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
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 avai
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,
Dear Kirk,
in $RDBASE/Code/ForceField/Wrap/testConstraints.py you'll find examples
how to set constraints on internal coordinates
with {MM,U}FFAddDistanceConstraint(), {MM,U}FFAddAngleConstraint(),
{MM,U}FFAddTorsionConstraint. You may also set harmonic positional
constraints on Cartesian coor
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
l
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