Chemical Formula Manipulation

ChemistryLab allows you to create and manipulate chemical formulas. It provides the Formula type (holds a formula string, multiple string representations, an atom composition map and a charge) and AtomGroup helper values, plus utilities to convert between notations (Phreeqc ↔ Unicode), to format/colour formulas, to perform arithmetic on formulas, and to validate atom symbols.

struct Formula{T<:Number}
    expr::String
    phreeqc::String
    unicode::String
    colored::String
    composition::OrderedDict{Symbol,T}
    charge::Int8
end

Formula construction

Formulas can be constructed:

• by parsing a string containing eventually fractional or decimal coefficients

f = Formula("C3AFS5//8H4.32")

Formula{Real}
    formula: C3AFS5//8H4.32 ◆ C₃AFS⅝H₄.₃₂
composition: C => 3, A => 1, F => 1, S => 5//8, H => 4.32
     charge: 0

• from a dictionary

fCaCO3 = Formula(Dict(:Ca => 1, :C => 1, :O => 3))

Formula{Int64}
    formula: CaCO3 ◆ CaCO₃
composition: Ca => 1, O => 3, C => 1
     charge: 0

• from atom groups

fCO2 = AtomGroup(:C) + AtomGroup(2,:O)

Formula{Int64}
    formula: CO2 ◆ CO₂
composition: O => 2, C => 1
     charge: 0

Charges can also be included during the creation in two different ways:

fHSO₄⁻ = AtomGroup(:H)+AtomGroup(:S)+AtomGroup(4,:O)+AtomGroup(:e)

Formula{Int64}
    formula: HSO4- ◆ HSO₄-
composition: H => 1, S => 1, O => 4
     charge: -1

Or:

fNa⁺ = AtomGroup(:Na)+AtomGroup(:Zz)

Formula{Int64}
    formula: Na+
composition: Na => 1
     charge: 1

Type of Formula

The type of the Formula struct being associated with the most complex type of the set of coefficients.

typeof(Formula("H2O"))

Formula{Int64}

typeof(Formula("C3AFS5//8H4.32"))

Formula{Real}

Change of type

Coefficient types can be converted a posteriori.

convert(Float64, Formula("H2O"))

Formula{Float64}
    formula: H2O ◆ H₂O
composition: H => 2.0, O => 1.0
     charge: 0