Dear Pavel and Sunhwan,
Please note that hydrogens should always be added for the embedding algorithm
to work properly (i.e. it’s not a walk around but what should be done).
See also Section “Working with 3D Molecules” in
https://www.rdkit.org/docs/GettingStartedInPython.html
Best regards,
Sereina
> On 7 Jul 2020, at 21:26, Sunhwan Jo <sunhw...@gmail.com> wrote:
>
>
> 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 <pavel_polishc...@ukr.net
>> <mailto:pavel_polishc...@ukr.net>> 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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>
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