https://github.com/lukasturcani/atomlite

Store your chemical data in a single file!
https://github.com/lukasturcani/atomlite

cheminformatics chemistry database

Last synced: about 2 months ago
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Store your chemical data in a single file!

• Host: GitHub
• URL: https://github.com/lukasturcani/atomlite
• Owner: lukasturcani
• License: other
• Created: 2023-05-02T16:37:54.000Z (over 1 year ago)
• Default Branch: master
• Last Pushed: 2024-04-25T10:26:24.000Z (8 months ago)
• Last Synced: 2024-05-01T15:31:42.526Z (8 months ago)
• Topics: cheminformatics, chemistry, database
• Language: Python
• Homepage: https://atomlite.readthedocs.io
• Size: 102 KB
• Stars: 12
• Watchers: 2
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

README

        
: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