Cysteines now become disulfides by the application of the disulfide patch.
1. The same goes for D-cysteine, homocysteine, D-homocysteine, beta-3-cysteine, penicillamine, d-penicillamine, and... any other disulfide residue type we hope to introduce.
2. So instead of incorporating two residue types, just type "FORMS_DISULFIDE_BOND" on the properties line of your params file (next to other standards like PROTEIN) and add a case to the disulfide patch.
3. A small number of integration test changes are expected. match_1n9l changes because it relies on the number of residue types in the name3map and it might require a special cysteine derived residue type without a HG to properly represent catalytic cysteines. dock_with_hotspot_place_simultaneously, remodel_disulfides_rosettascripts, inverse_rotamer_remodel have been bug-fixed, essentially--they were checking for a type().name() of CYD, which is a no-no in any version of Rosetta! @jadolfbr confirms that the antibody_designer test is likely responding to an uninitialized variable and that I should go ahead and merge.