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:
AllChem.SanitizeMol(mols[0],
sanitizeOps = AllChem.SanitizeFlags.SANITIZE_KEKULIZE \
| AllChem.SanitizeFlags.SANITIZE_SETAROMATICITY)
This will fix your problem.
Kind regards,
Paolo
On 05/14/2016 07:07 AM, Robert DeLisle wrote:
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 those structures, create a template based on the MCS and a
3D conformation of the structure of interest, and then generate a
constrained conformation of a query structure. I tried to comment the
attached code enough to lead you through the process.
What I find is that quite often, the ConstrainedEmbed() function fails
with the error "molecule doesn't match the core" which seems very odd
since the pairs for which it fails are very similar. The attached .png
shows one such pair and their MCS.
What I've found is that when I generate a 3D conformation for the
first structure and optimize it with MMFF (MMFFOptimize), this often
causes GetSubstructMatch to fail finding the MCS within the
structure. If instead I used UFFOptimize, everything seems to work OK
most of the time.
In my code, I've noted where the error occurs and flanked it with some
print statements to show what happens. Specficially, at like 36 I have
the MMFFOptimize line, and at 37 the UFFOptimize line. I've also
attached a set of structures for which MMFF fails.
While using UFFOptimize produces great results, I'm curious regarding
why MMFFOptimize creates a problem. And, whether this is a bug which
should be fixed, or just a glitch related to atom typing and other
parameterizations that occur with MMFF.
Thanks for any explanation or ideas.
-Kirk
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