[Rdkit-discuss] Ligand conversion problem from 2D to 3D

[Emre A. <emr...@gm...>]

Hello,

I want to convert the 2D ligands I downloaded as sdf format from the ZINC
library to 3D, but almost half of them are not converted to 3D. Some of
them are; ZINC000008214373, ZINC000001530666, ZINC000085545180. 208 ligands
are not converted to 3D in this way. When I run the script, I do not get
any warning or error in IDE. When I look at the output of my Try, Except
commands, I see "ZINC000008214373.sdf : rdDistGeom.EmbedMolecule(mol,
etkdgv3) = Failed
ZINC000008214373.sdf : rdForceFieldHelpers.UFFOptimizeMolecule(mol) =
Failed" It outputs like this for ligands that are not translated to 3D.
When I try different methods, the ligands are converted to 3D. I wonder if
there is something missing or wrong with my script. I would be grateful if
you can help me.

Thank you!

```
from rdkit import Chem
from rdkit.Chem import rdDistGeom
from rdkit.Chem import rdForceFieldHelpers
from rdkit.Chem import rdPartialCharges
import os

ligands_dir = "ligands"
output_dir = "new_ligands"
status_file = "process_status.txt"

if not os.path.exists(output_dir):
    os.makedirs(output_dir)

sdf_files = [f for f in os.listdir(ligands_dir) if f.endswith(".sdf")]

with open(status_file, 'w') as status:
    for sdf_file in sdf_files:
        input_path = os.path.join(ligands_dir, sdf_file)
        output_path = os.path.join(output_dir, sdf_file)
        mol = Chem.MolFromMolFile(input_path)

        # Add hydrogens
        try:
            mol = Chem.AddHs(mol, addCoords=True)
        except:
            status.write(f"{sdf_file} : Chem.AddHs(mol) = Failed\\n")
            continue

        # 3D embedding
        etkdgv3 = rdDistGeom.ETKDGv3()
        embed_status = rdDistGeom.EmbedMolecule(mol, etkdgv3)
        if embed_status == -1:
            status.write(f"{sdf_file} : rdDistGeom.EmbedMolecule(mol,
etkdgv3) = Failed\\n")

        # Compute Gasteiger charges
        try:
            rdPartialCharges.ComputeGasteigerCharges(mol)
        except:
            status.write(f"{sdf_file} :
rdPartialCharges.ComputeGasteigerCharges(mol) = Failed\\n")

        # UFF energy minimization
        try:
            rdForceFieldHelpers.UFFOptimizeMolecule(mol)
        except:
            status.write(f"{sdf_file} :
rdForceFieldHelpers.UFFOptimizeMolecule(mol) = Failed\\n")

        Chem.MolToMolFile(mol, output_path)
```