To add support for input structures with missing residues due to loop_replacement

[pablosanchezizquierdo]

The automatization will fail in the mutlist rule because get_mutlist.py exists if it finds missing residues. By just adding the -s flag to the script we force it to keep going even though it finds a missing residue and then it outputs the mutlists without those residues. We should only add this flag to the command when a loop_replaced input is used