Camelia, the Perl 6 bug

IRC log for #bioclipse, 2011-09-16

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All times shown according to UTC.

Time Nick Message
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05:41 sneumann Argh, I am having a terrible time creating a SMARTS/SMILES string to search for the backbone of flavonoids
05:41 sneumann An example is http://pubchem.ncbi.nlm.nih.gov/​summary/summary.cgi?cid=5282151
05:41 sneumann which has an apigening core structure.
05:41 sneumann I did a smiles like this http://pubchem.ncbi.nlm.nih.gov/edit2/index.htm​l?smiles=C1%3DCC%28%3DCC%3DC1C2%3DCC%28%3DO%29C​3%3DC%28C%3DC%28C%3DC3O2%29O%29O%29O&cnt=0
05:41 zarah sneumann's link is also http://tinyurl.com/6emtfen
05:42 sneumann and tried (several) ways to look for this as a substructure.
05:42 sneumann In RCDK this works:
05:42 sneumann library(rcdk)
05:42 sneumann ## http://pubchem.ncbi.nlm.nih.gov/​summary/summary.cgi?cid=5282151
05:42 sneumann vitexinrhamnoside <- parse.smiles(c("CC1C(C(C(C(O1)OC2C(C(C(OC2C3=C(C=C​(C4=C3OC(=CC4=O)C5=CC=C(C=C5)O)O)O)CO)O)O)O)O)O"))
05:42 sneumann do.typing(vitexinrhamnoside[[1]])
05:42 sneumann do.aromaticity(vitexinrhamnoside[[1]])
05:42 sneumann ## http://pubchem.ncbi.nlm.nih.gov/​summary/summary.cgi?cid=5280443
05:42 sneumann apigenin <- parse.smiles("C1=CC(=CC=C1C2=CC(​=O)C3=C(C=C(C=C3O2)O)O)O")[[1]]
05:42 sneumann flavonoid <- parse.smiles("C1=CC=CC=C1C3​=CC(=O)C2=CC=CC=C2O3")[[1]]
05:43 sneumann is.subgraph(apigenin, vitexinrhamnoside)
05:43 sneumann is.subgraph(flavonoid, vitexinrhamnoside)
05:43 sneumann But this SMILES is also from vitexin CC5OC(OC1C(O)C(O)C(CO)OC1c3c(O)cc(O)c2C​(=O)C=C(Oc23)c4ccc(O)cc4)C(O)C(O)C5(O)
05:43 sneumann and does not match. I am at a loss there
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06:16 sneumann got it to work, but no clue where I got which smiles that worked in the end. quite messy
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07:41 sneumann http://lwn.net/Articles/457312/bigpage
07:41 sneumann Git is not a Prius. Git is a Model T. Its plumbing and wiring sticks out all over the place. You have to be a mechanic to operate it successfully or you'll be stuck on the side of the road when it breaks down. And it will break down.
07:41 sneumann -- Nick Farina
07:41 sneumann Couldn't resist ;-)
07:42 egonw :)
07:43 egonw I fully agree
07:43 egonw with Git you don't have to go to an expensice garage just because you cannot fix a Prius yourself, because all logical is hidden in a single CPU under the hood somewhere :)
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07:54 olass When driving, it's sometimes difficult to know which branch to take. But you can be sure that lanes merge at some point, if you don't end up in a collision!
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13:08 CIA-96 bioclipse.statistics: Valentin Georgiev master * r9b01815 / plugins/net.bioclipse.r.business/src/net/b​ioclipse/r/business/RBusinessManager.java : Load R session if .RData file is found in bioclipse-workspace - http://git.io/qnvLMQ
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13:23 Topic for #bioclipse is now #bioclipse An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse
13:27 CIA-96 bioclipse.ds: Ola Spjuth modeling * ra521b2e / (10 files in 5 dirs): Implemented regmodel - http://git.io/XWqwFA
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