Hi Phuong,
In order to use AlignMol() you need to know the mapping (i.e. which atoms
should be aligned to which) between the two molecules, so this is good if
chemical A and chemical B share a common core or scaffold that you would
like to align. If you don't know the mapping in advance then you can use
the Open3D align functionality.
Here's an example showing how to use both approaches:
https://www.rdkit.org/docs/Cookbook.html#d-functionality-in-the-rdkit
And, what may be helpful, a thread from a couple years ago that gets into
some details about Open3DAlign:
https://www.mail-archive.com/[email protected]/msg05661.html
-greg
On Tue, Jul 31, 2018 at 1:18 AM Phuong Chau <[email protected]> wrote:
> Hello everyone,
>
> I am trying to build a code that can take input as a SMILES string of
> chemical A and output a 3D coordinates of chemical B that aligns with
> chemical A's 3D coordidates. I am searching through rdkit functions and
> found AlignMol() which returns RMS value and AlignMolConformers()--I am not
> sure what this function returns. Would you please help me to know which
> functions I should use in order to achieve my purpose?
>
> Thank you so much for your time and consideration.
> Phuong Chau
>
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