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> 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. > > > > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user >
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