Question: Rcpi issue - ChemmineOB Fp4 fingerprints
0
gravatar for josephjmcdonald
3.7 years ago by
United States
josephjmcdonald0 wrote:

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)

locale:
[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    

 

 

 

chemmineob fingerprint fp4 rcpi • 596 views
ADD COMMENTlink modified 2.6 years ago by Nan Xiao0 • written 3.7 years ago by josephjmcdonald0
Answer: Rcpi issue - ChemmineOB Fp4 fingerprints
0
gravatar for Thomas Girke
3.7 years ago by
Thomas Girke1.7k
United States
Thomas Girke1.7k wrote:

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

locale:
 [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            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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     

 
ADD COMMENTlink written 3.7 years ago by Thomas Girke1.7k
Answer: Rcpi issue - ChemmineOB Fp4 fingerprints
0
gravatar for Nan Xiao
2.6 years ago by
Nan Xiao0
Cambridge, MA
Nan Xiao0 wrote:

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.

Best,
-Nan

ADD COMMENTlink written 2.6 years ago by Nan Xiao0
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