Re: [Rdkit-discuss] Does RDKit support 3D small molecular alignment

[Greg L. <gre...@gm...>]

On Wed, Sep 25, 2013 at 2:45 AM, S.L. Chan <sl...@ya...> wrote:

> Hello Greg,
>
> By "3D similarity of aligned molecules based on molecular shape" do you
> mean
> ShapeTanimotoDist ?
>

 Correct; ShapeTanimotoDist and ShapeProtrudeDist (more suitable for
comparing molecules of different sizes).

 Also are there any integrated examples on how to use the pharmacophore
> packages
> like Chem.FeatMap, Chem.Pharm2D, Chem.Pharm3D etc. ? I found the manual
> pages
> but some more guidance would be helpful, preferably with the Python
> interface.
>

There is some documentation for using the 2D pharmacophore fingerprints and
chemical features in the "Getting Started" book:
http://www.rdkit.org/docs/GettingStartedInPython.html#chemical-features-and-pharmacophores

There's not currently anything for FeatMap or the Pharm3D functionality. If
there's demand from the rdkit community, I could start thinking about
adding something there.

-greg