commit f8e96f43603eb1c565e5f7a932c1ed0d8f07aee4
Merge: 7f4ba12 49e2272
Date: Tue Mar 8 15:42:39 2016 -0800
Merge pull request #1159 from RosettaCommons/tlinsky/reg_primary_sequence_neighborhood_selector
Add missing registrator for PrimarySequenceNeighborhood residue selector
commit 7f4ba121fd9cc15563566640faaf423e310d4e96
Merge: 1c13041 096cc7b
Date: Tue Mar 8 13:07:29 2016 -0800
Merge pull request #1149 from RosettaCommons/tlinsky/removeresidues_selector
Add residue selector support to DeleteRegionMover
commit 1c13041ac27e6c9458e4dd14aeb3d026269b4a28
Date: Tue Mar 8 14:00:00 2016 -0500
fixing SnugDock integration test
commit ab10e6ad233d846fc77a08b85c6035d6676a6e96
Merge: dacbaa4 510a66d
Date: Tue Mar 8 05:59:05 2016 -0800
Merge pull request #1166 from RosettaCommons/vmullig/peppredict_set
Adding an option to the simple_cycpep_predict app to let me set certain torsions
This is to allow me to predict larger peptide structures in cases in which I might have some idea of regions of secondary structure
commit dacbaa4ce9575faeb0f881a66f2d1ecb7cd63d1a
Merge: c691610 96c2f5c
Date: Tue Mar 8 02:12:46 2016 -0800
Merge pull request #1164 from RosettaCommons/vmullig/fix_sfxn
Fix remaining beta_nov15 unit test failures
This pull request fixes the remaining issues with the beta_nov15 energy function and mirror symmetry, cyclic geometry, etc.
Tasks:
Fix Ramachandran gly table symmetrization with the Shapovalov tables turned on.
Fix omega energy and derivative calculation for D-amino acids.
Fix oversensitivity of the electrostatics unit test. (Frank has already fixed the electrostatics issue; the test failure is a false alarm, now.)
Damn it -- I missed fa_intra_sol_xover4 and lk_ball_wtd. Add unit tests for these.
Fix cyclic scoring with lk_ball_wtd.
Beauty.
commit c691610b7605669031eba5eacf2feb572abaa71b
Date: Mon Mar 7 23:02:09 2016 -0800
fix path for git add help in code template generation.
commit 1820eabdda00fab1755a90e548501c1a862879d7
Date: Mon Mar 7 17:13:54 2016 -0800
Fix compile bug
commit 4f75e9ee8e0afde3e5686d256178a3481c8d9f98
Merge: 4417abe 8555325
Date: Mon Mar 7 16:34:35 2016 -0800
Merge pull request #1162 from RosettaCommons/dimaio/fix_xtal_refine
Small bugfix for xtal_ml scoreterm with new minimization scheme
commit 4417abefd0f2780b6e59c94418d9424614717511
Merge: 5512591 5aed17a
Date: Mon Mar 7 17:21:03 2016 -0500
Merge pull request #1158 from RosettaCommons/xrw_PDB_diagnostics
(This is the PR opener, repeated). This branch pulls in the PDB_diagnostic application written for the chemical XRW. The application just does the basic Rosetta exercises - score, repack, minimize. It also adds to the scorefile numbers of residues in all the categories supported directly by ResidueType. The key is that the application is not meant to run on a PDB (file), it's meant to run on THE PDB (all 115K+). There are two supports not in this PR - a data processing script in tools/ (will be merged there soon), and a godawful shell-script based job distributor that is robust against segfaults (will be merged noplace ever). Since we'll be discussing it at Winter RosettaCON I wanted it in master; also I'm tired of making special temp branches to merge this test code against the PDB-reading features it needs to test.
Note that the original history of the application was accidentally merged into an earlier XRW merge, but that merge was reverted after pushing. Thus this PR starts with an en-block reversion reversion to make the new code appear; its real history is further back.
The changes to not-obviously-this-application files are either cosmetic, or a bugfix in JD2 (boolean options should always check .value(), never .user(), so that the user can pass false...).
