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Question: output of propOB function ChemmineR
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gravatar for elisa.micarelli
9 months ago by
European Union
elisa.micarelli0 wrote:

Hi, 

I'm using the package ChemmineR and in particular I'm getting the Open Babel properties by propOB function, that should to generate the following descriptors  'abonds',  'atoms', 'bonds', 'dbonds', 'HBA1', 'HBA2', 'HBD', 'logP', 'MR',  'MW', 'nF', 'sbonds', 'tbonds', 'TPSA' as mentioned in help section, but actually some features returned are different: 

  "cansmi"   "cansmiNS" "formula"  "title"    "InChI"    "HBA1"    "HBA2"     "HBD"      "logP"     "MR"       "MW"       "nF"  "TPSA"  .

Is there a way to get the right descriptors?

Thanks in advance for your help.

Elisa

 

ADD COMMENTlink written 9 months ago by elisa.micarelli0

Dear Elisa,

This might be an oversight updating the help file. I let Kevin Horan comment on this. 

Are there specific descriptors you are interested in? As you know there are hundreds of them and propOB just generates a few common ones. With ChemmineR itself you can also generate quite few that complement (or sometimes overlap with those from OpenBabel). For instance take a look at this example from the main vignette (section here: https://goo.gl/UC6jFD):

library(ChemmineR)
data(sdfsample); sdfset <- sdfsample
propma <- data.frame(MF=MF(sdfset, addH=FALSE), MW=MW(sdfset, addH=FALSE),
                             Ncharges=sapply(bonds(sdfset, type="charge"), length),
                             atomcountMA(sdfset, addH=FALSE), 
                             groups(sdfset, type="countMA"), 
                             rings(sdfset, upper=6, type="count", arom=TRUE))
 propma[1:4,] 

              MF       MW Ncharges  C  H N O S F Cl RNH2 R2NH R3N ROPO3 ROH RCHO RCOR RCOOH RCOOR ROR RCCH RCN RINGS AROMATIC
CMP1  C23H28N4O6 456.4916        0 23 28 4 6 0 0  0    0    2   1     0   0    0    0     0     0   2    0   0     4        2
CMP2  C18H23N5O3 357.4069        0 18 23 5 3 0 0  0    0    2   2     0   1    0    0     0     0   0    0   0     3        3
CMP3 C18H18N4O3S 370.4255        0 18 18 4 3 1 0  0    0    1   1     0   1    0    1     0     0   0    0   0     4        2
CMP4 C21H27N5O5S 461.5346        0 21 27 5 5 1 0  0    0    1   3     0   0    0    0     0     0   2    0   0     3        3

Thomas

ADD REPLYlink modified 9 months ago • written 9 months ago by Thomas Girke1.6k

I apologize for the confusion. The man page for propOB in the ChemmineR package was not updated to reflect changes made to that function. The propOB function in ChemmineR just calls another function called prop_OB in the package ChemmineOB. That functions man page is up-to-date, but as I said, I forgot to propagate the change to ChemmineR. It will be fixed in the next version. 

 

Kevin Horan

ADD REPLYlink written 8 months ago by khoran0
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