Check Chemical Formula against Fiehn Seven Golden Rules

Evaluates whether a candidate chemical formula satisfies heuristic chemical rules based on Senior's valence rules (Senior 1951), Hydrogen-to-Carbon (H/C) ratios, heteroatom ratios (N/C, O/C, P/C, S/C, Halogen/C), and Double Bond Equivalents (DBE) as described by Kind & Fiehn (2007).

Usage

checkGoldenRules(formula, z = 0, min_hc = 0.1, max_hc = 6, max_dbe = 40)

Arguments

formula

Character string representing molecular formula (e.g. "C6H12O6").

z

Integer charge state (default: 0).

min_hc

Numeric minimum H/C ratio (default: 0.1).

max_hc

Numeric maximum H/C ratio (default: 6.0).

max_dbe

Numeric maximum DBE (default: 40.0).

Value

A list containing booleans indicating whether the formula passed Senior rules, H/C ratio, heteroatom ratios, DBE, nitrogen rule, and overall validity.

References

Kind, T., Fiehn, O. Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics 8, 105 (2007). doi:10.1186/1471-2105-8-105

Senior, J. K. Partitions and their connection with the problems of chemical structure. J. Chem. Phys. 19, 865-873 (1951).

Examples

checkGoldenRules("C6H12O6")
#> $valid
#> [1] TRUE
#> 
#> $senior_rules
#> [1] TRUE
#> 
#> $hc_ratio
#> [1] 2
#> 
#> $hc_pass
#> [1] TRUE
#> 
#> $heteroatom_pass
#> [1] TRUE
#> 
#> $dbe
#> [1] 1
#> 
#> $dbe_pass
#> [1] TRUE
#> 
#> $nitrogen_rule
#> [1] TRUE
#> 
checkGoldenRules("C3H32N12O3") # chemically impossible formula
#> $valid
#> [1] FALSE
#> 
#> $senior_rules
#> [1] TRUE
#> 
#> $hc_ratio
#> [1] 10.66667
#> 
#> $hc_pass
#> [1] FALSE
#> 
#> $heteroatom_pass
#> [1] TRUE
#> 
#> $dbe
#> [1] -6
#> 
#> $dbe_pass
#> [1] FALSE
#> 
#> $nitrogen_rule
#> [1] TRUE
#>