Hello Greg,
By "3D similarity of aligned molecules based on molecular shape" do you mean
ShapeTanimotoDist ?
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.
Thank you!
Ling
>________________________________
> From: Greg Landrum <[email protected]>
>To: Z.L. Deng <[email protected]>
>Cc: RDKit Discuss <[email protected]>
>Sent: Tuesday, September 24, 2013 12:15 AM
>Subject: Re: [Rdkit-discuss] Does RDKit support 3D small molecular alignment
>
>
>
>Hi,
>
>
>On Tue, Sep 24, 2013 at 1:05 AM, Z.L. Deng <[email protected]> wrote:
>
>Does RDKit support 3D small molecular alignment(flexible, rigid) and 3D
>molecular similarity calculation (Like surflex-sim do)?
>>
>>
>
>
>The code supports rigid alignment based on a user-provided atom mapping
>between the two molecules, and 3D similarity of aligned molecules based on
>molecular shape.
>
>
>There is also a proof-of-concept implementation of a rigid
>shape-based-alignment algorithm, but that's not something anyone should
>actually use.
>
>
>-greg
>
>
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