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Revisions №56

branch: release 「№56」
Commited by: Andy Watkins
GitHub commit link: 「fb3dbb3db2c16719」
Difference from previous tested commit:  code diff
Commit date: 2015-05-13 23:33:18

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.