Calculate total atomic mass of a compound.

total_atomic_mass.R

atomic_mass <- c( H = 1.008,  He = 4.0026, Li = 6.94,   Be = 9.0122,
                  B = 10.81,   C = 12.011,  N = 14.007,  O = 15.999,
                  F = 18.998, Ne = 20.180, Na = 22.990, Mg = 24.305,
                 Al = 26.982, Si = 28.085,  P = 30.974,  S = 32.06,
                 Cl = 35.45,  Ar = 39.948,  K = 39.098, Ca = 40.078,
                 Sc = 44.956, Ti = 47.867,  V = 50.942, Cr = 51.996,
                 Mn = 54.938, Fe = 55.845, Co = 58.933, Ni = 58.693,
                 Cu = 63.546, Zn = 65.38,  Ga = 69.732, Ge = 72.630,
                 As = 74.922, Se = 78.971, Br = 79.904, Kr = 83.798,
                 Rb = 85.468, Sr = 87.62,   Y = 88.906, Zr = 91.224,
                 Nb = 92.906, Mo = 95.95,  Tc = 98,     Ru = 101.07,
                 Rh = 102.91, Pd = 106.42, Ag = 107.87, Cd = 112.41,
                 In = 114.82, Sn = 118.71, Sb = 121.76, Te = 127.60,
                  I = 126.90, Xe = 131.29, Cs = 132.91, Ba = 137.33,
                 La = 138.91, Ce = 140.12, Pr = 140.91, Nd = 144.24,
                 Pm = 145,    Sm = 150.36, Eu = 151.96, Gd = 157.25,
                 Tb = 158.93, Dy = 162.50, Ho = 164.93, Er = 167.26,
                 Tm = 168.93, Yb = 173.05, Lu = 174.97, Hf = 178.49, 
                 Ta = 180.95,  W = 183.84, Re = 186.21, Os = 190.23,
                 Ir = 192.22, Pt = 195.08, Au = 196.97, Hg = 200.59,
                 Ti = 204.38, Pb = 207.2,  Bi = 208.98, Po = 209,
                 At = 210,    Rn = 222,    Fr = 223,    Ra = 226,
                 Ac = 227,    Th = 232.04, Pa = 231.04,  U = 238.03,
                 Np = 237,    Pu = 244,    Am = 243,    Cm = 247,
                 Bk = 247,    Cf = 251,    Es = 252,    Fm = 257,
                 Md = 258,    No = 259,    Lr = 266,    Rf = 267, 
                 Db = 268,    Sg = 269,    Bh = 270,    Hs = 277,
                 Mt = 278,    Ds = 281,    Rg = 282,    Cn = 285,
                 Nh = 286,    Fl = 298,    Mc = 290,    Lv = 293,
                 Ts = 294,    Og = 294)

total_atomic_mass <- function(compound, ref){
  compound <- 
    unlist(
      stringr::str_extract_all(
        string = compound,
        pattern = "[A-Z][a-z]{0,2}[1-9]{0,}[0-9]{0,}"
      )
    )

  element <- 
    unlist(
      stringr::str_extract(
        string = compound,
        pattern = "[A-Z][a-z]{0,2}"
      )
    )
  
  count <- 
    unlist(
      stringr::str_extract(
        string = compound,
        pattern = "[1-9]{1,}[0-9]{0,}"
      )
    )
  count[is.na(count)] <- 1
  
  # For assistance in debugging.  Do not delete.
  # data.frame(
  #   element = element,
  #   count = as.numeric(count),
  #   mass = ref[element],
  #   total_mass = as.numeric(count) * ref[element]
  # )
  
  sum(as.numeric(count) * ref[element])
}

total_atomic_mass("H2O", atomic_mass)