Hmm, that makes it distinctly trickier. Recursive SMARTS work at the level
of single atoms and their environment, rather than treating a group of
atoms together, so I suspect it isn't possible to create a single SMARTS to
give the match information you need in one go. I'd be very pleased to find
out I'm wrong!
If you could use a small script it's pretty trivial of course -
m = Chem.MolFromSmiles("CCNN")
p1 = Chem.MolFromSmarts("C-C")
p2 = Chem.MolFromSmarts("N-N")
m1 = m.GetSubstructMatches(p1)
m2 = m.GetSubstructMatches(p2)
m1 + m2
which gives ((0, 1), (2, 3)) as required, but if you have a specific need
for the 'single SMARTS' approach that's not much use. Sorry not to be more
helpful...
Chris Earnshaw
On 19 September 2017 at 16:50, James T. Metz <jamestm...@aol.com> wrote:
> Chris,
>
> Thank you for your interesting suggestion, but it is not quite what I
> need.
>
> For example, consider the molecule
>
> m = Chem.MolFromSmiles("CCNN")
>
> I am looking for one SMARTS that using the SMARTS pattern matching
> capability in RDkit would return 2 groups, each group containing the two
> atoms corresponding to CC and NN.
>
> Your suggested recursive SMARTS and code below
>
> pattern = Chem.MolFromSmarts('[$(C-C),$(N-N)]')
> match = m.GetSubstructMatches(pattern)
> match
>
> returns
>
> ((0,), (1,), (2,), (3,))
>
>
> The output I am trying to achieve, instead, is
>
>
> ((0,1), (2,3))
>
>
> Is there a single SMARTS that will do that?
>
>
> Regards,
>
> Jim Metz
>
>
>
>
>
>
> -----Original Message-----
> From: Chris Earnshaw <cgearns...@gmail.com>
> To: James T. Metz <jamestm...@aol.com>
> Cc: Rdkit-discuss@lists.sourceforge.net <rdkit-discuss@lists.
> sourceforge.net>
> Sent: Tue, Sep 19, 2017 10:13 am
> Subject: Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR
>
> Hi
>
> Will the recursive SMARTS [$(C-C),$(N-N)] not do the job?
>
> I'd parse this in English as 'an atom which is EITHER an aliphatic carbon
> singly bonded to an aliphatic carbon OR an aliphatic nitrogen singly bonded
> to an aliphatic nitrogen'.
>
> Regards,
> Chris Earnshaw
>
> On 19 September 2017 at 15:01, James T. Metz via Rdkit-discuss <
> rdkit-discuss@lists.sourceforge.net> wrote:
>
> Dante,
>
> Yes. In principle, if one can figure out all of the possible
> undesired cross
> matches.
>
> Since my goal is to do this in RDkit and generate groups of atoms
> that match, perhaps one approach is to simply use multiple RDkit pattern
> matching statements (with multiple SMARTS), generate the groups of atoms,
> then combine the lists, removing identical groups.
>
> Hmmm... Is there a more straightforward (elegant) solution?
>
> Regards,
> Jim Metz
>
>
>
> -----Original Message-----
> From: Dante <dante.esgrimi...@gmail.com>
> To: James T. Metz <jamestm...@aol.com>
> Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
> Sent: Tue, Sep 19, 2017 8:45 am
> Subject: Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR
>
> Hi Jim,
>
> Could you use the 'NOT' logical operator (!) in combination with recursive
> SMARTS to eliminate the cross-matches?
>
> Cheers,
>
> Dante
>
> On Tue, Sep 19, 2017 at 9:13 AM, James T. Metz via Rdkit-discuss <
> rdkit-discuss@lists.sourceforge.net> wrote:
>
> Hello,
>
> Is it possible to write a single SMARTS for two separate patterns involving
> a Boolean OR?
>
> For example, I want to write a single SMARTS that can match the
> patterns of
>
> [C]-[C]
>
> or
>
> [N]-[N]
>
> I realize that I could write something like
>
> [C,N]-[C,N]
>
> but that would also match "cross" patterns such as
>
> CN and NC which I don't want.
>
> I have tried to write
>
> ([C]-[C]), ([N\-[N]) but I have not been able to get that syntax or
> related
> expressions (variations of parentheses, brackets, etc) to work.
>
> Hence, if someone knows how to combine separate SMARTS expressions into
> a single expression with a Boolean OR, I would be grateful. Thank you.
>
> Regards,
> Jim Metz
>
>
>
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