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A SQLite chemical database.

Project description


Lukas Turcani



AtomLite is a Python library for simple molecular database on top of SQLite.

For an alternative to AtomLite, which provides stronger integration with RDKit, and a greater focus on cheminformatics, see chemicalite.


pip install atomlite


You can see a lot more examples in our docs but here is a taste of using AtomLite:

import atomlite
import rdkit.Chem as rdkit
# Create a database.
db = atomlite.Database("molecules.db")
# Create database entries.
entry1 = atomlite.Entry.from_rdkit("first", rdkit.MolFromSmiles("C"), {"prop1": "Hi"})
entry2 = atomlite.Entry.from_rdkit("second", rdkit.MolFromSmiles("CN"), {"prop2": 203})
# Add entries to database.
db.add_entries([entry1, entry2])
# Retrieve entries from database.
for entry in db.get_entries(["first", "second"]):
  molecule = atomlite.json_to_rdkit(entry.molecule)

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