[Rdkit-discuss] problem when doing Chem.MolFromSmiles()

[Chencheng Fan]

Hello everyone, I meet a problem that I don’t understand how it happens and how to solve it. First, I generate an rdkit_object from reading a mol file(Porphyrin molecule). Then generate Smiles from the rdkit_object and save the Smiles string in a parameter. Then use the parameter to generate rdkit_object. The code works well until now. However, if I directly try to generate rdkit_object from the Smiles string, it will return SMILES Parse Error:syntax error for input. I appreciate very much for your help!  Have a good day! Best wishes Cheng The mol file is:

Porphyrin.mol
Description: chemical/molfile

Code is: from __future__ import print_function import rdkit from rdkit import Chem from rdkit.Chem import AllChem Corefile='Porphyrin.mol' core_rdkit_object=Chem.MolFromMolFile(Corefile) core_smiles=Chem.MolToSmiles(core_rdkit_object) print('core_smiles',core_smiles) core=Chem.MolFromSmiles(core_smiles) print('rdkit_object',core) coreh=Chem.AddHs(core) AllChem.EmbedMolecule(coreh) print(Chem.MolToMolBlock(coreh)) core_smiles_2='C1=C/C2=C/c3ccc4n3[Zn]n3/c(cc/c3=C/C3=N/C(=C\4)C=C3)=C\C1=N2' core=Chem.MolFromSmiles(core_smiles_2) print(core) coreh=Chem.AddHs(core) AllChem.EmbedMolecule(coreh) print(Chem.MolToMolBlock(coreh)) Error is: core_smiles        C1=C/C2=C/c3ccc4n3[Zn]n3/c(cc/c3=C/C3=N/C(=C\4)C=C3)=C\C1=N2 rdkit_object.       <rdkit.Chem.rdchem.Mol object at 0x2ab4209e1b40> [11:50:20] UFFTYPER: Unrecognized atom type: Zn1+2 (9) [11:50:20] SMILES Parse Error: syntax error for input: 'C1=C/C2=C/c3ccc4n3[Zn]n3/c(cc/c3=C/C3=N/C(=C)C=C3)=C\C1=N2' None Traceback (most recent call last):  File "test-generate_core.py", line 21, in <module>    coreh=Chem.AddHs(core) Boost.Python.ArgumentError: Python argument types in    rdkit.Chem.rdmolops.AddHs(NoneType) did not match C++ signature:    AddHs(RDKit::ROMol mol, bool explicitOnly=False, bool addCoords=False, boost::python::api::object _onlyOnAtoms_=None, bool addResidueInfo=False)

_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss