In that case include the cdk-legacy module and use that version of SMSD.
Here's the GIST I previously wrote to align to a subgraph:
https://gist.github.com/johnmay/12797a89f4186bc7da881f1f4a706671
On Wed, 14 Aug 2019 at 18:21, Tim Dudgeon wrote:
> Hi John,
>
> Thanks for that info. I did look
Hi John,
Thanks for that info. I did look into SMSD, but found some problems
using it with the latest CDK [1,2].
Also, the maven version has not been updated since Jun 2016 so I wonder
if its still active?
Let me know if you want help with the utility function you mention.
Happy to help, b
2. Use SMSD or Edmund Duesbury's MCS code. SMSD is a separate library now
as we couldn't smoothly integrate the updates and had tests failing.
3. You can fix atoms in place with the *Set afix* option of the
layout. So you copy the coords from MCS you got, fix these in place whilst
you lay out the
I'm wanting to depict molecules that have been aligned to a the MCS of a
query molecule, and highlight the MCS.
Are there any examples of this? Seems like some of the relevant CDK code
is deprecated, but its not clear what should be used.
As an example:
1. I have a query molecule and a target
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