detect_formula_sets {IDSL.UFA}

Organic Class Detection by Repeated Unit Patterns

Description

This function sorts a vector of molecular formulas to aggregate organic compound classes with repeated/non-repeated substructure units. This function only works for molecular formulas with following elements: c("As", "Br", "Cl", "Na", "Se", "Si", "B", "C", "F", "H", "I", "K", "N", "O", "P", "S")

Usage

detect_formula_sets(molecular_formulas, ratio_delta_HBrClFI_C = 2,
mixed.HBrClFI.allowed = FALSE, min_molecular_formula_class = 2,
max_number_formula_class = 100, number_processing_threads = 1)

Arguments

molecular_formulas

a vector of molecular formulas

ratio_delta_HBrClFI_C

c(2, 1/2, 0). 2 to detect structures with linear carbon chains such as PFAS, lipids, chlorinated paraffins, etc. 1/2 to detect structures with cyclic chains such as PAHs. 0 to detect molecular formulas with a fixed structures but changing H/Br/Cl/F/I atoms similar to PCBs, PBDEs, etc.

mixed.HBrClFI.allowed

mixed.HBrClFI.allowed = c(TRUE, FALSE). Select 'FALSE' to detect halogenated-saturated compounds similar to PFOS or select 'TRUE' to detect mixed halogenated compounds with hydrogen.

min_molecular_formula_class

minimum number of molecular formulas in each class. This number should be greater than or equal to 2.

max_number_formula_class

maximum number of molecular formulas in each class

number_processing_threads

Number of processing threads for multi-threaded computations.

Value

A matrix of clustered classes of organic molecular formulas.

Examples

molecular_formulas <- c("C3F7O3S", "C4F9O3S", "C5F11O3S", "C6F9O3S", "C8F17O3S",
"C9F19O3S", "C10F21O3S", "C7ClF14O4", "C10ClF20O4", "C11ClF22O4", "C11Cl2F21O4",
"C12ClF24O4")
##
ratio_delta_HBrClFI_C <- 2 # to aggregate polymeric classes
mixed.HBrClFI.allowed <- FALSE # To detect only halogen saturated classes
min_molecular_formula_class <- 2
max_number_formula_class <- 20
##
classes <- detect_formula_sets(molecular_formulas, ratio_delta_HBrClFI_C,
mixed.HBrClFI.allowed, min_molecular_formula_class, max_number_formula_class,
number_processing_threads = 1)