Hello,
I know that chem B should be aligned to chem A, but I am not sure what to
do next with the AlignMol() since it returns a RMS value. How can I find
the 3D coords of B from the RMS value?
Thank you so much for your time and consideration.
Phuong Chau
On Mon, Jul 30, 2018 at 9:09 PM, Greg Landrum <[email protected]>
wrote:
> 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/rdkit-discuss@lists.
> sourceforge.net/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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>
--
Phuong Chau
Smith College '20
Engineering Major
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