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

Question

I tried to use CDPL Chem to read a RDKit output SDF file following this codebase. 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.

Answer 1

I found that this is because of the conflicts when importing rdkit and CDPL in the one file like reply from authors. They are trying to fix this problem in the next release.

I will close this post because there are no other ways to fix except splitting code into two files like the original source.