First: the reason the RDKit does not parse things like:
In [2]: p = Chem.MolFromSmarts('([Cl-].[Na+])')
[05:58:01] SMARTS Parse Error: syntax error while parsing: ([Cl-].[Na+])
[05:58:01] SMARTS Parse Error: Failed parsing SMARTS '([Cl-].[Na+])' for
input: '([Cl-].[Na+])'
In [3]: p =
Thanks Ivan -- very helpful.
Is there any consensus on idioms for identifying multiple moieties in the
same fragment? Do I have to use len(mol.GetSubstructMatches(patt)) > 1 as
some kind of selector and then do some kind of graph traversal routine to
see if any of the matches are covalently
Hi Curt,
According to
https://www.rdkit.org/docs/RDKit_Book.html#smarts-support-and-extensions ,
it's not supported:
Here’s the (hopefully complete) list of SMARTS features that are *not*
> supported:
>
>- Non-tetrahedral chiral classes
>
>
>- the @? operator
>
>
>- explicit atomic
Hi rdkit fiends!
The [Daylight SMARTS example page](
https://daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html)
gives several examples for "multiple group" smarts, including these strings:
([Cl!$(Cl~c)].[c!$(c~Cl)])
([Cl]).([c])
([Cl].[c])
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