MoleculeReader.__init__(MoleculeReader, str, str) did not match C++ signature

[mainguyenanhvu]

I tried to use CDPL Chem to read a RDKit output SDF file. However, I encountered an error:

    mol = CDPL_readSDF(temp_file)
  File "~/csv2sdf.py", line 462, in CDPL_readSDF
    reader = CDPLChem.MoleculeReader(input_sd_file)
Boost.Python.ArgumentError: Python argument types in
    MoleculeReader.__init__(MoleculeReader, str)
did not match C++ signature:
    __init__(_object* self, std::istream {lvalue} is, CDPL::Base::DataFormat fmt)
    __init__(_object* self, std::istream {lvalue} is, std::string fmt)
    __init__(_object* self, std::string file_name, CDPL::Base::DataFormat fmt, std::_Ios_Openmode mode=CDPL.Base._base.OpenMode(12))
    __init__(_object* self, std::string file_name, std::string fmt, std::_Ios_Openmode mode=CDPL.Base._base.OpenMode(12))
    __init__(_object* self, std::string file_name, std::_Ios_Openmode mode=CDPL.Base._base.OpenMode(12))

My import:

import CDPL.Chem as CDPLChem
import CDPL.ConfGen as CCfGen
from rdkit import Chem
from rdkit.Chem import AllChem

My output RDKit SDF file:

def prepare_mol_for_SDPL(smiles:str, columns: list, row: pd.Series, temp_file: str):
    """
    Adds hydrogens to the provided SMILES string.
    """
    mol = Chem.MolFromSmiles(smiles)
    mol = Chem.AddHs(mol)
    AllChem.Compute2DCoords(mol)
    for col in columns:
        mol.SetProp(col, str(row[col]))
    mol.SetProp("_InputInChIKey", str(Chem.inchi.InchiToInchiKey(Chem.inchi.MolToInchi(Chem.MolFromSmiles(smiles)))))
    mol.SetProp("_SMILES", str(Chem.MolToSmiles(mol)))
    mol.SetProp("_InChIKey", str(Chem.inchi.InchiToInchiKey(Chem.inchi.MolToInchi(mol))))
    writer = Chem.SDWriter(temp_file)
    writer.write(mol)
    writer.close()

My read function:

def CDPL_readSDF(input_sd_file: str) -> None:
    """
    Retrieves the structure data of each molecule in the provided SD file and outputs it to the console.

    Parameters:
    - input_sd_file (str): Path to the input SD file.

    Refs:
    - https://cdpkit.org/cdpl_python_tutorial/cdpl_python_tutorial.html#retrieving-structure-data-from-mdl-sd-files
    """
    # Create reader for MDL SD-files
    # reader = CDPLChem.FileSDFMoleculeReader(input_sd_file)
    reader = CDPLChem.MoleculeReader(input_sd_file)

    # create an instance of the default implementation of the Chem.Molecule interface
    mol = CDPLChem.BasicMolecule()

    # Iterate over each molecule in the file and retrieve structure data
    try:
        while reader.read(mol):
            return mol
            # try:
            #     if not CDPLChem.hasStructureData(mol):
            #         raise Exception('Error: no structure data available for molecule', Chem.getName(mol))
            #     return mol

            # except Exception as e:
            #     raise Exception('Error: processing of molecule failed: ' + str(e))

    except Exception as e: # handle exception raised in case of severe read errors
        raise Exception('Error: reading molecule failed: ' + str(e))

My main function:

for ind in df.index:
        smiles = df.loc[ind, args.smi_column]
        mol = None
        try:
            try:
                os.remove(temp_file)
            except:
                print()
            temp_file = output_file.replace('.sdf', '_temp.sdf')
            prepare_mol_for_SDPL(smiles, df.columns, df.loc[ind], temp_file)
            mol = CDPL_readSDF(temp_file)
            os.remove(temp_file)

p/s: I took a look at some refs: They both works:

• smi3d
• gen3d original code

Please help me to solve it. Thank you very much.

[seidelt]

Thank you for reporting! This is a duplicate of issue #19 and I will release a fix in the next days...