Integration and unit tests are a mess in master. There are two integration test changes legitimately caused by this code: the new itest PDB_diagnostic (will fail because it's new), and central_class_modification (will fail because I changed JobDistributor [the bugfix noted above]).
commit 5512591becb785321f20e0491cbdcfc36af4a0f7
Merge: 6ac50a8 6aba664
Date: Sun Mar 6 16:19:51 2016 -0700
Merge pull request #1155 from RosettaCommons/PyRosetta
Adding binding for core::io::Remarks.
Updating C++ PyMOL mover so it now accept address and port argument.
commit 6ac50a8641f27367ee82ada6b8d2718e092e8642
Merge: c566deb 2e93ca1
Date: Sun Mar 6 12:20:31 2016 -0800
Merge pull request #1142 from RosettaCommons/dimaio/refine_apix
Checking in code that allows refinement of voxel spacing in electron density maps.
There are several integration test failures; all are expected as they either: a) refine with density (normalization of density values has changed a bit), b) report all scoreterms (one was deleted), or c) small numeric changes which are related to removing a scoreterm.
commit c566deb21280963b741e2d83d5542c46984bf2aa
Merge: 695a350 ef24af5
Date: Sat Mar 5 20:38:56 2016 +0200
Merge pull request #1154 from RosettaCommons/kwikwag/peptiderive-integration-test-fix
Peptiderive: integration test - remove use of sed command so it works on mac
Expected integration test changes: `peptiderive`
commit 695a350c034e01f1f25764fc577ff839abe49d33
Merge: 5a56ef1 c5fb09a
Date: Fri Mar 4 15:54:54 2016 -0800
Merge pull request #1104 from RosettaCommons/dimaio/mirrorsymm
Add mirror symmetry support to Rosetta
This adds support for mirror symmetries to Rosetta. This was a collaboration completed by Frank Dimaio and Vikram K. Mulligan. Here's Frank's description of the changes:
---
This PR adds the ability for Rosetta to model symmetries with mirror operations. This builds upon Vikram's previous PR (#956) but attempts to address some of the concerns of Andrew.
Specifying mirror symmetry: Mirror symmetry is specified through the use of an "inverse virtual" residue which defines a left-handed local coordinate system. These inverse virtuals may be used to define mirror symmetries as follows:
symmetry_name C2_big__2
E = 2VRT0 + 1(VRT0:VRT1)
anchor_residue 13
virtual_coordinates_start
xyz VRT0 1.0,0.0,0.0 0.0,1.0,0.0 0.0,0.0,0.0
xyzM VRT1 1.0,0.0,0.0 0.0,1.0,0.0 0.0,0.0,0.0
virtual_coordinates_stop
..
Above, xyzM declares an inverse virtual residue. Connecting this inverse virtual to a subunit makes the connected subunit inverted. The above snippet declares a Cs symmetric system with a mirror plane in XY.
MirrorSymmetricConformation is a new class derived from SymmetricConformation, and has additional data members that remember which subunits and which jumps are linked by mirroring. It overrides a handful of conformation manipulation functions. It also ensures that the correct chirality type is maintained for symmetric copies. MirrorSymmetricConformation is created by default when make_symmetric_pose encounters a symmdef file with mirrored virtuals.
Kinematics are handled entirely by the AtomTree. This is done by adding two booleans to Jump specifying the handedness of the upstream and the downstream stubs. The functions make_jump, from_stubs, and fold_in_rb_deltas have been updated accordingly, and a tiny bit of logic is added to JumpAtom when starting refolding from an inverted residue. Note that if the upstream and downstream handedness are different, then the jump "rotation" is no longer a rotation but a reflection. The variable names have not been updated to reflect this.
Packing is handled by modifying SymmetricRotamerSet_ so that orient_rotamer_set_to_symmetric_partner uses the Conformation-computed symmetric transforms instead of orient_onto_residue. This allows for the same code to be used with both mirrored and non-mirrored symmetric conformations, and does not require peptoid-specific code as there is currently. However, this change will lead to small numeric changes in symm packing tests.
