commit fb3dbb3db2c1671927112d0c58350a73191cceb4
Merge: 56b655b 739f250
Date:   Wed May 13 23:33:18 2015 -0400

    Cysteines now become disulfides by the application of the disulfide patch.
    1. The same goes for D-cysteine, homocysteine, D-homocysteine, beta-3-cysteine, penicillamine, d-penicillamine, and... any other disulfide residue type we hope to introduce.
    2. So instead of incorporating two residue types, just type "FORMS_DISULFIDE_BOND" on the properties line of your params file (next to other standards like PROTEIN) and add a case to the disulfide patch.
    3. A small number of integration test changes are expected. match_1n9l changes because it relies on the number of residue types in the name3map and it might require a special cysteine derived residue type without a HG to properly represent catalytic cysteines. dock_with_hotspot_place_simultaneously, remodel_disulfides_rosettascripts, inverse_rotamer_remodel have been bug-fixed, essentially--they were checking for a type().name() of CYD, which is a no-no in any version of Rosetta! @jadolfbr confirms that the antibody_designer test is likely responding to an uninitialized variable and that I should go ahead and merge.

commit 56b655b26f4ae26f06ef7f8ab13d016872667486
Date:   Wed May 13 16:19:08 2015 -0700

    Fix unused variable

commit 98e02a0c0502e22ce1550ac74d253917777b157b
Date:   Wed May 13 16:02:08 2015 -0700

    Fixing a bug in pdb_to_map pilot app (missed a file)

commit fbcbb7cc252c3b7e840471be310527681572d565
Date:   Wed May 13 15:57:54 2015 -0700

    Fixing a bug in pdb_to_map pilot app

commit 48ba06583f3da77d1dbc6482e893843236d7480e
Merge: 64b54b3 74fcc4a
Date:   Wed May 13 11:29:37 2015 -0500

    Merge pull request #513 from RosettaCommons/roccomoretti/re-startfrom
    
    Update StartFrom ligand docking mover
    
    * Fix a bug where (in practice) only the first position would ever be chosen if multiple positions were given in the XML tag.
    * Unify the JSON file handling - you can now put multiple positions for the same protein in the same JSON file. Also, you can mix and match specification type, and it now recognizes default (no-tag) specifications.
    * Add the ability to specify the start from positions with the heavyatom positions in a PDB file - useful if you want to place the ligand graphically with PyMol.
    * Add option to place the ligand based on the neighbor atom (the constant point for conformer overlay) rather than the all-atom coordinate centroid.
    * Generally clean up the code
    
    New unit tests, but otherwise no tests expected.

commit 64b54b3f2b1ebacd6355a2b7441d64fc87e874ae
Merge: ab78dc0 c17cb8c
Date:   Wed May 13 11:28:33 2015 -0500

    Merge pull request #514 from RosettaCommons/roccomoretti/autoruntime
    
    Add -run:maxruntime_bufferfactor option to JD2
    
    
    
    On the cluster that I use, there's a hard time limit cutoff - exceed your requested time, and your job gets mercilessly killed and you get an email about it. This isn't necessarily good for output files, and if you're running a lot of jobs your email can be spammed if you misjudged timing.
    
    You could use -run:maxruntime, which will stop Rosetta with a clean exit if you exceed the setting - although you have to give yourself plenty of space, as JD2 only checks this when launching a new job. This means it's easy to run over - particularly if the cluster node is slower than your test run machine.
    
    Enter the new -run:maxruntime_bufferfactor option. This allows you to specify a real number which is the multiple of the estimated (currently average) job runtime. If you're within that time of the maxruntime value, you'll exit cleanly with a "too little time remaining" message. The estimated job runtime is calculated from the actual runtimes of the jobs on the run.
    
