On 07/25/2017 05:45 AM, Katrina Lexa wrote:
Hi All,
I'm relatively new to RDKit, so I apologize for what may be a silly
question. I'd like to generate a set of local minimum conformations
around my input conformation, using a set of defined flat bottom
potentials (0.2, 0.6, 1.0, and 1.4), in order to better compare my bound
conformation with its unrestrained minimum.
Ultimately, I'd like to write a script that reads in one input 3D
conformation and prints out the energy and rmsd (and structure) of those
local minimums as well as the lowest energy unrestrained conformation.
There are plenty of examples of conformer generation scripts for RDKit,
but I'm struggling with the constraints piece. I see the MMFFFixedAtoms
& MMFFPositionConstraints code, but based on the code it's not obvious
to me whether it's possible to implement either as a constraint on all
atoms in my input molecule. Is there a way or is there another route I
should be taking?
Maybe this can give you some inspiration:
"3D diverse conformers generation using rdkit"
https://github.com/UnixJunkie/smi2sdf3d
Thanks for the help,
Katrina
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