Marta,
On Tue, Jul 5, 2016 at 11:14 AM, Marta Stępniewska-Dziubińska <
[email protected]> wrote:
>
> To be honest, I expected it to fail :)
>
I'm glad to hear that!
I want to find structures with a defined topology, but allow for
> different bond types. My first idea was to use SMARTS with ~ bonds,
> and it works fine with GetSubstructMatch.
>
Assuming that I'm understanding the idea correctly, your best bet is
probably to use BondCompare.CompareAny. Here's a simple demonstration:
In [15]: m1 = Chem.MolFromSmiles('C=CC')
In [16]: m2 = Chem.MolFromSmiles('CCC')
In [17]: FindMCS((m1,m2),
bondCompare=rdFMCS.BondCompare.CompareAny).smartsString
Out[17]: '[#6]=,-[#6]-[#6]'
I don't really need MCS, I just used it to check different patterns.
> But I expected that FindMCS will throw an exception, rather than
> produce SMARTS it cannot parse.
>
Agreed. Here's the bug report: https://github.com/rdkit/rdkit/issues/968
If you keep an eye on that (or subscribe to it) in github you'll see when
it's fixed.
Best,
-greg
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