Greg and Paolo,
Thank you both! Both of those pieces were exactly what I needed.
-Kirk
On Fri, Apr 22, 2016 at 10:15 PM, Greg Landrum <greg.land...@gmail.com>
wrote:
> Hi Kirk,
>
> Paolo has already pointed out the tools to use if you want to have control
> over the process. There's also a convenience function available,
> AllChem.ConstrainedEmbed(), that makes the process a bit easier:
>
> http://www.rdkit.org/docs/api/rdkit.Chem.AllChem-module.html#ConstrainedEmbed
>
> Best,
> -greg
>
>
>
> On Fri, Apr 22, 2016 at 10:14 PM, Robert DeLisle <rkdeli...@gmail.com>
> wrote:
>
>> In working with RDKit I've been able to align 2D structures based upon a
>> common core of MCS using
>>
>> AllChem.GenerateDepictionMatching2DStructure(m,p)
>>
>> The next step for me is to generate 3D structures and align them based
>> upon that same common core. Obviously this leads to multiple steps, not
>> the least of which is generating conformations that are consistent across
>> the common core for the various molecules. I seem to recall the ability to
>> generate a conformation and minimize it (either UFF or MMFF) and apply
>> constraints based upon an input substructure, but I cannot find the details.
>>
>> Any tips to accomplish this one?
>>
>> -Kirk
>>
>>
>>
>>
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