Merge pull request #4173 from RosettaCommons/roccomoretti/fix_patch_dangling_conn_icoor
Attempt to fix (some) issues with the dangling ICOOR connect. (Stopgap fix for issue #4153.) So
Add something to SET_POLYMER_CONNECT patch operation to re-do the dangling connections based on ideal xyz geometry and other atoms in the residue type. To work best, this means that the SET_POLYMER_CONNECT should come after SET_ICOOR records in the patch file. This doesn't fix everything, and those patches with issues should probably still be fixed to give a proper ICOOR record.