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 coordinates with
{MM,U}FFAddPositionConstraint() and fix atoms by setting their gradient
to 0 during minimization with AddFixedPoint().
The relevant Python API documentation is here:
http://www.rdkit.org/docs/api/rdkit.ForceField.rdForceField.ForceField-class.html
Cheers,
p.
On 04/22/2016 09:14 PM, Robert DeLisle wrote:
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 least of which is generating conformations that are consistent
across the common core for the various molecules. I seem to recall
the ability to generate a conformation and minimize it (either UFF or
MMFF) and apply constraints based upon an input substructure, but I
cannot find the details.
Any tips to accomplish this one?
-Kirk
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