The reason constraint embed didn’t work is the molecule simply can’t be
embedded using the rdkit’s algorithm.
> In [25]: mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
>
>
> In [26]: AllChem.EmbedMolecule(mol_child)
>
> Out[26]: -1
See more discussion here:
https://github.com/rdkit/rdkit/issues/2996
<https://github.com/rdkit/rdkit/issues/2996>
The SMILES you posted looks valid to me and doesn’t look that complicated, but
the anyway I think
somehow the RDKit’s algorithm tripped up and couldn’t finish embedding without
some help. Hope
someone with more in-depth insight can help here.
Anyway, for a walk around, adding H seems to do the trick:
> In [39]: mol = AllChem.AddHs(mol_child)
>
>
> In [40]: AllChem.EmbedMolecule(mol)
>
> Out[40]: 0 # worked
>
> In [41]: AllChem.ConstrainedEmbed(mol, mol_parent)
>
> Out[41]: <rdkit.Chem.rdchem.Mol at 0x7fe8000f6f80> # also worked
>
Sunhwan
> On Jul 7, 2020, at 12:36 AM, Pavel Polishchuk <[email protected]>
> wrote:
>
> 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>_______________________________________________
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