Open arthuc01 opened 5 years ago
This works....
> formula <- get.formula('C6H19KN2O10', charge = 1) > isvalid.formula(formula,rule=c("nitrogen","RDBE")) [1] FALSE
But when I try....
> formula <- get.formula('C5H13KN9O5', charge = 1) > isvalid.formula(formula,rule=c("nitrogen","RDBE")) Error in .jcall(rdbeRule, "D", "validate", molecularFormula) : java.lang.NullPointerException
I'm trying to validate formulae generated with generate.formula
library(rcdk) molFormula <- function(mz){ ppm = (2/1000000)*mz temp <- generate.formula(mz, window=(2/1000000)*mz, elements=list(c("C",0,120), c("H",0,180), c("N",0,20), c("O",0,20), c("S",0,20), c("Na",0,1), c("K",0,1) ), validation=FALSE, charge =1) df <- data.frame(matrix(ncol = 4, nrow = 0)) x <- c("formula", "mass", "charge", "ppmError") colnames(df) <- x for (i in temp) { print(i@string) formula <- get.formula(i@string, charge = 1) print(isvalid.formula(formula,rule=c("nitrogen","RDBE"))) } return (df) } mz <-318.06768 formulae <- molFormula(mz)
This works....
But when I try....
I'm trying to validate formulae generated with generate.formula