Merge pull request #1666 from RosettaCommons/vmullig/add_betapatch_test Adding beta_patch scoring test. The -beta_patch flag is currently completely untested. I WILL break this without a test.

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Merge pull request #1665 from RosettaCommons/hahnbeom/beta_patch_fix simple fix to FastDesign + beta_patch

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Merge pull request #1657 from RosettaCommons/roccomoretti/san_benchmark Hook sanitizers into the benchmark testing system. I was slightly mistaken in the earlier sanitizer pull request, in that setting up unit/integration tests for different "mode" builds are more complicated. This pull request sets things up so the test system can run the sanitizer unit/integration tests. (They currently fail, but they run.) Also, we've been rather overzealous in the integration test ignore settings. e.g. we excluded "time", which will also exclude lines containing "runtime error" or other such ("antimetabolite", for example). I tweaked the ignore exceptions to be more specific, as a consequence massive integration test changes are expected, as lines which were ignored will be ignored no longer. If there is some tracer line which I revealed which should probably be hidden, feel free to add a specific line to the ignore_list: just be as specific with the regex as possible, to avoid inadvertent hiding of lines.

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Merge pull request #1658 from RosettaCommons/roccomoretti/atompaircst_pdbnumber_fix Fix PDB number parsing in Constraints Around July of this year a change was made to the constraint parsing code, such that how PDB numbering for chain A in constraint files was altered. This bug has been fixed, and a new unit test which should catch a similar error has been added. With some changes in the demos repository that have already been made, this should fix all of the tutorials tests, allowing us to enable those for routine running.

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Merge pull request #1662 from RosettaCommons/lqtza/make-antibody-relax-consistent FastRelax() in antibody.cc now respects coordinate constraints.

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Merge pull request #1647 from RosettaCommons/orlypolo/add-FPD-metrices Orlypolo/add fpd metrices

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Merge pull request #1661 from RosettaCommons/vmullig/kinclose_symm Adding unit tests for symmetric bridgeObjects behaviour (underlying all kinematic closure). I need to make sure that mirror-image systems yield mirror-image solutions. Which they do. Good.

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Merge pull request #1337 from RosettaCommons/aleaverfay/jd3_jobdist_jobqueen_interface Fleshed out interface between JD3's JD and JQ when the JQ is interested in describing multiple-round protocols. The JQ describes the interdependencies between batches of jobs using a directed graph; each node represents a batch of jobs (all of which are independent of each other) and a directed edge from i to j implies that the jobs for node j will not be started until after the jobs from node i have completed.

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Merge pull request #1642 from RosettaCommons/jaumebonet/psipred_input Psipred parser function overload.

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Merge pull request #1655 from RosettaCommons/sergey/mi PyRosetta: Adding support for multiple inheritance, adding bindings for operator* and operator/, adding PyMOL-Rosetta server script.

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Merge pull request #1656 from RosettaCommons/tjbrunette/place_motifs_master Tjbrunette/place motifs master adds the code for Jorge/Will's place motifs mover to master.

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Merge pull request #1503 from RosettaCommons/roccomoretti/rts_type Separate the concept of a ResidueTypeSet "type" from a RTS "name" There is (or should be) a distinction between the "type" of a ResidueTypeSet (e.g. "Fullatom"/"Centoid") and the "name" of the ResidueTypeSet. For example, we have an fa_standard RT, but doesn't that imply there could be an fa_nonstandard? This pull request attempts to separate out the concept of a TypeSet type (as an enum), and replace the instances of using names as comparisons with types (where it makes sense). This means that you can now ask "is this residue a 'fullatom' residue type, rather than asking "is this ResidueType a member of the fa_standard ResidueTypeSet. A bunch of integration test changes expected, as I made SwitchResidueTypeSet much less chatty when it's "switching" a pose that already has residues of the desired type.

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Merge pull request #1654 from RosettaCommons/roccomoretti/fix_gcc47_segfault Fix GCC segfault issue. Older versions (4.7.2, 4.8.1) of GCC have internal compiler errors (the compiler segfaults) with code in SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh. Separating out the variable initialization over two lines 'fixes' the issue and allows Rosetta to be compiled.

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Merge pull request #1649 from RosettaCommons/hahnbeom/cartbonded_redefine redefining names of subterms in cart_bonded:

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Merge pull request #1652 from RosettaCommons/vmullig/chunli_metal_issue Fixing crash with -auto_setup_metals when poses were resized Correcting issue that lead to crashes whenever -auto_setup_metals was used with a pose that was subsequently resized. Since NamedAtomPairConstraint and NamedAngleConstraint didn't implement a remap_resid() function, the parent class (AtomPairConstraint or AngleConstraint) function was called, resulting in the NamedAtomPairConstraint being replaced with an AtomPairConstraint, or the NamedAngleConstraint being replaced with an AngleConstraint, with atom IDs set to zero.

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Beautifying two files

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