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.
Installation
pip install atomliteQuickstart
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", "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}
db.get_property_df(["$.prop1", "$.prop2"])shape: (2, 3) ┌────────┬─────────┬─────────┐ │ key ┆ $.prop1 ┆ $.prop2 │ │ --- ┆ --- ┆ --- │ │ str ┆ str ┆ i64 │ ╞════════╪═════════╪═════════╡ │ first ┆ hi ┆ 100 │ │ second ┆ thing ┆ 203 │ └────────┴─────────┴─────────┘
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Release files for atomlite 4.5.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| atomlite-4.5.0.tar.gz | 86.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| atomlite-4.5.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 97.6 kB
Release files / atomlite-4.5.0.tar.gz
| Download URL | atomlite-4.5.0.tar.gz |
|---|---|
| Size | 86.7 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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Yes |
| Uploaded via |
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Release files / atomlite-4.5.0-py3-none-any.whl
| Download URL | atomlite-4.5.0-py3-none-any.whl |
|---|---|
| Size | 10.9 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
uv/0.7.2
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