Implement a "custom core"-like filter

[IAlibay]

Create a filter based on a user supplied SMARTS string that would effectively define the maximum core region that could be retained within a mapping.

Anything that falls outside of that region would be automatically treated as alchemical.

[jthorton]

Because Kartograf is sensitive to alignment, there is a chance that the full custom core would not be present in the suggested mapping before this filter is applied, in that case it should just return the maximum part of the common core as possible.