Rcpi issue - ChemmineOB Fp4 fingerprints
Entering edit mode
Last seen 5.9 years ago
United States

Having difficulties generating fingerprints from Rcpi tutorial. any assistance would be greatly appreciated.

From section 3.2 of Rcpi manual, the following steps are successful:

> require(Rcpi)
> fdamdd.smi=system.file('vignettedata/FDAMDD.smi',package='Rcpi')
> x.smi=readMolFromSmi(fdamdd.smi,type='text')

The next step results in error:

> x3=extractDrugOBFP4(x.smi,type='smile')
Error in ChemmineOB::fingerprint_OB("SMI", molecules[i], "FP4") : 
  unused argument ("FP4")

traceback() yields:

> traceback()
2: ChemmineOB::fingerprint_OB("SMI", molecules[i], "FP4")
1: extractDrugOBFP4(x.smi, type = "smile")

I am running openbabel, version 2.3.1, as suggested from post:

ChemmineOB cannot find installed open-babel

sessionInfo() yields:

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] Rcpi_1.4.0           ChemmineOB_1.6.1     caret_6.0-57        
 [4] ggplot2_1.0.1        lattice_0.20-33      ChemmineR_2.18.1    
 [7] BiocInstaller_1.16.5 AnnotationDbi_1.28.2 GenomeInfoDb_1.2.5  
[10] IRanges_2.0.1        S4Vectors_0.4.0      Biobase_2.26.0      
[13] BiocGenerics_0.12.1  RSQLite_1.0.0        DBI_0.3.1           

loaded via a namespace (and not attached):
 [1] Biostrings_2.34.1   bitops_1.0-6        BradleyTerry2_1.0-6
 [4] brglm_0.5-9         car_2.0-25          codetools_0.2-14   
 [7] colorspace_1.2-6    digest_0.6.8        doParallel_1.0.8   
[10] fingerprint_3.5.2   fmcsR_1.8.0         foreach_1.4.2      
[13] GO.db_3.0.0         GOSemSim_1.24.1     grid_3.1.2         
[16] gtable_0.1.2        gtools_3.4.2        iterators_1.0.7    
[19] lme4_1.1-10         magrittr_1.5        MASS_7.3-44        
[22] Matrix_1.2-2        MatrixModels_0.4-1  mgcv_1.8-7         
[25] minqa_1.2.4         munsell_0.4.2       nlme_3.1-122       
[28] nloptr_1.0.4        nnet_7.3-11         pbkrtest_0.4-2     
[31] plyr_1.8.3          png_0.1-7           proto_0.3-10       
[34] quantreg_5.19       rcdk_3.3.2          rcdklibs_1.5.8.4   
[37] Rcpp_0.12.1         RCurl_1.95-4.7      reshape2_1.4.1     
[40] rJava_0.9-7         rjson_0.2.15        scales_0.3.0       
[43] SparseM_1.7         splines_3.1.2       stringi_0.5-5      
[46] stringr_1.0.0       tools_3.1.2         XVector_0.6.0      
[49] zlibbioc_1.12.0    




fingerprint FP4 ChemmineOB Rcpi • 824 views
Entering edit mode
Thomas Girke ★ 1.7k
Last seen 7 months ago
United States

I can only comment on how to generate these FP4 fingerprints directly with ChemmineR/ChemmineOB (see below). With the current Rcpi that seems to call ChemmineOB in this step I am getting the same error. 

> library(Rcpi); library(ChemmineR)
> fdamdd.smi=system.file('vignettedata/FDAMDD.smi',package='Rcpi') # Same example
> smiset <- read.SMIset(fdamdd.smi) # Import and store as SMIset object
> sdfset <- smiles2sdf(smiset) # Coerce to SDFset object class
> fpset <- fingerprintOB(sdfset, "FP4") # Generate FP4
> fpset
An instance of a 512 bit "FPset" of type "FP4" with 796 molecules

Note, to convert the resulting FPset into character or matrix, you do the usual:
> as.character(fpset)
> as.matrix(fpset) 


> sessionInfo()

R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:
[1] stats     graphics  utils     datasets  grDevices methods   base     

other attached packages:
[1] ChemmineOB_1.7.1      ChemmineR_2.21.10     Rcpi_1.5.0            RSQLite_1.0.0         DBI_0.3.1             BiocInstaller_1.19.14 vimcom_1.2-5         
[8] setwidth_1.0-4        colorout_1.1-0       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.1           plyr_1.8.3            XVector_0.9.4         rcdklibs_1.5.8.4      iterators_1.0.7       bitops_1.0-6          tools_3.2.2          
 [8] zlibbioc_1.15.0       digest_0.6.8          gtable_0.1.2          png_0.1-7             foreach_1.4.2         parallel_3.2.2        proto_0.3-10         
[15] rJava_0.9-7           fmcsR_1.11.4          stringr_1.0.0         Biostrings_2.37.8     S4Vectors_0.7.23      IRanges_2.3.26        stats4_3.2.2         
[22] grid_3.2.2            Biobase_2.29.1        AnnotationDbi_1.31.19 rcdk_3.3.2            GOSemSim_1.27.4       GO.db_3.2.2           ggplot2_1.0.1        
[29] reshape2_1.4.1        magrittr_1.5          codetools_0.2-14      scales_0.3.0          BiocGenerics_0.15.11  MASS_7.3-44           fingerprint_3.5.2    
[36] colorspace_1.2-6      stringi_0.5-5         RCurl_1.95-4.7        munsell_0.4.2         doParallel_1.0.8      rjson_0.2.15     

Entering edit mode
Nan Xiao • 0
Last seen 10 months ago
Cambridge, MA

Hi Joe and Thomas,

- thanks a lot for the feedback. Together with the other build & check issues, this problem has been fixed in the development and release branch now. Please wait about one day for the propagation of the latest daily build.



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