Merge pull request #383 from RosettaCommons/kwikwag/peptiderive-talaris Peptiderive: merge second round of fixes to the PeptiDerive protocol and adjacent logic. Note that this includes some fixes to pose::util and to unit testing infrastructure. Detailed change list below. DisulfideInsertionMover - unit tests - RosettaScripts support PeptideDeriverFilter unit tests - use -in:missing_density_to_jump 1 - change input PDB to check more edge cases: discontinuous chains, short segments, and zero-isc segments. Bug fixes in basic Rosetta code - fix `return_nearest_residue()` and `addVirtualResAsRoot()` in pose::util - fix test core files to reuse `get_commandline_with_additional_options()` and always use `initialize_rng()` Logic fixes - anchor residue in the receptor for receptor-peptide jump is now nearest residue to the peptide - make jump id is returned from `build_receptor_peptide_pose()` (as it changes when using `-in:missing_density_to_jump 1`) - fix #371 : remove truncated terminus variant type before adding full terminus variant type - use iterators for the `next_cutpoint` logic; this fixed some logic flaws - fix incorrect pose PDB being output as best linear - change translation magnitude to 2e6 Option tune-ups - compressed report output (`report_gzip` option) - output PDBs by default

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Oops! Did not mean to check the last commit into master directly! Reverting it, and will test on branch.

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updating tolerance on angle_deriv function from 1.0e-3 to 1.0e-8. This was causing major issues in derivs for a new Mg energy function I was developing, and took a while to track down!

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Merge pull request #503 from RosettaCommons/sjf/FilterScan_thresholdvector Sjf/filter scan thresholdvector

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Merge pull request #499 from RosettaCommons/tlinsky/tlinsky/subroutinefix Subroutine mover now sets last move status based on status of its mover_

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Merge pull request #500 from RosettaCommons/vmullig/z_is_for_zibo_that_good_enough_for_me Adding output of parameters in PDB file REMARK lines When doing parametric design, it's nice to be able to have the parameters in the REMARK lines of the output PDB file. This adds that. Tasks: -- Add option (enabled by default) to enable/disable this behaviour. -- Add PDB remark line function to the base core::parametric::ParametersSet class. -- Add override of this function to the protocols::helical_bundle::BundleParametersSet class. -- Add remark line function to the protocols::helical_bundle::BundleParameters class. -- Update documentation. Expected integration test changes: -- All PDB files in all bundlegridsampler, helical_bundle, perturb_helical_bundle integration tests should now have additional REMARK lines. The LayerDesign_ncaas integration test also uses the MakeBundle mover, so it will also have additional lines of output in its PDB files.

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Merge pull request #497 from RosettaCommons/vmullig/gamma_aas Adding gamma-amino acids to the properties list Also: - Tweaking some core code that was preventing mainchain torsions from being identified properly in C-aminomethylated terminal resiudes (resulting in changes to my backbonegridsampler integration test). - Updating protein patches to work with gamma-amino acids. - Adding GABA to the database (gamma-aminobutyric acid -- basically gamma-homoglycine).

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Merge pull request #496 from RosettaCommons/tlinsky/residue_name3_selector Add option to ResidueNameSelector to select by name3

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Merge pull request #491 from RosettaCommons/tlinsky/disulfidize_andor Disulfidize now has option to find disulfides with good score OR match_rt

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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.

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Merge pull request #492 from RosettaCommons/vmullig/minor_tweak_1 Minor change to backbonegridsampler_nstruct_mode integration test.

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Merge pull request #478 from RosettaCommons/roccomoretti/bowdlerize Remove some of the known user-facing swearing in Rosetta

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adding xray/electron scattering factors for metal ions.

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Merge pull request #474 from RosettaCommons/tlinsky/genericmc Fix uninitialized variables/segfault in GenericMonteCarloMover

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Merge pull request #477 from RosettaCommons/roccomoretti/no_scores_in_pdb Add option -out:file:no_scores_in_pdb This prevents addition of the scoretable and the extra scores at the end of Rosetta PDB output. The default is to preserve the current behavior (with the score table in output).

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Merge pull request #485 from RosettaCommons/smoe/no_raw_strings_prior_to_cpp11 smoe/no raw strings prior to cpp11 Concerning \n across platforms see http://stackoverflow.com/questions/3671462/is-n-multi-character-in-c or Rocco's comment :+1: Many thanks.

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