decomposeIsotopes it doesnt seem to apply element min/max

[Rennepink]

Hi,

Thank you for the great package!
I'm trying to test it to generate possible molecules based on isotopic score.
min <- c("C3","H0","N0", "S0", "Cl0", "O0", "Br")
I have two questions:
1- It doesn't seem like that the function decomposesiotope is applying the minimum number of 3 carbon, when it generates formulas? There are few formulas with no carbon at all!
cbind(getFormula(molecules), getScore(molecules), getValid(molecules))

2- what is the order of the generated formulas, and how are they generated? Is it based on matching isotopic pattern?

I try to use isotopScore function to calculate isotopic score for my formulas that are generated using above:
molecule <- c("C8F17SO3")
masses <- c(498.9328, 500.9350, 499.9372)
intensities <- c(102, 10, 5)
isotopeScore(molecule, masses, intensities, elements = NULL, filter = NULL, z = -1)
This gives me error "$ operator is invalid for atomic vectors"

Thank you in advance for your time!

[janlisec]

Hi @Rennepink,
I am currently trying to solve issues which did arise over the last years. Si, in case you are still using Rdisop:

Regarding the first part of your issue, the functions decomposeMass and decomposeIsotopes do respect minimum and maximum allowed values for elements when specified as a moledular formula. For the next release of Rdisop I updated the help section with appropriate examples:

> # use m/z=48 as an example
> getMolecule("CHOF")$exact
[1] 48.00114
> ele <- initializeElements(c("C","H","N","O","P","S","F"))
> getFormula(decomposeMass(48, mzabs = 0.003, elements = ele))
[1] "C4"   "H3NP" "CHOF"
> # works
> getFormula(decomposeMass(48, mzabs = 0.003, elements = ele, minElements = "H"))
[1] "H3NP" "CHOF"
> getFormula(decomposeMass(48, mzabs = 0.003, elements = ele, maxElements = "H2"))
[1] "C4"   "CHOF"
> getFormula(decomposeMass(48, mzabs = 0.003, elements = ele, maxElements = "H2", minElements = "CHF"))
[1] "CHOF"

Regarding the second part of your issue, the function isotopeScore does allow to calculate what you intended. However, you need to provide it with a molecule as a parameter and not a formula. Also, the masses parameter should be ordered. So, to write your example corretly:

> molecule <- getMolecule("C8F17SO3")
> masses <- c(498.9328, 499.9372, 500.9350)
> intensities <- c(102, 10, 5)
> Rdisop::isotopeScore(molecule, masses, intensities)
    C8F17O3S 
2.435789e-13 

Here, I also did amend the help section with appropriate examples for the next release.