Infernal mapping not working for "depaired" and "constrained" structures

[AntonPetrov]

Infernal-driven mapping does not work in 2 cases:

1. For tRNAs there is a depairing step to remove non-canonical basepairs so that the number of basepairs is different between the template and the Infernal-driven mapping. As a result, R2DT falls back to Traveler mapping between the structures.

2. The same situation occurs during constrained folding, except the basepairs are added to the mapping.

The solution would be either not to use Infernal driven mapping in these cases in the first place, or modify the template on the fly, removing basepairs for depaired structures or adding basepairs for constrained folding. Example sequences can be found in the Mito-vert and constraint unit tests.