    So if you're launching an eight hour run on a cluster, you can simply add "-run:maxruntime 28800 -run:maxruntime_bufferfactor 1.5" to your commandline/options, and if there isn't enough time to complete 1.5 jobs (on average) in the remaining time before the 8 hours is up, Rosetta will exit cleanly (though with an error message). No timing test runs or mental math required - it should work if you jobs take 33 s or if they take 3333 s. (Rosetta should stop at 7h59m36s and 7h24m24s, respectively.)
    
    This option is off by default, even when maxruntime is on, so no test changes are expected. The default behavior should stay the same for all Job Distributor types, although I'm not sure how well things work for MPI and the like when the new option is active.

commit ab78dc0d619beff7bcc9a467e34790967bbea1f1
Merge: 6df7379 5a0c3d1
Date:   Mon May 11 15:09:23 2015 -0700

    Merge pull request #504 from RosettaCommons/rhiju/dimaio_uniform_rotation_sampler
    
    adding UniformRotationSampler.hh, developed by Frank Dimaio

commit 6df73793257be459acc15a035cad92ee51ca74b2
Merge: 67d33b5 673d00d
Date:   Mon May 11 14:27:38 2015 -0400

    Merge pull request #424 from RosettaCommons/sh-maxim/DunbrackLibs
    
    Sh maxim/dunbrack libs

commit 67d33b548ef8cd8186a50d1c48a321db60b6f1b0
Date:   Sun May 10 16:29:01 2015 -0700

    A small bugfix for hybrid when mixing template-based and extended (de novo) models in a single run

commit 6e415ac23f31ee779b7abcdf432a3d658dd57b3e
Date:   Sun May 10 16:26:48 2015 -0700

    Updating a pilot app

commit c0350fc39046a94561ab36502afc9e3a75002073
Merge: 95bda5e 1acc231
Date:   Sat May 9 07:43:20 2015 -0500

    Merge pull request #509 from RosettaCommons/pocket-optimization
    
    Sets current_tag_ on all movers in a mover container, added pocket_relax...

commit 95bda5ea28cdb4f8f01cc864c8cae796dc22d9e6
Merge: 0884ee4 6736ea9
Date:   Fri May 8 23:38:49 2015 -0700

    Merge pull request #507 from RosettaCommons/raywangyr/denovo_modelbuilding
    
    Raywangyr/denovo modelbuilding
    
    merging apps for de novo model building in near-atomic resolution cryoEM maps

commit 0884ee4627694f5bc67f066a1eb7aefc0439f975
Merge: d14058c 01b0707
Date:   Sat May 9 08:42:56 2015 +0300

    Merge pull request #512 from RosettaCommons/sjf/FilterScan_thresholdvector
    
    Sjf/filter scan thresholdvector

commit d14058cfe1fb275e7e610ac4fefa630787307a17
Merge: 77a7fec 6d6ff27
Date:   Fri May 8 15:56:58 2015 +0200

    Merge pull request #511 from RosettaCommons/wpotrzebowski/fiber_diffraction_defs
    
    Wpotrzebowski/fiber diffraction defs

commit 77a7fec8a0421fd769dc64f95f956191640a77ea
Merge: 5b784f5 1508cd7
Date:   Thu May 7 12:59:10 2015 -0500

    Merge pull request #506 from RosettaCommons/rhiju/angle_deriv_tol
    
    updating tolerance on angle_deriv function from 1.0e-3 to 1.0e-8.
    
    This fix does cause changes in several integration tests that carry out minimizes. In several cases, the final energy is noticeably better than before (by many Rosetta units), but in most cases changes to final energies are less than 0.1 Rosetta units.

commit 5b784f5579543e2c7b0508379f6139886bfea186
Merge: c49b7e0 d0a964d
Date:   Thu May 7 12:44:02 2015 -0500

    Merge pull request #505 from RosettaCommons/rhiju/turn_off_cmake_warning
    
    turning off -inline_functions as generic flag in cmake builds

commit c49b7e0427baadce167b7acc7db388accffe3ca5
Date:   Thu May 7 00:11:36 2015 -0500

