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.

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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?