Fix atom name bug in alternate ResidueType::add_atom() This does not affect the standard add_atom() function, so no change expected. New unit test function added.

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Changed JD2 behavior to fail and exit when a bad RosettaScript is parsed and fixed 2 integration tests that were not running The affected tests that were failing silently are: write_mol_file and features If you care about these tests, you might want to make sure they work properly now. If multiple inputs were passed, the prior behavior was to iterate over all of these inputs, even if a bad RosettaScript was used that wouldn't work on any of them. I added a new catch block in JD2 to specifically catch RosettaScripts option exceptions (already existing) and reraise this exception, instead of trying to continue as before. The other problem that this fixes is if an integration test used a bad RosettaScript, perhaps because the script's parse_my_tag function changed, this would only be picked up by the initial test server run, and would fail silently after that. The script parsing error wasn't picked up because JD2 exited with a "0" exit code. This commit merges branch 'kylebarlow/bugs' into master Expected test changes: write_mol_file (wasn't running before, should at least run now) features (wasn't running before, should at least run now)

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Cleaning up random *.orig files.

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merge from master -- allows modeling of cyclic-diAMP in RNA puzzle 2 by FARFAR, using CHAIN_CONNECTION format that allows non-contiguous sets of residues to be input.

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parameterize strength of stub constraint for matcher The scaffold_matcher app relies on backbone stub constraints. Previously, this was hard-coded to the relatively arbitrary value of 5.0. Now it's a command-line parameter (stub_constraint_strength).

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Merge branch 'master' of github.com:RosettaCommons/main add clang version to build system, uncomment line in buns

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Merge branch 'master' to commit fixes to linux debug build Fixes linux debug build

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updates to RNA_DataInfo fixes -- thanks to Daniel for prior fixes to build.

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Merge branch 'master' of github.com:RosettaCommons/main

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Fixes (some of) rhiju's code that break rosetta's linux gcc build. 1. Place placeholders for your unused variables: src/core/scoring/rna/data/RNA_ChemicalMappingEnergy.cc 2.(40) RNA_DataInfo::RNA_DataInfo( RNA_DataInfo const & src ) : utility::pointer::ReferenceCount(src) { . . . }

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One more file to FIx pyrosetta compilation Missing def MACRO in CoordinateArray_RMSD_FlatLookup.hh

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Merge branch 'master' of github.com:RosettaCommons/main Bugfixes to FragmentLookupFilter and QCP that break pyrosetta compilation

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Merge from rhiju/dms_score bracnh: includes new score term for RNA chemical mapping (for now, just dimethyl sulfate reactivities). In integration tests, cosmetic changes due to one additional residue type, and change in score type names (in jd2_database tests). I am also seeing changes to match_1n9l & cstfile_to_theozyme, which look like late floating point deviations on my Mac, but I will monitor output from test server.

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Added an overloaded operator= in SymmetricConformation with an 'other' of type Conformation. This fixes a bug where copying a symmetric pose used Conformation's operator= instead of SymmetricConformation's, and failed to copy its symmetry type.

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Merge branch 'master' of github.com:RosettaCommons/main

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Adding exception handling to ParsedProtocol to address a segmentation fault bug triggered when a mover in the protocol throws an exception. Cosmetic tracer output changes for clarity. Unit Tests: All Pass

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