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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