Reagents

Pourfecto uses the Reagent interface of CHESSCore. The Solid, Liquid, and Gas types, registration, and unit conversions all belong to CHESSCore. Its Reagents & Species page describes them.

This page describes the one part of that interface that Pourfecto workflows use directly: creating reagents from a name.

Creating reagents on the fly

Most Pourfecto workflows do not need reagents to be registered. string_to_component takes a name and a concrete Reagent subtype. It returns the registered reagent if one exists. Otherwise it creates a reagent with only a name, leaves the physical properties missing, and shows a warning. Given Organism instead of a reagent type, it parses an organism name in the same way, and an organism name that is neither registered nor in the form "genus species strain" is an error.

using Pourfecto, CHESSCore

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

julia> string_to_component("custom buffer", Liquid)
┌ Warning: reagent custom buffer not registered. parsing custom buffer assuming it is a chemical. No chemical properties known.
└ @ CHESSCore ...
custom buffer

The returned reagent identifies the reagent in planning and labeling. Calculations that need molecular weight or density, such as conversions between mass and moles or between mass and volume, need a registered reagent. CHESSCore's Reagents & Species page describes registration with the @reagent macro, register_lab, and the reagent_context keyword, and component_to_string, the inverse of string_to_component.

Pourfecto's examples and tests use this form, and Pourfecto calls it when it parses reagent names from stock tables.