Since everything is added to the atomtree framework, derivatives/minimization works as-is (at least using Phil's new_sym_min framework, which I'm hoping to make default). Note that the current code assumes that there are NO mirror virtuals within the asymmetric unit. If there is a want/need for such support (I'm not sure I see what advantage it offers) it can be done, but I think JumpAtom::get_dof_axis_and_end_pos needs to be aware of the jump handedness for derivatives to work correctly.
MirrorSymm specific code has been added to ensure that the proper type of conformation is created from setup_symmetric_code, and for dumping silent files. Other than these two instances, the conformation should work transparently in any other mover that works with symmetric conformations. In theory, it should work fine with various docking protocols, multicomp, etc., but I have not tested these.
Finally, I'm using this PR as an opportunity to update some of the SymAtomTreeMinimizer logic. Phil's -new_symm_min flag is now default (pending a few more tests) ... it no longer requires scalefactors on interactions occurring through multiple cloned jumps. The old behavior available through -old_symm_min.
---
Tasks:
- [x] Add core functionality to allow one to get a mirror-image type efficiently (and without any string parsing).
- [x] Add clone_flipping_chirality() function to Residue class.
- [x] Revert my reversion (9c8a8ee) to re-merge my changes into Frank's branch (Vikram).
- [x] Unit tests for this.
- [x] Add MirrorSymmetricConformation class.
- [x] Finish the flip_chirality() function (Vikram).
- [x] I can't assume that the asymmetric unit is symmetry copy 1. Fix this in MirrorSymmetricConfromation::update_residue_identities(). (See line marked "Assumes that the asymmetric unit is copy 1."). (Vikram). *fixed -fpd*
- Finish the detect_disulfides() function (Vikram). -- Put off to a future pull request
- Unit test for detect_disulfides() (Vikram). -- Put off to a future pull request
- [x] Update packer to handle mirrored symmetry (Frank).
- [x] Update Atomtree to handle inverted stubs (Frank).
- [x] Get derivatives working (make sure *get_dof_axis_and_end_pos* is right for inverted stubs) (Frank).
- [x] Unit tests for three cases above (Frank).
- [x] Make aa_composition_energy (or, more generally, ResidueArrayAnnealableEnergies) symmetry-aware (Vikram).
- [x] Unit test: aa_composition energy + design.
- [x] Revert a6eae0ea471c964a369e8fc640b33b3476bef9fe and d007c35d0b9bbc2546b84fc35d8ca76905b58c80 (in that order). These were added temporarily to disable the post-packing step at which residue types were inverted.
- [x] Revisit this -- this will be broken again, since residue-type flipping was taken out of SymmetricRotamerSet_::orient_rotamer_set_onto_symmetric_copy().
- [x] Fix the node list -- issue when prevent_repacking used on some residues.
- [x] Add unit test for this (prevent_repacking used on a subset of residues + aa_composition).
- [x] Document this.
- [x] Fix issue with creating covalent bonds between symmetry subunits (Vikram).
- [x] Make this part of the integration test.
- [x] Integration test.
- [x] Address integration tests currently failing to run (INV_VRT issue).
- [x] Fix PyRosetta build.
- [x] Ensure that SymmetricConformation::declare_chemical_bond() works properly with mirror symmetry.
- [x] Documentation.
- [x] Beauty.
Also:
- [x] Strips out a little more of the old Lua junk.
- [x] Fixes D-amino acid base name to be the D-name rather than the L-name.
- [x] Fixes a bug in SymmetricConformation::declare_chemical_bond. Previously, not all symmetry copies were properly getting the bond. Now they all do.
