IsalChem: Representation of Molecules by Sequences of Instructions

This is a repository for IsalChem, a novel formal language intended to represent chemical compounds, described in the paper Representation of Molecules by Sequences of Instructions

This repository contains the source code and scripts employed in the study that introduce a novel approach to chemical nomenclature. The article presents a method based on a reduced instruction set that defines a language in which every string represents a valid molecule. Notably, minor alterations in these strings typically correspond to small modifications in the corresponding molecular structures. Computational experiments demonstrate a strong correlation between distances and standard chemical similarity measures in this string space. This innovative approach facilitates integration with state-of-the-art computational intelligence systems, including deep learning models, for advanced chemical information processing.

Installation Instructions:

To set up the required environment, please execute the following commands:

conda install python=3.11

conda install pip numpy networkx python-pptx

pip install rdkit

mkdir sequence