Kevin,
Thank you for your quick reply and the references. It seems like you've
thought about this problem a bit and the ring concatenation bit is a great
idea. However, I couldn't download/use your code off of Github. Is there
any chance you could copy/paste me some of the VB? Or put it in a gist on
github?
Thanks!
zach cp
On Mon, Jan 8, 2018 at 12:42 PM, Kevin Lawson <klawson...@gmail.com> wrote:
> Hi Zach
>
> LICSS (https://github.com/KevinLawson/excel-cdk) tackles this problem by
> using text manipulation of Smiles. This approach is made robust by using
> the 'Dot Disconnect' trick, described in this context by the authors of
> SMILIB: (Schüller, Andreas & Schneider, Gisbert & Byvatov, Evgeny. (2003).
> SMILIB: rapid assembly of combinatorial libraries in SMILES notation. QSAR
> & Combinatorial Science. 22. 719 - 721. 10.1002/qsar.200310008). Basically,
> R groups are combined by denoting the connection points with the notation
> used for ring junctions and using a '.' to concatenate the two fragments to
> be joined. This creates legal SMILES for the enumerated molecules. In
> LICSS, this SMILES is then checked and standardised by reading in each
> enumerated SMILES string into CDK and re-outputing SMILES for the resulting
> AtomContainer. The text manipulation of the SMILES is very fast and LICSS
> accomplishes this with simple Visual Basic. If you are interested in the
> VBA code for enumeration, install LICSS, then with the VBA window in Excel
> open [Alt F11] look at the EnumerateWorkSheet subroutine (and the doRecEnum
> function it calls) - both in the SSS module. If you don't have Excel then I
> can send you the code as text which you could adapt and improve as
> necessary...
>
> Best wishes
>
> Kevin
>
> On Mon, Jan 8, 2018 at 4:53 PM, Zach Charlop-Powers <
> zach.charlop.pow...@gmail.com> wrote:
>
>> Hi CDK-Users,
>>
>> I am wondering if anyone has a suggestion on the best way to
>> combinatorially expand R groups.
>>
>> Lets say that I have three R groups and three possibilities for each
>> group. What would be the best way to generate all 27 of the compounds? I
>> can imagine it would be possible to use string replacement in SMILES but
>> that seems a bit brittle. Is there a way to do PseudoAtom substitution
>> with CDK itself? I'm asking here before poking around the API in the
>> hopes that this is an easy problem that is already solved.
>>
>> Thanks,
>> zach cp
>>
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