Hi all,I have an issue with ConstrainedEmbed and I cannot figure out what exactly causes this. I have a molecule C[C@@H]1CCCCC1=O with 3D coordinates in 1.mol file (attached). And I want to generate coordinates for another structure with this core -
C[C@@H]1CC[C@H](O)CC1=O.
This is usual way which causes issue with embedding and the corresponding error.
mol_parent = Chem.MolFromMolFile('1.mol')
mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
try:
mol = AllChem.ConstrainedEmbed(mol_child, mol_parent)
except ValueError as e:
print(e)
If I add explicit hydrogens the issue disappears.
mol_parent = Chem.MolFromMolFile('1.mol')
mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
mol = AllChem.ConstrainedEmbed(Chem.AddHs(mol_child), mol_parent)
If I do not use pre-defined coordinates - everything works well.
mol_parent = Chem.MolFromSmiles('C[C@@H]1CCCCC1=O')
AllChem.EmbedMolecule(mol_parent)
mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
mol = AllChem.ConstrainedEmbed(mol_child, mol_parent)
Does ugly coordinates in 1.mol file cause the embedding issue? Or the
issue is caused by some implicit properties of a molecule? How to solve
this properly?
Kind regards, Pavel.
1.mol
Description: MOL mdl chemical test
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
