Hello
This may be just an example that you picked out of many, however why don't
you just make this atom an 'any atom'? It's in a ring and normally hydrogen
don't come up in rings.
Best
Peter
On Thu, 17 Sep 2015 at 6:24 am, Andrew Dalke <[email protected]>
wrote:
> On Sep 16, 2015, at 9:57 PM, Bodle, Christopher R wrote:
> > I am having trouble with RDKit correctly interpreting the SMARTS
> character [!#1], which should be interpreted as "any atom not hydrogen.
>
> I've been looking at your emails but it's difficult for me to figure out
> what you are doing. Can you generate a smaller reproducible?
>
> My guess is that you are looking at the RDKit depiction of a molecule
> generated from a SMARTS string. This is a query molecule. As I recall,
> this is incomplete, and there is an open call out for someone interested in
> generating a better query depiction. If that's the case, then what you see
> is inability of the renderer to display a "not". This shouldn't affect the
> ability to match a molecule.
>
> I also don't understand this:
>
> > My SMARTS input:
> > [#6]-1(=[!#1]-[!#1]=[!#1]-[#7](-[#6]-1=[#16])-[#1])-[#6]#[#7]
> >
> > Now when I do Chem.MolFromSmarts, my mol representation has hydrogens at
> those three positions, and as such I can't do sanitization of the molecule
> because since it has hydrogens in the !#1 positions, there is a valency
> conflict.
>
> It doesn't make sense to me to do sanitization of molecule that came from
> a SMARTS query.
>
> It looks like you have tried to convert a query-based molecule into a more
> chemical molecule. That is, I can reproduce some of what you report by
> using:
>
> >>> from rdkit import Chem
> >>> mol =
> Chem.MolFromSmarts("[#6]-1(=[!#1]-[!#1]=[!#1]-[#7](-[#6]-1=[#16])-[#1])-[#6]#[#7]")
> >>> Chem.MolToSmiles(mol)
> '[H]N1[H]=[H][H]=C(C#N)C1=S'
>
> This produces a nearly meaningless conversion. For example, consider:
>
> >>> mol = Chem.MolFromSmarts("[#92,#93][$(N=N)]")
> >>> Chem.MolToSmiles(mol)
> '[*][U]'
> >>> mol = Chem.MolFromSmarts("[#93,#92][$(N=N)]")
> >>> Chem.MolToSmiles(mol)
> '[*][Np]'
>
> When there is a choice of atoms, it picks the first, given 'U' and 'Np'
> when I swap the two element numbers. And it shows a recursive SMARTS as a
> '*'.
>
> As far as I can tell, the "[!#1]" works correctly. Here's a case where it
> matches an 'N':
>
> >>> pat = Chem.MolFromSmarts("C-[!#1]-C")
>
> >>> mol = Chem.MolFromSmiles("CNC")
> >>> mol.HasSubstructMatch(pat)
> True
>
> RDKit won't parse a 2-valent hydrogen by default:
>
> >>> mol = Chem.MolFromSmiles("C[H]C")
> [00:15:07] Explicit valence for atom # 1 H, 2, is greater than permitted
>
> but if I disable sanitization, I can show that the pattern doesn't match
> this molecule:
>
> >>> mol = Chem.MolFromSmiles("C[H]C", sanitize=False)
> >>> mol.HasSubstructMatch(pat)
> False
>
> And to double-check that the sanitize flag isn't doing something odd:
>
> >>> mol = Chem.MolFromSmiles("C[N]C", sanitize=False)
> >>> mol.HasSubstructMatch(pat)
> True
>
> Since the SMARTS pattern doesn't work for you, but does seem to work for
> me, could you give a test case which is just the SMILES/SMARTS or
> molfile/SMARTS combination which gives the failure? That is, without the
> incomplete scaffolding that you showed.
>
>
> Cheers,
>
> Andrew
> [email protected]
>
>
>
>
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