Re: [Rdkit-discuss] Ligand conversion problem from 2D to 3D
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
Date: Wednesday, January 10, 2024 at 8:47 AM
To: 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; ZINC08214373, ZINC01530666, ZINC85545180. 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; ZINC08214373, ZINC01530666, ZINC85545180. 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
"ZINC08214373.sdf : rdDistGeom.EmbedMolecule(mol, etkdgv3) = Failed
ZINC08214373.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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[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; ZINC08214373, ZINC01530666, ZINC85545180. 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 "ZINC08214373.sdf : rdDistGeom.EmbedMolecule(mol,
etkdgv3) = Failed
ZINC08214373.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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[Rdkit-discuss] mmpdb 3.1
Hi everyone, We have released mmpdb 3.1, which you can get from https://github.com/rdkit/mmpdb . mmpdb 3.0, released May 2023, merged three development tracks: - create and query 1-cut med chem transformations as described in Awale et al., The Playbooks of Medicinal Chemistry Design Moves, J. Chem. Inf. Model. 2021, 61, 2, 729–742 - support indexing large datasets on a distributed cluster - replace the hash-based fingerprint environment with a SMARTS/pseudo-SMILES description Version 3.1 adds support for the 2- and 3-cut med chem transformations described by Awale et al. There are also a few feature improvements, some performance tuning, and bug fixes. See the CHANGELOG for details. Andrew da...@dalkescientific.com ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
