Feature mapping diagnostic

[lohedges]

BioSimSpace.Align.matchAtoms now tells users when it has probably returned a sub-optimal mapping. After computing the default MCS it looks for mapped atoms that have an unmapped heavy-atom neighbour of the same element on both molecules, i.e. attachment points where the search stopped symmetrically, which usually means a pairable atom was missed. If it finds any, it re-runs the MCS with ringMatchesRingOnly relaxed and compares: only if the second mapping preserves every original pair and extends it sensibly (heavy to heavy, hydrogen to hydrogen) does it emit a UserWarning suggesting mcs_kwargs={'ringMatchesRingOnly': False}. The check is purely observational, i.e. the originally computed mapping is always what gets returned, and it fires only where the advice can be acted on, so it is suppressed for internal callers such as rmsdAlign, flexAlign, the ROI path and ATM setup, which offer no way to pass MCS options through. The existing test set produces no false positives, but this is something that should be monitored over the current development cycle.

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