 jkerssem (sorry, /me is infected with the SemWeb virus: everything must resolve for everyone!)
11:04 egonw jkerssem++
11:21 jkerssem gah...
11:21 jkerssem found the documentation archive... the atoms aren't even mentioned...
11:21 jkerssem (yay ctrl+f :-))
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11:41 jkerssem does anyone have a recent email-address for Christian Hoppe?
11:43 jkerssem (the most recent I could find was 2004..)
11:45 egonw no, don't think we have that
11:45 jkerssem ah well, lets try the old one then...
11:45 jkerssem git-log claims he added the vdw-radii
11:45 egonw let's see what we can pull in from a recent EMBOSS
11:46 jkerssem but there's something happening there, because the radii are definitely not the ones for pure atoms
11:46 jkerssem ooh, that sounds good...
11:50 egonw oh, wow... the good old CVS days...
11:50 egonw how I missed those...
11:50 egonw well, cannot find anything really obvious... but please check http://emboss.sourceforge.net/developers/cvs.html
11:50 jkerssem from what I've seen/read/heard, CVS was "bad, but the best available"
11:51 egonw hahahah... was it the author?
11:51 jkerssem well, no, but that is the general feel I get from "the `net"
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11:56 jkerssem okay, cvs maybe after lunch...
11:56 jkerssem in the meanwhile, I finished to patches
11:56 jkerssem *two
12:00 maclean Heh. Three extra lines to add CML support for SMSD tool :)
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12:01 maclean now : lunch.
12:12 jkerssem wow, only three lines? impressive!
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12:44 maclean jkerssem : well, 3 lines that call the N lines of the CMLReader...
12:45 maclean So relying on Egon's work, really :)
12:46 egonw make sure to cite the IJC paper
12:46 maclean Ok, will do.
12:47 maclean "International Jewish Correspondence", right? Not "Internet Journal of Criminology" :)
12:47 maclean (j/k)
12:51 maclean "Processing CML Conventions in Java"  Internet Journal of Chemistry.
12:51 egonw right
12:51 egonw http://www.citeulike.org/u​ser/egonw/article/1375509
12:52 maclean "Did you mean: http://scholar.google.co.uk/scholar?hl=en&as_​sdt=0,5&q=Processing+XML+Conventions+in+Java" - no google, I did not.
12:52 zarah maclean's link is also http://tinyurl.com/4kl3mh5
12:52 maclean Argh. Copy/paste links!
12:52 egonw http://scholar.google.co.uk/schola​r?cites=4542863800501950288&as​_sdt=2005&sciodt=0,5&hl=en
12:52 zarah egonw's link is also http://tinyurl.com/4an2j4u
12:53 maclean Yes, I noticed a common element in those citing papers :) A certain "E Willighagen..."
12:54 egonw yeah, let's try to change that
13:00 maclean Hah. Take that, Scribd! That doc wasn't even finished. It was original work, though.
13:02 maclean http://www.scribd.com/doc/514​57272/graphs-groups-symmetry
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