rvianello/razi

A cheminformatics extension for the SQLAlchemy database toolkit.

razi's Issues

I get a runtime error, can't execute the sql

I use razi and sqlchemy generate a similary sql like

SELECT "RdkitMol_c5".id, "RdkitMol_c5".canonical_smiles, "RdkitMol_c5".canonical_smiles_key, mol_to_pkl("RdkitMol_c5".rdkit_mol) AS rdkit_mol, bfp_to_binary_text("RdkitMol_c5".rdkit_bfp) AS rdkit_bfp 
FROM "RdkitMol_c5" JOIN "Molecules_c5" ON "Molecules_c5".canonical_smiles = "RdkitMol_c5".canonical_smiles 
WHERE "RdkitMol_c5".rdkit_bfp # morganbv_fp('Cc1ccc2nc(-c3ccc(NC(C4N(C(c5cccs5)=O)CCC4)=O)cc3)sc2c1')

but after the sql execute, I get a runtime error:

  File ".conda\envs\3.7\lib\site-packages\sqlalchemy\engine\result.py", line 393, in <listcomp>
    return [make_row(row) for row in rows]
  File ".conda\envs\3.7\lib\site-packages\razi-0.0.0-py3.7.egg\razi\rdkit_postgresql\types.py", line 43, in process
RuntimeError: Unexpected row value type for a Mol instance

when I try to select less field. I generate a sql

SELECT bfp_to_binary_text("RdkitMol_c5".rdkit_bfp) AS rdkit_bfp 
FROM "RdkitMol_c5" JOIN "Molecules_c5" ON "Molecules_c5".canonical_smiles = "RdkitMol_c5".canonical_smiles 
WHERE "RdkitMol_c5".rdkit_bfp # morganbv_fp('Cc1ccc2nc(-c3ccc(NC(C4N(C(c5cccs5)=O)CCC4)=O)cc3)sc2c1')

then I get a runtime error too,

 File ".conda\envs\3.7\lib\site-packages\sqlalchemy\engine\result.py", line 393, in <listcomp>
    return [make_row(row) for row in rows]
  File "code\razi\razi\rdkit_postgresql\types.py", line 85, in process
    "Unexpected row value type for a Bfp instance")
RuntimeError: Unexpected row value type for a Bfp instance

seem like sqlalchemy can't generate select result. I don't konw what happen? Dost anybody can help me ?

`operator does not exist: bfp %% bfp` error

SQLAlchemy>2.0.0 is using different dialect and handles % sign differently. As a result, the operators defined in tanimoto_sml function are parsed as %% and this causes the operator does not exist: bfp %% bfp error.