cdkr
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Problem with isvalid.formula
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)