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https://github.com/propensive/charisma

Represent chemical formulae in Scala
https://github.com/propensive/charisma

chemical-elements chemical-formulas scala

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Represent chemical formulae in Scala

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# 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 Plan



Charisma has not yet been published. The medium-term plan is to build Charisma

with [Fury](https://github.com/propensive/fury) and to publish it as a source build on

[Vent](https://github.com/propensive/vent). This will enable ordinary users to write and build

software which depends on Charisma.



Subsequently, Charisma will also be made available as a binary in the Maven

Central repository. This will enable users of other build tools to use it.



For the overeager, curious and impatient, see [building](#building).



## 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 `ChemicalFormula`s,

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



`ChemicalElement`s, `Molecule`s, `ChemicalFormula`s and `ChemicalEquation`s 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](https://en.wikipedia.org/wiki/Chemical_formula#Hill_system).



## Status



Charisma is classified as __embryotic__. For reference, Scala One 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](https://github.com/propensive/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`](https://github.com/propensive/wrath/releases/latest), 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](https://github.com/propensive/charisma/labels/beginner).



We suggest that all contributors read the [Contributing

Guide](/contributing.md) 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](https://propensive.com/).



## Name



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



### Pronunciation



`/kəˈɹɪzmə/`



In general, Scala One 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](https://en.wikipedia.org/wiki/Bohr_model).



## License



Charisma is copyright © 2024 Jon Pretty & Propensive OÜ, and

is made available under the [Apache 2.0 License](/license.md).