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, but not sure right now how to approach it.
CDK rendering is so beautiful!
Tim
1.https://github.com/asad/SMSD/issues/9
<https://github.com/asad/SMSD/issues/9>
2. https://github.com/asad/SMSD/issues/10
On 14/08/2019 16:05, John Mayfield wrote:
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<IAtom> afix* option of the
layout. So you copy the coords from MCS you got, fix these in place
whilst you lay out the rest.
One day I will get around to adding a utility function for this but
there is some example code on the mailing list for No. 3, look for
emails from someone at Dotmatics albeit with a substructure match.
On Tue, 13 Aug 2019 at 17:01, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
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 molecule and they share
significant MCS, often with the query being a complete subgraph of
the
target.
2. I identify the MCS
3. Using that MCS I layout the target molecule (e.g. generate 2D
coordinates) fixing the parts that are in the MCS to the coordinates
from the query structure.
4. I then depict that layed out molecule colouring the MCS.
I know how to do #4 - its steps #2 and #3 that I'm unsure about.
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