    Fixing Rosetta build on Intel on Stampede

commit 5509736b35221a18f9d8b165b76197192bfca06a
Merge: 81ce15d 7348eca
Date:   Wed May 6 13:52:52 2015 -0700

    Merge pull request #508 from RosettaCommons/tlinsky/named_atom_constraint
    
    Add NamedAngleConstraint

commit 81ce15de47cf6580b547d54a64d0d54a589bb474
Merge: 85947d8 a64dda4
Date:   Wed May 6 09:42:08 2015 -0500

    Merge pull request #481 from RosettaCommons/justinrporter/env_release
    
    Fixes to AbinitoLoopCM. Minimal changes; no unit test differences, one integration test change that's likely a red herring.

commit 85947d8708130a52c78210d88a1ef8b7f731340f
Merge: 2d5aee3 6ae346a
Date:   Tue May 5 13:13:52 2015 -0500

    Merge pull request #487 from RosettaCommons/roccomoretti/no_boostserialize
    
    Remove USEBOOSTSERIALIZE code from Rosetta
    
    This was an old attempt to serialize Rosetta objects. It's no longer being maintained, and when Rosetta does get serialization it will be with a different technique. As we can always recover the code from the git history, there's no reason to keep it in master.

commit 2d5aee3ff4465c7593a5af51a3d9bdf97fad461b
Merge: e03980a 5769e5d
Date:   Tue May 5 13:12:33 2015 -0500

    Merge pull request #495 from RosettaCommons/roccomoretti/xml_dualspace_fix
    
    Fix behavior of XML FastRelax with dualspace.
    
    The XML version of FastRelax completely ignored any commandline flags about dualspace and cartesian. This was counter-intuitive for people here in the Meiler lab. Fix this such that commandline flags are honored by default. (Explicit settings in the tag override, of course.)

commit e03980aa1f47dadfc8b0b761ab5f50c8476d4abb
Date:   Tue May 5 12:48:26 2015 -0400

    Update default-torsions.txt
    
    The C-N-CA-CB and N-C-CA-CB improper torsions for CYS were being scored, but the corresponding torsions for CYD were not being scored. I confirmed with Frank that this is an error, one that I wished to fix before handling the whole disulfide patch merge--this is a simple enough bugfix that it doesn't require a pull request.

commit b67378c9a1c38c879ba1dd863d921cab57bd648f
Merge: 45508cc fe84e7b
Date:   Tue May 5 10:02:21 2015 +0300

    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

commit 45508ccc949a97ef2ea7ac86bd043e50e50b973c
Date:   Mon May 4 11:55:40 2015 -0700

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

commit 90620e19595bd9873dd09aa0c07fe26ed7fdbed6
Date:   Mon May 4 11:47:03 2015 -0700

    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!

commit 41a4e97231097db8a6af66b6ed4bc4ddc13a6c28
Merge: 9b976d7 510940c
Date:   Mon May 4 21:24:59 2015 +0300

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

commit 9b976d7a8a7878840b545e736b34b9305503879b
Merge: e2650d1 0826ba4
Date:   Sun May 3 17:02:06 2015 -0700

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

commit e2650d124e62ac31d222955399ae4fbe185040d2
Merge: 94328a6 a2c6e82
Date:   Sat May 2 16:07:01 2015 -0700

    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.

commit 94328a691ef69e64bdfefdc1d094e5827f912b9b
Merge: 2af92e1 8e3fcda
Date:   Sat May 2 04:25:07 2015 -0700

    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).

commit 2af92e1b5223be0a7929ff850a5908ce8ab75efb
Merge: 076ceaa 523bfc7
Date:   Fri May 1 09:12:50 2015 -0700

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

commit 076ceaa43b1c56019da625eac68719819974a0f8
Merge: 840ffd5 2f154dd
Date:   Thu Apr 30 17:18:53 2015 -0700

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