Merge pull request #1027 from RosettaCommons/jkleman/foldtree-fix Jkleman/foldtree fix Fixing foldtree bug for membrane protein ligand docking in MinimizeMover

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Merge pull request #1014 from RosettaCommons/everyday847/fix_map_at_problem Revised chirality detection to handle incomplete termini sensibly

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Merge pull request #1026 from RosettaCommons/roccomoretti/graphviz Graphviz output for ResidueTypes Just a little utility function I had lying around which allows you to create a Graphviz DOT file from the connectivity of a ResidueType. New, unused functionality (aside from unit test) -- no test changes expected.

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Merge pull request #1023 from RosettaCommons/sergey/f PyRosetta: Adding extra ‘notebook’ option to rosetta.init to allow redirect of Rosetta Tracer output to Python Jupyter notebook logs

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Merge pull request #1018 from RosettaCommons/vmullig/fix_valgrind_unit_issue Fixes source/destination overlap error with Valgrind in ParamsDataStorageTests unit tests. I was sloppy with a sprintf() statement in the unit test.

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Merge pull request #1021 from RosettaCommons/dimaio/hybridize_realign_fix Small bugfix for the auto-realign code in hybridize

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Merge pull request #1019 from RosettaCommons/lqtza/pten_floppy_tail Lqtza/pten floppy tail

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Merge pull request #1017 from RosettaCommons/revert-1016-revert-1015-vmullig/hbond_resselect Adding support for ResidueSelectors to the HbondsToResidueFilter (reverting the reversion) Reverts RosettaCommons/main#1016 (which reverted the premature merge) If the user provides a ResidueSelector, the filter will only count hydrogen bonds between the specified residue and residues in the selection. In the absence of a ResidueSelector, the old behaviour (counting hydrogen bonds between the specified residue and all pose residues) will be preserved. Tasks: - Add ResidueSelectorCOP to HbondsToResidueFilter class private member variables. - Parse ResidueSelector in parse_my_tag() function. - Add ResidueSelector functionality in apply() function. - Integration test. - Documentation.

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Merge pull request #1016 from RosettaCommons/revert-1015-vmullig/hbond_resselect Revert "Adding support for ResidueSelectors to the HbondsToResidueFilter." Accidentally merged prematurely, prior to testing and whatnot. Reverting.

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Merge pull request #1015 from RosettaCommons/vmullig/hbond_resselect Adding support for ResidueSelectors to the HbondsToResidueFilter.

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Merge pull request #1013 from RosettaCommons/tlinsky/residue_count_selector Add residue_selector option to residuecountfilter

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make the creation of the template files sorted as to prevent stochastic diffs in the logs that can show up on the test server.

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Merge pull request #1011 from RosettaCommons/rfalford12/fix_cppcheck_errors Fix Cppcheck errors

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Merge pull request #951 from RosettaCommons/vmullig/disulf_pep Add support for disulfides to the simple_cycpep_predict app This will add simple support for disulfides to the simple_cycpep_predict app. If the -require_disulfides flag is used, then the app will require that solutions have disulfide bonds between all residues of types that can form disulfide bonds. Every set of pairwise disulfide combinations will be tried. Tasks: - Add flags to the options system for requiring disulfides, and for cutoff energies. - Have these flags actually do something in the app. - Add a mover for disulfide construction and checking (trying all permutations or just a user-defined connectivity). - apply() function. - parse_my_tag() function. - Support for ResidueSelectors. - Support for odd numbers of disulfide-forming residues + integration test. - Integration test. - Documentation. - Handle the special case of an odd number of disulfide-forming residues OR throw an error (for now). - Add disulfide construction and checking to the parsed protocol called for every closure solution. - Add a post-relaxation check for disulfide energy. - The depermute() function needs to preserve disulfide linkages. - Test with Gaurav's test cases. - Update documentation. Put off to another pull request: x Add a unit test for symmetric glycine scoring when the -symmetric_gly_tables flag is used. x Debug asymmetries in gly scoring that currently persist. x Add a way for users to specify a desired disulfide connectivity. @gbhardwaj

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Merge pull request #1012 from RosettaCommons/kalekundert/explicit-python2 Specify ``python2.7`` instead of ``python2``

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Merge pull request #1010 from RosettaCommons/vmullig/graphics_issue Fix an issue with BOINC graphics The graphics app incorrectly defaults to sphere mode if it initializes itself before the shared memory object created by the worker app has been initialized fully. This addresses that. Tasks: - Add a wait_for_shared_memory_initialization() function that halts the graphics app until the worker app has finished initializing shared memory.

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