An implementation of Roger Sayle's SmiZip algorithm for compressing short strings
Project description
SmiZip is a compression method for short strings. It was developed by Roger Sayle in 1998 while at Metaphorics LLC to compress SMILES strings.
This repo is an implementation in Python of the SmiZip algorithm as described by Roger in a presentation in 2001.
Quick start
Install as follows:
pip install smizip
Let’s compress a .smi file that originated with RDKit:
python3 scripts/compress.py
SMILES strings must be encoded and decoded with the same n-grams. These are listed in a JSON file. Several JSON files are included by default but you can create your own by training on a dataset (find_best_ngrams.py), or by modifying existing ones (add_char_to_json.py).
Let’s
This codebase was developed by Noel O’Boyle based on the information in that presentation.`
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