pcl: add_ccs2csv.R: Update

pubchemlite/R/add_ccs2csv.R

@@ -34,26 +34,43 @@ message("Number of MF rows: ", NROW(dt_mf_csv))
 
 data.table::setnames(dt_ccs,"smi","SMILES",skip_absent = T)
 
-## Turn adduct into a number of columns.
-dt_tr_ccs <- data.table::dcast(dt_ccs, SMILES ~ adduct, value.var = "ccs")
-message("Number of dcast CCS rows: ",NROW(dt_tr_ccs))
+res <- dt_ccs[,.(SMILES=smi,adduct,ccs)][dt_mf_csv,on="SMILES",nomatch=NULL]
 
-## Wrangle names.
-add_nm <- grep("\\[.+",colnames(dt_tr_ccs),val=T)
-message("Adducts: ",add_nm)
+idsmi <- dt_mf_csv[,.(Identifier,SMILES)]
+res <- res[idsmi,on="Identifier",nomatch=NA]
 
-new_add_nm <- paste("pred_CCS_A2",add_nm,sep="_")
-data.table::setnames(dt_tr_ccs,add_nm,new_add_nm)
-mf_nms <- colnames(dt_mf_csv)
 
-sel_add_cols <- if (!is.null(SEL_ADDUCTS))
-                    paste0("pred_CCS_A2_",SEL_ADDUCTS) else new_add_nm
+uniq_smiles_merged <- db_res[,unique(SMILES)]
+uniq_smiles_pcl <- dt_mf_csv[,unique(SMILES)]
 
-all_nms <- c(mf_nms,sel_add_cols)
+diff <- setdiff(uniq_smiles_pcl,uniq_smiles_merged)
 
-res <- dt_tr_ccs[dt_mf_csv,on="SMILES",nomatch=NA][,..all_nms]
-message("Number of res rows: ",NROW(res))
+data.table::fwrite(res,file=fn_mf_res_csv,sep=",",quote = "auto",na = "")
+message("Unique SMILES entries in pure PCL: ", uniq_smiles_pcl)
+message("Unique nonempty SMILES entries in PCL with CCS: ", uniq_smiles_merged)
+message("Number of SMILES in pure PCL with missing CCS: ", diff)
+
+## Obsolete?
+## ## Turn adduct into a number of columns.
+## dt_tr_ccs <- data.table::dcast(dt_ccs, SMILES ~ adduct, value.var = "ccs")
+## message("Number of dcast CCS rows: ",NROW(dt_tr_ccs))
+
+## ## Wrangle names.
+## add_nm <- grep("\\[.+",colnames(dt_tr_ccs),val=T)
+## message("Adducts: ",add_nm)
+
+## new_add_nm <- paste("pred_CCS_A2",add_nm,sep="_")
+## data.table::setnames(dt_tr_ccs,add_nm,new_add_nm)
+## mf_nms <- colnames(dt_mf_csv)
+
+## sel_add_cols <- if (!is.null(SEL_ADDUCTS))
+##                     paste0("pred_CCS_A2_",SEL_ADDUCTS) else new_add_nm
+
+## all_nms <- c(mf_nms,sel_add_cols)
+
+## res <- dt_tr_ccs[dt_mf_csv,on="SMILES",nomatch=NA][,..all_nms]
+## message("Number of res rows: ",NROW(res))
+## data.table::fwrite(res,file=fn_mf_res_csv,sep=",",quote = "auto",na = "")
 
 
-data.table::fwrite(res,file=fn_mf_res_csv,sep=",",quote = "auto",na = "")