On Mon, Oct 30, 2017 at 10:14 PM, Andy Jennings <andy.j.jenni...@gmail.com>

> Next question on this topic, as I can't find it from digging into various
> sources.
> The solution you pointed me to works very well. I'm now expanding it to
> compare the 'color' between two conformations from different molecules. I
> cannot, however, see how to do this. Is there an option such as
> 'confId1/confId2' like the ShapeTanimotoDist routine?

Interesting question. It looks like the answer is currently "no".
The underlying C++ feature objects do have a setActiveConformer() method
that would allow you to do this, but it seems like this isn't currently
available in Python.

It's not hard to fix that (and I will), but that doesn't help you
immediately. In the short term, you probably need to create single
conformer molecules for this. Here's a way to do that:

In [6]: AllChem.EmbedMultipleConfs(m)

In [7]: nm = Chem.Mol(m)

In [8]: nm.RemoveAllConformers()

In [10]: nm.AddConformer(m.GetConformer(2),assignId=True)
Out[10]: 0

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