notmywing/stoikts

Chemical formulae parser/tokenizer written in TypeScript.

Stoik

Stoik is a TypeScript library for parsing and evaluating chemical formulas.

Installation

To install Stoik, run the following command:

npm install stoik

Usage

To use Stoik in your project, import the evaluate function as well as any other necessary functions for your project:

import { tokenize, evaluate, toRPN, Molecule } from "stoik";

To evaluate a chemical formula using Stoik, you can use the evaluate function. This function takes a chemical formula as input and returns a Molecule instance, which is essentially an extension of Map and contains the atoms and their frequencies in the molecule. For example:

const formula = "H2O";

evaluate(formula); // Map {"H" => 2, "O" => 1}

// Formulas can consist of fairly complicated operations as well.
evaluate("5(H2O)3((FeW)5CrMo2V)6CoMnSi");

// The result of the expression above is equivalent to:
new Molecule([
	["H", 30],
	["Co", 5],
	["Cr", 30],
	["Fe", 150],
	["Mn", 5],
	["Mo", 60],
	["O", 15],
	["Si", 5],
	["V", 30],
	["W", 150],
]);

Tokenization and Parsing

Alternatively, it's possible to evaluate formulas step-by-step, if you need to alter any of the steps.

The tokenize function combines the tokenization and parsing functionality. It is capable of detecting malformed formulas to some extent. However, if the input is not a valid formula, the function is not guaranteed to return a sequence that will correctly evaluate into a Molecule.

// First, tokenize the formula to get a Denque sequence of tokens.
const tokens = tokenize(formula);
// new Denque([
//   [TokenType.Atom, "H"],
//   [TokenType.Subscript],
//   [TokenType.Number, 2],
//   [TokenType.Add]
//   [TokenType.Atom, "O"]
// ]);

Before supplying the tokens to evaluate, they first have to be converted to the Reverse Polish Notation using toRPN. Like tokenize, this function is not guaranteed to return a valid sequence of tokens if the input is inherently incorrect.

// Next, convert the tokens to Reverse Polish Notation (RPN) using the toRPN function. Note the different order.
const RPN = toRPN(tokens);
// new Denque([
//   [TokenType.Atom, "H"],
//   [TokenType.Number, 2],
//   [TokenType.Subscript],
//   [TokenType.Atom, "O"],
//   [TokenType.Add]
// ]);

Finally, the RPN token sequence can be supplied to evaluate to evaluate the formula. This will throw a concise error if the input is incorrect.

evaluate(RPN); // Map {"H" => 2, "O" => 1}

Molecule Class

The Molecule class includes methods for performing basic arithmetic operations on molecules. By default, these methods return new Molecule instances, which means that they do not mutate the original molecule. However, each method also has a mutable counterpart (e.g. add and addMut) that can be used to modify the original molecule instead.

An AtomLiteral is a type that represents a valid atom in a chemical molecule. It must be either a single uppercase letter (e.g. "H" for hydrogen), or a combination of an uppercase letter followed by a lowercase letter (e.g. "Cl" for chlorine).

Molecule objects can be constructed in several ways:

• With no arguments, to create an empty molecule
• With a single AtomLiteral argument, to create a molecule containing a single atom at a frequency of 1
• With a single AtomLiteral and a number argument, to create a molecule containing a single atom at a specified frequency
• With a Molecule argument, to create a new molecule with the same atoms and frequencies as the input molecule
• With an array of tuples, where each tuple contains an AtomLiteral and an optional number, to create a molecule containing the atoms and frequencies specified in the input array

The Molecule class also contains several methods for manipulating molecules:

• The set method can be used to add or update the frequency of an atom in the molecule
• The add method can be used to add a molecule to this molecule
• The subtract method can be used to subtract a molecule from this molecule
• The multiply method can be used to multiply this molecule by a number
• All other methods provided by the standard Map class

In addition, the Molecule class has a fromAtom static method that can be used to quickly create a molecule containing a single atom at a specified frequency.

Design and Implementation

Stoik uses a combination of recursive descent parsing and the Shunting-yard algorithm to parse and evaluate chemical formulas. The tokenize function uses a simple state machine to split the input string into tokens, and the evaluate function uses a stack to evaluate the formula in RPN.

License

Stoik is licensed under the LGPL 3.0 license. See the LICENSE file for details.