Hi Emre!
You can get more detailed info on failed conformer generations through
rdDistGeom.EmbedFailureCauses, see:
https://greglandrum.github.io/rdkit-blog/posts/2023-05-17-understanding-confgen-errors.html
Bests,
--
Amy He
Hadad Lab @ OSU
he.1...@osu.edu
From: Emre Apaydın <emreapaydin1...@gmail.com>
Date: Wednesday, January 10, 2024 at 8:47 AM
To: rdkit-discuss@lists.sourceforge.net <rdkit-discuss@lists.sourceforge.net>
Subject: [Rdkit-discuss] Ligand conversion problem from 2D to 3D
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
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)
```
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