EmbedMolecule() returns the coordinates 0, 0, 0 for some peptides derived from MolFromHELM

[KYU49]

Describe the bug
After version 2024_03_1, which changes EmbedMolecule() incompatibly, EmbedMolecule() returns the coodinates 0, 0, 0 for all atoms of some peptides derived from MolFromHELM.
e.g.

ATOM      1  N   PHE A   1       0.000   0.000   0.000  1.00  0.00           N  
ATOM      2  CA  PHE A   1       0.000   0.000   0.000  1.00  0.00           C  
ATOM      3  C   PHE A   1       0.000   0.000   0.000  1.00  0.00           C  
...

To Reproduce
The below python codes works well on rdkit ver. 2023.03.3, but it does not work for seq3 on ver. 2024.03.2.

    seq1 = "GGGGGGG"    # EmbedMolecule() works well
    seq2 = "FFFFFF"     # EmbedMolecule() works well
    seq3 = "FFFFFFF"    # EmbedMolecule() returns coordinates 0, 0, 0 without any error

    tempPdbName = "./" + seq1 + ".pdb"
    m = Chem.MolFromHELM("PEPTIDE1{" + str.join(".", list(seq1)) + "}$$$$")
    AllChem.EmbedMolecule(m)
    Chem.MolToPDBFile(m, tempPdbName)

    tempPdbName = "./" + seq2 + ".pdb"
    m = Chem.MolFromHELM("PEPTIDE1{" + str.join(".", list(seq2)) + "}$$$$")
    AllChem.EmbedMolecule(m)
    Chem.MolToPDBFile(m, tempPdbName)
    
    tempPdbName = "./" + seq3 + ".pdb"
    m = Chem.MolFromHELM("PEPTIDE1{" + str.join(".", list(seq3)) + "}$$$$")
    AllChem.EmbedMolecule(m)
    Chem.MolToPDBFile(m, tempPdbName)

Expected behavior
The pdb files of seq3 has non-zero coodinates like seq1 and seq2.

Configuration (please complete the following information):

• RDKit version: 2024_03_1 (not work), 2023_03_3 (work well)
• OS: Windows 10
• Python version (if relevant): 3.9
• Are you using conda?: Yes
• If you are using conda, which channel did you install the rdkit from?: conda-forge

[joseerlang]

Hi there ,

following the documentation of the code you provide, it seems that the problem you have is that you are missing to explicitly add the hydrogens to the molecule before calling the EmbedMolecule method. With the code below you should be fine with the seq3 case. The change from what I see in Greg's source code @greglandrum , is made in this ticket #3807

import rdkit
from rdkit.Chem import AllChem,rdmolops
from rdkit import Chem
seq1 = "GGGGGGG"    # EmbedMolecule() works well
seq2 = "FFFFFF"     # EmbedMolecule() works well
seq3 = "FFFFFFF"    # EmbedMolecule() returns coordinates 0, 0, 0 without any error

tempPdbName = "./" + seq3 + ".pdb"
m = Chem.MolFromHELM("PEPTIDE1{" + str.join(".", list(seq3)) + "}$$$$",)
m= rdmolops.AddHs(m)
AllChem.EmbedMolecule(m)
Chem.MolToPDBFile(m, tempPdbName)

[KYU49]

Thank you for your help. I was struggling to understand the cause of the problem, so your guidance was very helpful. I checked the ticket you mentioned, and it seems that displaying an error would make it clearer.