Add examples

examples/read_database.py

@@ -0,0 +1,29 @@
+"""Read all the molecules in a database."""  # noqa: INP001
+
+import argparse
+from pathlib import Path
+
+import atomlite
+
+
+def main() -> None:
+    """Run the example."""
+    args = _parse_args()
+    db = atomlite.Database(args.database)
+    for entry in db.get_entries():
+        molecule = atomlite.json_to_rdkit(entry.molecule)  # noqa: F841
+        # do something with molecule
+
+
+def _parse_args() -> argparse.Namespace:
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "database",
+        help="Path to the atomlite file.",
+        type=Path,
+    )
+    return parser.parse_args()
+
+
+if __name__ == "__main__":
+    main()

examples/write_chembl.py

@@ -0,0 +1,43 @@
+"""Write the ChEMBL database to an AtomLite file."""  # noqa: INP001
+
+import argparse
+from pathlib import Path
+
+import atomlite
+import rdkit.Chem as rdkit  # noqa: N813
+
+
+def main() -> None:
+    """Run the example."""
+    args = _parse_args()
+    chembl = rdkit.SDMolSupplier(args.chembl)
+    db = atomlite.Database(args.output)
+    for i, mol in enumerate(chembl):
+        db.add_entries(
+            atomlite.Entry.from_rdkit(
+                key=str(i),
+                molecule=mol,
+                properties=mol.GetPropsAsDict(),
+            ),
+            commit=False,
+        )
+    db.connection.commit()
+
+
+def _parse_args() -> argparse.Namespace:
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "chembl",
+        help="Path to the ChEMBL sdf database file.",
+        type=Path,
+    )
+    parser.add_argument(
+        "output",
+        help="Path to the output atomlite file.",
+        type=Path,
+    )
+    return parser.parse_args()
+
+
+if __name__ == "__main__":
+    main()