Dear Sereina,
I'll have a look. I suspect it might have something to do with the MMFF94
aromaticity model, but it could also be a bug.
I'll get back to you later.
Cheers,
p.
> On 3 Aug 2016, at 08:00, Sereina <sereina.rini...@gmail.com> wrote:
>
> Dear all,
>
> I stumbled upon a - to me - rather strange behavior with
> MMFFHasAllMoleculeParams().
>
> I want to generate a molecule from SMILES, check if all MMFF parameters are
> present, add hydrogens and generate conformers. However, the outcome (error
> or not error) depends on the order of checking of the MMFF parameters and
> adding hydrogens.
>
> Everything is fine if I first add the hydrogens:
> In [1]: m = Chem.MolFromSmiles('Cc1nc(=O)c(C[NH3+])c(-c2c[nH]c3ccccc23)[nH]1')
>
> In [1]: m = AllChem.AddHs(m)
>
> Out[2]: AllChem.MMFFHasAllMoleculeParams(m)
> Out[2]: True
>
> In [3]: AllChem.EmbedMultipleConfs(m, numConfs=100)
> Out[3]: <rdkit.rdBase._vecti at 0x111761950>
>
> But here’s what happens when I first check the MMFF parameters:
> In [4]: m = Chem.MolFromSmiles('Cc1nc(=O)c(C[NH3+])c(-c2c[nH]c3ccccc23)[nH]1')
>
> In [5]: AllChem.MMFFHasAllMoleculeParams(m)
> Out[5]: True
>
> In [6]: m = AllChem.AddHs(m)
>
> In [7]: AllChem.EmbedMultipleConfs(m, numConfs=100)
> RDKit ERROR: [08:41:02] Explicit valence for atom # 11 N, 4, is greater than
> permitted
> ---------------------------------------------------------------------------
> ValueError Traceback (most recent call last)
> <ipython-input-17-6b197697e61c> in <module>()
> ----> 1 AllChem.EmbedMultipleConfs(m, numConfs=100)
>
> ValueError: Sanitization error: Explicit valence for atom # 11 N, 4, is
> greater than permitted
>
> Interestingly, if I do the check first, but then remove the hydrogens before
> adding hydrogens, things work again:
> In [8]: m = Chem.MolFromSmiles('Cc1nc(=O)c(C[NH3+])c(-c2c[nH]c3ccccc23)[nH]1')
>
> In [9]: AllChem.MMFFHasAllMoleculeParams(m)
> Out[9]: True
>
> In [10]: m = AllChem.RemoveHs(m)
>
> In [11]: m = AllChem.AddHs(m)
>
> In [12]: AllChem.EmbedMultipleConfs(m, numConfs=100)
> Out[12]: <rdkit.rdBase._vecti at 0x111761a50>
>
> I cannot really explain the behavior. It only happens for some molecules. Is
> MMFFHasAllMoleculeParams() modifying the molecule, i.e. already addying
> hydrogens?
>
> Best,
> Sereina
> ------------------------------------------------------------------------------
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
------------------------------------------------------------------------------
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
