run_script: Predict MS^2 fragment spectra from SMILES code.

In fioRa: Mass-Spectra Prediction Using the FIORA Model

Predict MS^2 fragment spectra from SMILES code.

Description

A wrapper around the python script 'fiora-predict' using the fiora open source model to generate a MS^2 spectra for a compound with known SMILES code.

Usage

run_script(
  x = data.frame(Name = "Example_0", SMILES = "CC1=CC(=O)OC2=CC(OS(O)(=O)=O)=CC=C12",
    Precursor_type = "[M-H]-", CE = 17, Instrument_type = "HCD"),
  min_prob = 0.001,
  annotation = FALSE,
  fiora_script = NULL,
  fmt = c("list", "df")
)

Arguments

x	A data frame containing columns Name (compound names), SMILES (SMILES code of the compounds, Precursor_type (currently "[M-H]-" or "[M+H]+"), CE (Collision energy) and Instrument_type (i.e. HCD).
min_prob	Minimum peak probability to be recorded in the spectrum.
annotation	Return SMILES for fragments if TRUE.
fiora_script	Path to python script fiora-predict.
fmt	Set fmt to 'df' to simplify the return value to a data frame (named list otherwise).

Details

This wrapper will generate a fiora ready input file (csv-format) based on the user parameters which is stored as a temp file. It will ensure that the current version of the fiora package is installed in a respective python environment. It will use 'system2()' to run the python script 'fiora-predict' and import its result back into R using the internal function 'read_fiora()'. You can try different installed version of 'fiora' by providing the path the the script explicitly.

Value

A list with the fiora results for the specified compound(s).

Examples

## Not run: 
  # !!! running this example will install the python module `fiora`
  td <- fioRa::test_data
  x <- setNames(data.frame(
    t(sapply(td[2:11], function(x) { strsplit(x, ",")[[1]] }))),
    strsplit(td[1], ",")[[1]]
   )
  foo <- run_script(x = x)
  foo[[1]][["spec"]]
  # modify parameters
  run_script(x = x[1,,drop=FALSE], min_prob = 0.05)

  # use a different fiora environment/model
  s_pth <- "c:/Users/jlisec/AppData/Local/r-miniconda/envs/fiora-0.1.0/Scripts/fiora-predict"
  foo2 <- run_script(x = x, fiora_script = s_pth)

  foo2[[1]][["spec"]]

  for (i in 1:length(foo)) {
    cat("\n")
    print(names(foo)[i])#'
    print(foo[[i]][["spec"]])
    print(foo2[[i]][["spec"]])
  }

## End(Not run)

fioRa documentation built on Nov. 11, 2025, 5:11 p.m.