Thanks, Curt! I'll give those a look. It'll give me a very good reason to
start digging into SciPy a bit more and exploit the added functionality
that will bring.
Regarding my original question and for anyone else that might be
interested...
I did indeed find an answer through a lot of code
Next up is clustering...
I've got about 350 structures to cluster and I've worked through the
example code from the RDKit Cookbook (
http://www.rdkit.org/docs/Cookbook.html#clustering-molecules). All seems
well and good there, but I would like to see the dendrogram. I see that
there is a
Dear Robert,
the reason of the failure is that MMFF uses its own aromaticity model
(see
http://www.rdkit.org/docs/GettingStartedInPython.html#working-with-3d-molecules).
Therefore, after calling
AllChem.MMFFOptimizeMolecule(mols[0])
you will need to add the following call:
RDKitters,
I'm working on a project in which I want to align a collection of
structures with their most similar structures and display the results in
PyMOL. To accomplish this, I've built a Python script similar to the one
attached here in which I start with pairs of structures, find the MCS of
4 matches
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