chemschema 0.0.1__py3-none-any.whl

chemschema/bingo/comparators.py

@@ -0,0 +1,13 @@
+from sqlalchemy import text
+from sqlalchemy.types import UserDefinedType
+
+
+class BingoMolComparator(UserDefinedType.Comparator):
+    def substructure(self, query, parameters=""):
+        return self.expr.op("@")(text(f"('{query}', '{parameters}')::bingo.sub"))
+
+    def smarts(self, query, parameters=""):
+        return self.expr.op("@")(text(f"('{query}', '{parameters}')::bingo.smarts"))
+
+    def equals(self, query, parameters=""):
+        return self.expr.op("@")(text(f"('{query}', '{parameters}')::bingo.exact"))

chemschema/bingo/functions.py

@@ -0,0 +1,27 @@
+from chemschema.utils import get_column_name
+from sqlalchemy import text
+
+
+class bingo_func:
+    name = "bingo"
+    mol_type_name = "bingo.molecule"
+    fingerprint_type_name = "bingo.fingerprint"
+
+    @staticmethod
+    def substructure(mol_column, query, parameters=""):
+        return text(f"{mol_column} @ {query, parameters}::bingo.sub")
+
+    @staticmethod
+    def smarts(mol_column, query, parameters=""):
+        return text(f"{mol_column} @ {query, parameters}::bingo.smarts")
+
+    @staticmethod
+    def equals(mol_column, query, parameters=""):
+        mol_column = get_column_name(mol_column)
+        return text(f"{mol_column} @ {query, parameters}::bingo.exact")
+
+    @staticmethod
+    def similarity(mol_column, query, bottom=0.0, top=1.0, metric="Tanimoto"):
+        # get table name if the columnis mapped
+        mol_column = get_column_name(mol_column)
+        return text(f"{mol_column} @ {bottom, top, query, metric}::bingo.sim")

chemschema/bingo/index.py

@@ -0,0 +1,30 @@
+from sqlalchemy.schema import Index
+
+
+# @compiles(BingoMolIndex, 'postgresql')
+# def compile_bingo_rxn_index(element, compiler, **kw):
+#     expr = list(element.expressions)[0]
+#     print(expr)
+#     return "CREATE INDEX %s ON %s USING bingo_idx (%s bingo.reaction)" % (
+#         element.name,
+#         compiler.preparer.format_table(expr.table),
+#         compiler.process(expr, include_table=False)
+#     )
+class BingoMolIndex(Index):
+    def __init__(self, name, mol_column):
+        super().__init__(
+            name,
+            mol_column,
+            postgresql_using="bingo_idx",
+            postgresql_ops={mol_column: "bingo.molecule"},
+        )
+
+
+class BingoBinaryMolIndex(Index):
+    def __init__(self, name, mol_column):
+        super().__init__(
+            name,
+            mol_column,
+            postgresql_using="bingo_idx",
+            postgresql_ops={mol_column: "bingo.bmolecule"},
+        )

chemschema/bingo/types.py

@@ -0,0 +1,18 @@
+from sqlalchemy.types import UserDefinedType
+from chemschema.bingo.comparators import BingoMolComparator
+
+
+class BingoMol(UserDefinedType):
+    cache_ok = True
+    comparator_factory = BingoMolComparator
+
+    def get_col_spec(self):
+        return "varchar"
+
+
+class BingoBinaryMol(UserDefinedType):
+    cache_ok = True
+    comparator_factory = BingoMolComparator
+
+    def get_col_spec(self):
+        return "bytea"

chemschema/rdkit/types.py

@@ -0,0 +1,6 @@
+from sqlalchemy.types import UserDefinedType
+
+
+class Mol(UserDefinedType):
+    def get_col_spec(self):
+        return "mol"

chemschema/utils.py

@@ -0,0 +1,19 @@
+from sqlalchemy.sql import ColumnElement
+from sqlalchemy.orm import InstrumentedAttribute
+from sqlalchemy.schema import Column
+from typing import Union
+
+
+def get_column_name(
+    mol_column: Union[InstrumentedAttribute, Column, ColumnElement, str],
+) -> str:
+    """Helper to get column name regardless of input type"""
+    if hasattr(mol_column, "table"):
+        # Handle ORM attributes
+        table_name = mol_column.table.name
+        column_name = mol_column.name
+        return f"{table_name}.{column_name}"
+    elif hasattr(mol_column, "name"):
+        # Handle Table columns
+        return mol_column.name
+    return str(mol_column)

chemschema-0.0.1.dist-info/METADATA

@@ -0,0 +1,31 @@
+Metadata-Version: 2.3
+Name: chemschema
+Version: 0.0.1
+Summary: Extensions for SQLAlchemy to work with chemical cartridges
+Keywords: chemistry
+Author: Anton Siomchen
+Author-email: Anton Siomchen <41703271+asiomchen@users.noreply.github.com>
+License: Apache-2.0
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Utilities
+Classifier: Topic :: Database
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3 :: Only
+Requires-Dist: datamol>=0.12.5
+Requires-Dist: geoalchemy2>=0.18.0
+Requires-Dist: psycopg[binary]>=3.2.9
+Requires-Dist: rdkit>=2025.3.6
+Requires-Dist: sqlalchemy>=2.0.43
+Requires-Python: >=3.10
+Project-URL: homepage, https://github.com/asiomchen/chemschema
+Project-URL: repository, https://github.com/asiomchen/chemschema
+Description-Content-Type: text/markdown
+
+# ChemSchema
+
+[WIP]

chemschema-0.0.1.dist-info/RECORD

@@ -0,0 +1,14 @@
+chemschema/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+chemschema/base.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+chemschema/bingo/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+chemschema/bingo/comparators.py,sha256=l63YLOD5YyMfVt5AcpsfcJYJWuS70JiWMXqgP3ec26Q,520
+chemschema/bingo/functions.py,sha256=h71bch7lSd_3cuMx5jDtr_pcHOxMoMF3EPOFBIzgCQA,948
+chemschema/bingo/index.py,sha256=91F3mnKNRLL-pjTLvJ7DuywaarNjfcvOn5mNeICm3NQ,919
+chemschema/bingo/types.py,sha256=iXOJ0L4RZjsYytuiG2Mt3tYKyreaVB-69kboNBmjaSQ,415
+chemschema/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+chemschema/rdkit/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+chemschema/rdkit/types.py,sha256=xHmz5a-Fr5Ne3f-0a9K5hb4EGoIqNXMj8RifTFLPN2o,124
+chemschema/utils.py,sha256=LXBMKv0ZlcOL7dBexW-n257bb8fS6eIaoBZ5latzVoI,642
+chemschema-0.0.1.dist-info/WHEEL,sha256=Pi5uDq5Fdo_Rr-HD5h9BiPn9Et29Y9Sh8NhcJNnFU1c,79
+chemschema-0.0.1.dist-info/METADATA,sha256=WwQI-UZkoqBu9IGKV8h8jhqHeoVjNxDYF4nQvQC376U,1112
+chemschema-0.0.1.dist-info/RECORD,,

chemschema-0.0.1.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: uv 0.8.17
+Root-Is-Purelib: true
+Tag: py3-none-any