Parse Chemical Formulas
Count the charge and number of elements in a chemical formula.
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character, a chemical formula
numeric, multiplier for the elemental counts in each formula
logical, add together the elemental counts in all formulas?
logical, include zero counts for elements?
makeup parses a chemical formula expressed in string notation, returning the numbers of each element in the formula. The formula may carry a charge, indicated by a + or - sign, possibly followed by a magnitude, after the uncharged part of the formula. The formula may have multiple subformulas enclosed in parentheses (but the parentheses may not be nested), each one optionally followed by a numeric coefficient. The formula may have one suffixed subformula, separated by * or :, optionally preceded by a numeric coefficient. All numbers may contain a decimal point.
makeup calls a sequence of supporting functions depending on specific characters present in the formula. If the formula has a charge, it is first parsed using
count.charge. If the formula has subformulas, in parentheses or as a suffix, they are separated and counted using
count.formulas. Finally, the elements in each subformula are counted using
count.elements processes a simple chemical formula that must adhere to the following pattern: it starts with an elemental symbol; all elemental symbols start with an uppercase letter, and are followed by another elemental symbol, a number (possibly fractional, possibly signed), or nothing (the end of the formula).
Any sequence of one uppercase letter followed by zero or more lowercase letters is recognized as an elemental symbol by
makeup will issue a warning for elemental symbols that are not present in
makeup can handle numeric and length > 1 values for the
formula argument. If the argument is numeric, it identifies row number(s) in
thermo$obigt from which to take the formulas of species. If
formula has length > 1, the function returns a list containing the elemental counts in each of the formulas. If
count.zero is TRUE, the elemental counts for each formula include zeros to indicate elements that are only present in any of the other formulas.
multiplier argument must have either length = 1 or length equal to the number of formulas. The elemental count in each formula is multiplied by the respective value. If
sum is true, the elemental counts in all formulas (after any multiplying) are summed together to yield a single bulk formula.
count.charge returns a list with named elements
uncharged, indicating, respectively, the numeric value of the charge, and the original formula string excluding the charge.
count.formulas returns a numeric vector with names refering to each of the subformulas or the whole formula if there are no subformulas.
makeup return numeric vectors with names refering to each of the elemental symbols in the formula. For
makeup, if more than one formula is provided, a list of numeric vectors is returned, unless
sum is TRUE.
Many other functions in CHNOSZ rely on
makeup for their operation:
entropy for calculating properties of chemical compounds from their elements;
i2A for constructing stoichiometric matrices (with
subcrt for checking mass balance of chemical reactions; and others.
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# the composition of a simple compound makeup("CO2") # 1 carbon, 2 oxygen # the formula of lawsonite, with a parenthetical part and a suffix makeup("CaAl2Si2O7(OH)2*H2O") # fractional coefficients are ok redfield <- c(106, 16, 1) reddiv10 <- makeup("C10.6N1.6P0.1") stopifnot(10*reddiv10 == redfield) # the coefficient for charge is a number with a *preceding* sign # e.g., ferric iron, with a charge of +3 is expressed as makeup("Fe+3") # transcribing the formula the way it appears in many # publications produces a likely unintended result: # 3 iron atoms and a charge of +1 makeup("Fe3+") # these all represent a single negative charge, i.e., electron makeup("-1") makeup("Z0-1") makeup("Z-1+0") # hypothetical compounds with negative numbers of elements makeup("C-4(O-2)") # -4 carbon, -2 oxygen makeup("C-4O-2") # -4 carbon, 1 oxygen, -2 charge makeup("C-4O-2-2") # -4 carbon, -2 oxygen, -2 charge # the 'sum' argument can be used to check mass and charge # balance in a chemical reaction formula <- c("H2O", "H+", "Z0-1", "O2") (mf <- makeup(formula, c(-1, 2, 2, 0.5), sum=TRUE)) stopifnot(all(mf==0))
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