Merge pull request #242 from RosettaCommons/daslab Daslab -- minor updates Merging! A few integration test changes in stepwise tests: • Test changes other than stepwise are 'usual suspects' -- broken tests or kic_fragments • cosmetic changes: getting rid of NativeRMSDScreener in cases without native. • in SWA, score offset from the way rna_bulge is computed; use of ftol vs. atol leads to some differences in minimization. • RMSD computation fixed in SWA. cosmetic changes. • cosmetic changes from reducing number of etable instantiations.

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Merge pull request #243 from RosettaCommons/justinrporter/env_release Integrating two bug fixes (18dde7b and f59f518) to master. No integration or unit test breakages expected, other than the usual suspects.

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Merge pull request #241 from RosettaCommons/justinrporter/env_release Merging several bug fixes to the environment. No expected unit test changes, no expected integration or performance test failures except the usual suspects.

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Merge pull request #238 from RosettaCommons/sjf/short_circuit_hairpin2 Sjf/fix_seqprof_cons_for_covalent_modifications

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Fixing Windows PyRosetta build

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Merge pull request #237 from RosettaCommons/hahnbeom/patchs Hahnbeom/patchs: bug fix & speed up & control option for context-dependence

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Merge pull request #228 from RosettaCommons/jkleman/mp_updates MP_UPDATES: * compute_structure_based_membrane_position: makes sure the embeddings show in positive z direction * EmbeddingDef: = constructor now takes a boolean whether the embeddings should show in positive z direction = implemented invert function that inverts the normal * Embedding: = constructor from pose and topology makes sure total embedding normal always shows in positive z direction = implemented invert function that inverts the normals of all EmbeddingDefs * AddMembraneMover: = debug check_pdb_for_mem to read in MEM in PDB file; it now goes through every residue in the pose to identify the MEM residue and matches that up with the user input; this means that reading in a membrane residue from the commandline works now * Types: = created core/conformation/membrane/types file that contains all membrane default values = replaced (hopefully) all instances with the default values in types * moved membrane_axis from docking into protocols3/membrane/geometry/util * MEM.params: = for fullatom, changed normal to length 15 * Conformation: = update_membrane_position now normalizes first and sets the points from the vectors - this is correct behavior: this function should now always be called with the vector for the normal and not with the point Unit tests: pass Integration tests: expected changes

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Merge pull request #235 from RosettaCommons/hahnbeom/patchs warning error removed

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Merge branch 'nawsad/flexpepdesign' merged nawsad/flexpepdesign branch into master. made a small change to task factory to allow design of the peptide if -design_peptide flag in on

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Merge pull request #229 from RosettaCommons/rhiju/allow_backtrace This was working with no integration test changes (except the 2 sensitive ones), and I put the backtrace functions in an "ifdef __GNUC__" to only be used in 'standard' Mac/Linux builds (gcc & clang). [I just tried a merge from master, but unfortunately several builds are broken there -- will check to see if master is restored soon.]

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Merge pull request #231 from RosettaCommons/rfalford12/membrane_symdock_updates Updates to membrane symmetric docking protocol = Add single membrane residue at the root of the symmetry fold tree = Adding method to compute the spanning topology of the full symmetric complex (compared to the asymmetric unit) = Updating pilot app to correctly configure the membrane residue and MembraneInfo for symmetry = Adding additional settings to membrane symmetric docking protocol to bypass filters, use REP criteria for side into contact and verify alignment of symmetry axis with the membrane normal Test Status = Integration test changes - expected = unit tests - all pass

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Merge pull request #233 from RosettaCommons/hahnbeom/patchs Hahnbeom/patchs

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fixing compile failures from warning

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merge

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Merge pull request #224 from RosettaCommons/jkleman/debug_interface_scores Jkleman/debug interface scores * DockingPrepackProtocol: move membrane axis from DockingPrepackProtocol to metrics * write_additional_pdb_pdb: deleted membrane functionality because not needed any more * DockingSlideIntoContact: slide axis is now in the membrane for membrane proteins * MembranePositionFromTopology: added error checking for empty SpanningTopology * compute_structure_based_membrane_position: added error checking for empty SpanningTopology * added option for local refine to MPDockingMover integration test changes: all ok: mostly added (useful) Tracer statements for docking, few numerical instabilities

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Merge pull request #227 from RosettaCommons/nollikai/coupled_moves_constraints Adding the following updates to the coupled_moves protocol: 1) Adding option to gzip pdb output 2) Adding option to use min_pack for initial repacking 3) Adding output of initial sequence / design positions 4) Adding option to use user specified constraints coupled_moves integration test is expected to fail following these updates.

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