atomlite

:Author: Lukas Turcani :Docs: https://atomlite.readthedocs.io

======== AtomLite

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_.

.. _SQLite: https://docs.python.org/3/library/sqlite3.html .. _chemicalite: https://github.com/rvianello/chemicalite

Installation

.. code-block:: bash

pip install atomlite

Quickstart

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

.. code-block:: python

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", "prop2": 100}) entry2 = atomlite.Entry.from_rdkit("second", rdkit.MolFromSmiles("CN"), {"prop1": "thing", "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) print(entry.properties)

::

{'prop1': 'hi', 'prop2': 100} {'prop1': 'thing', 'prop2': 203}

.. code-block:: python

db.get_property_df(["$.prop1", "$.prop2"])

::

shape: (2, 3) ┌────────┬─────────┬─────────┐ │ key ┆ $.prop1 ┆ $.prop2 │ │ --- ┆ --- ┆ --- │ │ str ┆ str ┆ i64 │ ╞════════╪═════════╪═════════╡ │ first ┆ hi ┆ 100 │ │ second ┆ thing ┆ 203 │ └────────┴─────────┴─────────┘

.. _docs: https://atomlite.readthedocs.io