Reagents

Pourfecto searches for ways to combine reagents to create desired chemical solutions. Pourfecto uses the JLIMS interface internally to identify and compute properties of different reagents. In most Pourfecto workflows, however, you do not need to work with reagents directly . Pourfecto can create JLIMS objects on the fly from reagent names in tables, CSV files, or other user inputs. This page is for advanced users who want a deeper understanding and more control of Pourfecto's behavior.

JLIMS Chemical types

All chemicals in JLIMS are subtypes of Chemical. The built-in concrete chemical types are:

• [JLIMS.Solid]
• [JLIMS.Liquid]
• [JLIMS.Gas]

Each type represents the phase of the chemical at standard temperature and pressure (STP). For Pourfecto, only Solid and Liquid types are relevant.

Chemical properties

Every Chemical subtype used by JLIMS has four fields:

JLIMS uses these properties to automatically compute unit conversions, such as a chemical mass to moles. If a property is unknown, it can be set to missing.

For example, a chemical with no known molecular weight, density, or PubChem ID can still be represented:

using JLIMS
unknown = JLIMS.Solid("unknown reagent", missing, missing, missing)

Creating reagents from strings in Pourfecto

The main Pourfecto interface for working with reagents is string_to_reagent.

using JLIMS
string_to_reagent("water", u"mL")
string_to_reagent("sodium chloride", u"mg")
string_to_reagent("ethanol", JLIMS.Liquid)
string_to_reagent("sodium chloride", JLIMS.Solid)

Pourfecto first checks whether the reagent is already registered in JLIMS or another custom module. If it is registered, the registered chemical object is returned.

If the reagent is not registered, Pourfecto creates a new chemical object on the fly with the given name and unknown physical properties.

For example:

julia> string_to_reagent("custom buffer", u"mL")
┌ Warning: reagent custom buffer not registered. parsing custom buffer assuming it is a chemical. No chemical properties known.
└ @ Pourfecto ...
custom buffer

The returned object is still usable as a reagent identifier in Pourfecto, but its chemical properties are set to missing.

Inferring chemical type from units

For convenience, Pourfecto can infer whether an unregistered reagent should be treated as a JLIMS.Solid or a JLIMS.Liquid based on the unit associated with it. Both JLIMS and Pourfecto use the Unitful.jl package for unit definitions and conversions.

string_to_reagent(str::AbstractString, unit::Unitful.Units)

This is especially useful when parsing [stock] tables. For example, reagents measured by mass are interpreted as solids, while reagents measured by volume are interpreted as liquids.

using Unitful

string_to_reagent("sodium chloride", u"mg")
string_to_reagent("water", u"mL")

The unit-based parser uses the following conventions for unknown reagents:

For example:

julia> string_to_reagent("unknown salt", u"mg")
┌ Warning: reagent unknown salt not registered. parsing unknown salt assuming it is a chemical. No chemical properties known.
└ @ Pourfecto ...
unknown salt

creates a Solid.

julia> string_to_reagent("unknown solvent", u"mL")
┌ Warning: reagent unknown solvent not registered. parsing unknown solvent assuming it is a chemical. No chemical properties known.
└ @ Pourfecto ...
unknown solvent

creates a Liquid.

Explicitly choosing the chemical type

You can also explicitly specify the chemical type to use if the reagent is not registered.

string_to_reagent(str::AbstractString, chem_type::Type{<:Chemical})

For example:

using JLIMS

buffer = string_to_reagent("custom buffer", Liquid)
salt = string_to_reagent("custom salt", Solid)
gas = string_to_reagent("oxygen mixture", Gas)

This form is useful when the unit alone is not enough to infer the intended phase.

If the reagent is already registered, the registered chemical is returned and chem_type is ignored as a fallback.

Converting reagents back to strings

Pourfecto can also convert a chemical object back into a stable string identifier using reagent_to_string.

reagent_to_string(chem)

For registered chemicals, this returns the registry key that can be parsed again later.

For unregistered chemicals created on the fly, it returns the chemical name.

chem = string_to_reagent("custom buffer", Liquid)

reagent_to_string(chem)

returns:

"custom buffer"

This is useful for serialization, DataFrame export, JSON export, and converting Pourfecto objects into text-based formats.

Registered reagents

Registered reagents are chemicals already known to JLIMS or to a custom lab module. You may want to register chemicals explicitly when you need:

• accurate molecular weights
• accurate densities
• PubChem identifiers
• reliable mass-to-mole conversions
• reliable mass-to-volume conversions
• shared lab-wide chemical definitions

Reagents can be registered with the JLIMS.@chemical macro in custom modules . For example:

module MyChemicals
    using JLIMS
    using Unitful

    JLIMS.@chemical water "water" Liquid 18.015u"g/mol" 1.00u"g/mL" 962
    JLIMS.@chemical sodium_chloride "sodium chloride" Solid 58.44u"g/mol" 2.16u"g/ml" 5234
end 

After registration, Pourfecto can resolve those chemicals by name by including MyChemicals module in the chem_context argument of string_to_reagent:

using Pourfecto, MyChemicals
string_to_reagent("water", u"mL"; chem_context=[MyChemicals])
string_to_reagent("sodium_chloride", u"mg";chem_context=[MyChemicals])

Pourfecto returns the chemical objects registered in the MyChemicals module.