Re: [Rdkit-discuss] ConstrainedEmbed issue

[Sunhwan Jo <sun...@gm...>]

Makes sense :)


> On Jul 7, 2020, at 12:35 PM, Sereina Riniker <ser...@gm...> wrote:
> 
> 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 <https://www.rdkit.org/docs/GettingStartedInPython.html>
> 
> Best regards,
> Sereina
> 
> 
> 
>> On 7 Jul 2020, at 21:26, Sunhwan Jo <sun...@gm... <mailto:sun...@gm...>> 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 <pav...@uk... <mailto:pav...@uk...>> 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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