Hi Greg,

Actually this question is relevant to my recent thread about aligning MCS
of 2 compounds. As also seen in the code I have posted in my last email, I
first generate N conformers of each query compound and then optimize them
using distance restraints in order to superimpose their MCS with that of
the reference ligand. So I tried the new code as you suggested and although
less, I still get wrong geometries for some compounds, particularly in the
aromatic rings. I tried to repair the wrong conformers by copying the
original bondlengths, angle and dihedral values from my starting
conformation which always has correct geometry. However I get the following
errors whenever I encounter aromatic atoms:

from Chem.rdMolTransforms.SetDihedralDeg()

> ValueError: bond (j,k) must not belong to a ring

from Chem.rdMolTransforms.SetAngleDeg()

> ValueError: bonds (i,j) and (j,k) must not both belong to a ring

from Chem.rdMolTransforms.SetBondLength()

> ValueError: bond (i,j) must not belong to a ring

How can I reset the bondlengths, angles and dihedrals of the aromatic rings
to their initial values?


On 23 February 2017 at 20:52, Greg Landrum <greg.land...@gmail.com> wrote:

> One thing you both might find useful is generating conformers using the
> new ETKDG code. The parameters for this are described in the documentation.
> Look for the "Working with 3D molecules" section of the getting started
> guide.
> That code should solve most, if not all, of the problems you are
> discussing.
> -greg
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