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girke-lab / chemmine-ei

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find out why some descrptors are missing #55

Closed khoran closed 11 years ago

khoran commented 11 years ago

Hi Kevin,

Something seems to be broken with probOB() in the current release of R-3.0.2 and Bioc 2.13. When I run it then the result contains many empty columns. For instance:

library(ChemmineR) data(sdfsample) propOB(sdfsample[1:4]) cansmi cansmiNS formula HBA1 HBA2 HBD InChI logP MR MW nF s smarts title TPSA CMP1 NaN NaN NaN 37 10 2 NaN 3.0288 119.9234 456.4916 0 NaN NaN NaN 123.00 CMP2 NaN NaN NaN 28 7 3 NaN 0.9234 101.3202 357.4069 0 NaN NaN NaN 104.94 CMP3 NaN NaN NaN 24 8 2 NaN 2.9535 101.4132 370.4255 0 NaN NaN NaN 125.35 CMP4 NaN NaN NaN 35 11 1 NaN 1.3127 123.4607 461.5346 0 NaN NaN NaN 134.68

khoran commented 11 years ago

I looked at these more closely. I think I can get "cansmi", "cansmiNS", "title", and "formula" to return the proper strings. You have to call a different function when the return result is a string, the normal function which is currently used for all of them returns NaN for string returning descriptors. For "InChI", "s" and "smarts", those are not really descriptors, they are meant to work with the "--filter" argument of the obabel command and expect to be given a smarts or InChI pattern.

Version 1.0.1 and 1.1.1 now properly display the string valued descriptors and do not contain the filter descriptors.