Updating release_debug_no_symbols build mode by adding -ffloat-store compilation flag. This should make this mode more ‘debug-like’. Adding this flag also lead to hard failure of previously passed fragmentpicker_integration_demo integration test.
Merge pull request #557 from RosettaCommons/kimdn/sw_unit
[update of SandwichFeatures]
- added unit test
- much better dependency definition (3 features are required)
- clearer comment in integration test
Merge pull request #527 from RosettaCommons/revert-517-jadolfbr/antibody_design
Revert "Jadolfbr/antibody design" temporarily
Since this merge seems to have caused intermittent instabilities in a number of integration tests in release_debug mode, I'm temporarily reverting it until we can track down the source of those instabilities. (This isn't meant as a condemnation or criticism of you, @jadolfbr! I know that the problems didn't show up when you tested this branch in commits.) Once we figure out what's going wrong, we can re-merge.
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.
Merge pull request #494 from RosettaCommons/vmullig/fix_atomtree_mover
Removing FoldTree reordering in the parse_my_tag() function of the AtomTree mover.
If the user does not want a FoldTree rooted on residue 1, he/she should not get a Foldtree rooted on residue 1.
No integration test changes or unit test failures expected.
Merge pull request #471 from RosettaCommons/vmullig/z_is_for_zibo_that_good_enough_for_me
Adjusting z1_offset parameter in helical bundle code to match Grigoryan paper's convention.
This adds a correction factor so that z1_offset is measured as the offset along the global z-axis, in Angstroms, rather than as the offset along the local helix axis. This is intended to match Grigoryan and DeGrado (2011) J. Mol. Biol. 405(4):1079-1100.
Tasks:
-- Add correction factor.
-- Double-check that this does, indeed, produce the correct offsets.
-- Update documentation.
-- Also, switch convention for inverted helices. (They now move in the opposite direction to right-side-up helices).
Expect integration test changes to z0_offset and z1_offset integration tests for the BundleGridSampler and PerturbBundle movers.
Merge pull request #445 from RosettaCommons/vmullig/fix_remodel_AP_issue
Fixing an issue with the RemodelMover
Fixing an owning pointers issue where an owning pointer was being requested from an object created as a reference on the stack in the RemodelMover.