smizip 1.0.1

Quick start

Install as follows:

pip install smizip

Let’s compress and decompress a .smi file that contains canonical SMILES from RDKit using n-grams trained for this purpose listed in rdkit.slow.json (available from the GitHub site):

smizip    -i test.smi  -o test.smiz  -n example-ngrams/rdkit.slow.json
smizip -d -i test.smiz -o test.2.smi -n example-ngrams/rdkit.slow.json

To create your own JSON file of n-grams, you can train on a dataset (find_best_ngrams), or modify an existing JSON (add_char_to_json).

To use from Python:

import json
from smizip import SmiZip

json_file = "rdkit.slow.json"
with open(json_file) as inp:
   ngrams = json.load(inp)

zipper = SmiZip(ngrams)
zipped = zipper.zip("c1ccccc1C(=O)Cl") # gives bytes
unzipped = zipper.unzip(zipped)

Note

You should include \n (carraige-return) as a single-character n-gram if you intend to store the zipped representation in a file with lines terminated by \n. Otherwise, the byte value of \n will be assigned to a multi-gram, and zipped SMILES will be generated containing \n.

A similar warning goes for any SMILES termination character in a file. If you expect to store zipped SMILES that terminate in a TAB or SPACE character, you should add these characters as single-character n-grams. Otherwise the zipped representation may contain these and you won’t know which TABs are terminations and which are part of the representation.