Charisma

Representations of chemicals

Charisma provides a simple representation of chemical elements and formulas in Scala.

Features

• provides representations (with names) of the 118 chemical elements known since 2015
• lightweight syntax for constructing molecules from multiples of elements
• serialization to Unicode strings

Availability

Getting Started

Chemical Entities

Charisma provides representations of several increasingly-complex entities from chemistry,

• chemical elements
• molecules
• chemical formulas
• chemical equations which can be constructed, usually by composing other entities.

Chemical Elements

The 118 chemical elements known, and assigned names since 2015 are all represented in the PeriodicTable object, as members named after their chemical symbol. For example, Hydrogen is PeriodicTable.H and Chlorine is PeriodicTable.Cl. Each element is an instance of ChemicalElement, which defines its atomic number, name in English (noting that "Sulphur" and "Aluminium" are preferred over "Sulfur" and "Aluminum") and chemical symbol.

Molecules

Elements can be combined to produce molecules, instances of Molecule. To combine multiple atoms of the same element into a molecule, we apply an integer type parameter to that element, for example PeriodicTable.O[2] is O₂ and PeriodicTable.C[60] would be C₆₀.

Different elements can be combined using the * operator. So salt, NaCl, would be Na*Cl. Or sulphuric acid, H₂O₄S, could be constructed as, H[2]*S*O[4]*S.

Chemical Formulas

A ChemicalFormula is the addition of several molucules, combined in integer multiples using the * operator, and with other molecules with the + operator. For example, the products of photosynthesis, C₆H₁₂O₆ + 6O₂ (sugar and oxygen), could be written, C[6]*H[12]*O[6] + O[2]*6.

Chemical equation

A ChemicalEquation describes a relationship between two ChemicalFormulas, and can be constructed using one the arrow operators between two chemical formulas. These arrow operators represent different relationsips between the sides of the equation, and are as follows:

• -->: net forwards
• <->: resonance
• <=>: both directions
• <~>: equilibrium
• ===: stoichiometric

These different relationships are reprensented by the enumeration, Reaction.

The ChemicalEquation#balance method will determine if the equation is balanced, that is, the number of atoms of each element is the same on the left and right sides of the equation.

Generality

A ChemicalElement principally represents the type of an atom and is not, in general, interchangeable with a Molecule. But in many circumstances, it can also serve to conveniently represent an atom of that element itself. So while a ChemicalElement is not a Molecule, both have the supertype, Molecular.

Likewise, ChemicalElement, Molecule and ChemicalFormula (as well as Molecular) are all subtypes of a further generalization, Formulable for types that can represent a chemical formula.

Generally, it is better to program to the Molecular and Forbulable interfaces, rather than Molecule or ChemicalFormula, for the greatest flexibility.

Molecular properties

Molecular values may be ionized with a positive or negative integer charge. For unit charges, a unary + or - may prefix a Molecular value, e.g. +Na or -C[2]*H[3]*O[2] (acetate). The charges of ions or ionic compounds will be added when combined, so +Na*(-Cl) (salt) will produce the chargeless compound, NaCl.

A non-unit charge may be specified for any molecule with its ion method, specifying its integral charge value.

Molecules in a chemical equation can also be identified as having a particular physical state, namely solid, liquid, gas or aqueous. These four states are represented by the enumeration, PhysicalState as Solid, Liquid, Gas and Aqueous, and can be specified for any Molecular value with its as method. For example, (Na*Cl).as(Aqueous) represents an aqueous salt solution.

By default, a molecule's state is unspecified, represented by the Unset value, and any combination of molecules with physical states set (other than integer multiplication) will unset their physical states, since the resultant state cannot be easily and reliably predicted. Therefore, in the earlier example, (Na*Cl).as(Aqueous), the parentheses are important as the aqueous state would otherwise be specified for Chlorine, but unset immediately upon combining with Sodium.

Rendering

ChemicalElements, Molecules, ChemicalFormulas and ChemicalEquations all have Show instances which will render the types as text, using appropriate Unicode characters for subscripts.

Since the different elements in a molecule could be written in any order with the same meaning, they are canonically written using the Hill System.

Status

Charisma is classified as embryotic. For reference, Soundness projects are categorized into one of the following five stability levels:

• embryonic: for experimental or demonstrative purposes only, without any guarantees of longevity
• fledgling: of proven utility, seeking contributions, but liable to significant redesigns
• maturescent: major design decisions broady settled, seeking probatory adoption and refinement
• dependable: production-ready, subject to controlled ongoing maintenance and enhancement; tagged as version 1.0.0 or later
• adamantine: proven, reliable and production-ready, with no further breaking changes ever anticipated

Projects at any stability level, even embryonic projects, can still be used, as long as caution is taken to avoid a mismatch between the project's stability level and the required stability and maintainability of your own project.

Charisma is designed to be small. Its entire source code currently consists of 252 lines of code.

Building

Charisma will ultimately be built by Fury, when it is published. In the meantime, two possibilities are offered, however they are acknowledged to be fragile, inadequately tested, and unsuitable for anything more than experimentation. They are provided only for the necessity of providing some answer to the question, "how can I try Charisma?".

1. Copy the sources into your own project

   Read the fury file in the repository root to understand Charisma's build structure, dependencies and source location; the file format should be short and quite intuitive. Copy the sources into a source directory in your own project, then repeat (recursively) for each of the dependencies.

   The sources are compiled against the latest nightly release of Scala 3. There should be no problem to compile the project together with all of its dependencies in a single compilation.

2. Build with Wrath

   Wrath is a bootstrapping script for building Charisma and other projects in the absence of a fully-featured build tool. It is designed to read the fury file in the project directory, and produce a collection of JAR files which can be added to a classpath, by compiling the project and all of its dependencies, including the Scala compiler itself.

   Download the latest version of wrath, make it executable, and add it to your path, for example by copying it to /usr/local/bin/.

   Clone this repository inside an empty directory, so that the build can safely make clones of repositories it depends on as peers of charisma. Run wrath -F in the repository root. This will download and compile the latest version of Scala, as well as all of Charisma's dependencies.

   If the build was successful, the compiled JAR files can be found in the .wrath/dist directory.

Contributing

Contributors to Charisma are welcome and encouraged. New contributors may like to look for issues marked beginner.

We suggest that all contributors read the Contributing Guide to make the process of contributing to Charisma easier.

Please do not contact project maintainers privately with questions unless there is a good reason to keep them private. While it can be tempting to repsond to such questions, private answers cannot be shared with a wider audience, and it can result in duplication of effort.

Author

Charisma was designed and developed by Jon Pretty, and commercial support and training on all aspects of Scala 3 is available from Propensive OÜ.

Name

One person's charisma may lead to figurative chemistry with another.

Pronunciation

/kəˈɹɪzmə/

In general, Soundness project names are always chosen with some rationale, however it is usually frivolous. Each name is chosen for more for its uniqueness and intrigue than its concision or catchiness, and there is no bias towards names with positive or "nice" meanings—since many of the libraries perform some quite unpleasant tasks.

Names should be English words, though many are obscure or archaic, and it should be noted how willingly English adopts foreign words. Names are generally of Greek or Latin origin, and have often arrived in English via a romance language.

Logo

The logo shows a deuterium atom, according to the Bohr model.

License

Charisma is copyright © 2024 Jon Pretty & Propensive OÜ, and is made available under the Apache 2.0 License.