The conformation generated is 2D and how to make sure it is a proper conformer as output?

[mw742]

Hello

Thank you for your work and it is useful for fast generating conformers.

I just have a small technical issue here and want to ask.

So I tried to run the default generating conformers using smiles for any random molecule as input.

I tried to run the template command for benzene "python -u script/gen.py --config_path ./config/qm9_default.yml --generator ConfGF --smiles c1ccccc1“
and "python -u script/gen.py --config_path ./config/qm9_default.yml --generator ConfGFDist --smiles c1ccccc1"
but the output rdmol reading from the .pkl files are both 2D and do not contain 3D coordinates.

As first, I though it is benzene and it might be flat.

Then I tried a random example like CCCC, "python -u script/gen.py --config_path ./config/qm9_default.yml --generator ConfGF --smiles CCCC" and the output is also 2D unless I embed it using Rdkit, but if I use Rdkit to embed, then it will change the coordinates of the output and the conformer is actually refine by Rkdit, as shown below:

"(confgf) popzq@GPUSrv:~/桌面/ConfGF-main/Diamond/qm9_default$ python
Python 3.7.16 (default, Jan 17 2023, 22:20:44)
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.

import pandas as pd
data = pd.read_pickle('ConfGF_CCCC.pkl')
print(data)
Data(atom_type=[14], bond_edge_index=[2, 26], d_gen=[128, 1], d_recover=[128, 1], edge_index=[2, 128], edge_length=[128, 1], edge_name=[128], edge_order=[128], edge_type=[128], is_bond=[128], num_pos_gen=[1], num_pos_traj=[1], pos=[14, 3], pos_gen=[14, 3], pos_traj=[70000, 3], rdmol=<rdkit.Chem.rdchem.Mol object at 0x7fa28856d8f0>, smiles="CCCC")
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
rdmol_object = data.rdmol
conf = rdmol_object.GetConformer()
Traceback (most recent call last):
File "", line 1, in
ValueError: Bad Conformer Id
positions = conf.GetPositions()
Traceback (most recent call last):
File "", line 1, in
NameError: name 'conf' is not defined
AllChem.EmbedMolecule(rdmol_object, randomSeed=42)
Traceback (most recent call last):
File "", line 1, in
NameError: name 'AllChem' is not defined
from rdkit import AllChem
Traceback (most recent call last):
File "", line 1, in
ImportError: cannot import name 'AllChem' from 'rdkit' (/home/popzq/anaconda3/envs/confgf/lib/python3.7/site-packages/rdkit/init.py)
from rdkit.Chem import AllChem
AllChem.EmbedMolecule(rdmol_object, randomSeed=42)
0
conf = rdmol_object.GetConformer()
positions = conf.GetPositions()
if positions.shape[1] == 3:
print("The molecule has 3D coordinates.")
else:
print("The molecule has 2D coordinates.")
...
The molecule has 3D coordinates.

"

I was just wondering, is there any way I can get the original model generating 3D output, instead of using Rkdit to generate a conformer? Is that any issue I might miss in running this model?