- [x] Fixes aa_composition and other ResidueArrayAnnealableEnergies so that they work properly with symmetry.
commit 5a56ef1d55718d5678bcd116ed5950f4ad35efd1
Merge: 7210bf2 7c29e45
Date: Fri Mar 4 14:28:11 2016 -0800
Merge pull request #1153 from RosettaCommons/hahnbeom/beta_fix
Correcting my mistake with elec_cp_reps.dat
commit 7210bf2badce25e343b5923293afad670bcc5a2b
Merge: b35db93 8a2cb07
Date: Fri Mar 4 13:25:46 2016 -0800
Merge pull request #1080 from RosettaCommons/tlinsky/tlinsky/fldsgn_bugfixes
Enhancement to sheetconstraintgenerator
commit b35db93b9c008ac0071af5b9ffae64fc19730b29
Date: Fri Mar 4 15:18:30 2016 -0600
Update batch_distances to avoid use of a header in apps/pilot/
Now that it's a public app, it can't rely on non-release (pilot) code.
commit 12ea1e47252bb66933d8ddb14c350f0757e2cf7a
Merge: c498726 136e672
Date: Fri Mar 4 11:40:05 2016 -0800
Merge pull request #1141 from RosettaCommons/hahnbeom/beta_soft
all the beta_nov15 related unit tests fails, as expected. others are fine.
commit c498726f1569a73eeb18dca752c142aacbe137bd
Merge: a7cd732 dfd0f0b
Date: Fri Mar 4 13:59:45 2016 -0500
Merge pull request #1138 from RosettaCommons/kimdn/master_dn_fixed
* SEWING
[sewing_hasher] automatic detailed score_file_name (just commented in
master to prevent integration test failure), default num_segments_to_match = 1, updated comments
[MonteCarloAssemblyMover] From now on, an option
(remove_non_contiguous_assembly_) is true by default
[ModelTrimmer] New options (leave_certain_model_ids, leave_models_with_H_terminal_ss,
model_should_have_at_least_1_H) added, if
'leave_parallel_way_H_bonded_models_by_terminal_strands_only' do
'leave_models_with_E_terminal_ss' in advance
[RepeatAssemblyMover] New option (threshold_score_of_complete_cycle,
default value is -0.5) is introduced
[SEWING overall] Minor code-cleanups
* SandwichFeatures
[WriteToFileFromSandwichFeatures] Code cleanup
[WriteToDBFromSandwichFeatures] Added a more reference regarding beta hairpin types
commit a7cd732c4d8c27f71ed3f98cdf591aeae9f4a164
Merge: e25eca5 5b18c6c
Date: Fri Mar 4 17:00:58 2016 +0200
Merge pull request #1152 from RosettaCommons/kwikwag/peptiderive-integration-test-fix
Peptiderive: remove Rosetta version from integration test
Expected integration test changes: `peptiderive`
commit e25eca5d7d200650dbf40083952e93dd1e762801
Merge: 62ad846 5e50139
Date: Fri Mar 4 00:55:36 2016 -0800
Merge pull request #1143 from RosettaCommons/jadolfbr/antibodies/remove_creators_from_headers
This moves (my) antibody task operation creators to their own file. Also makes files for sewing creators.
As @aleaverfay has pointed out, TaskOp creators should be in their own file to decrease compile time of init.cc.
A note has also been added to init.TaskOperationCreators.ihh
commit 62ad8468118e995b2a741731347a32e058ff9c8d
Merge: 725b46c a328c57
Date: Thu Mar 3 22:34:50 2016 -0800
Merge pull request #1151 from RosettaCommons/vmullig/fixbetanov15
Trying to fix failing beta_nov15 unit tests.
There was a call to oneletter_code_from_aa() that didn't first check whether the AA enum passed to it was an L- or D-amino acid. This adds a check.
commit 725b46c9564dfa83ec54ca9d2eacf3c3894cf40b
Merge: 28f9b4c f02f366
Date: Thu Mar 3 18:56:18 2016 -0800
Merge pull request #1150 from RosettaCommons/dimaio/fix_beta_for_d_aas
A few fixes to beta_nov15 to ensure: a) L- and D-AAs are scored equivalently, and b) symmetric_gly_tables is respected for bb-dep omega.
commit 28f9b4c90d57121ee698745e7531a682fbbfff01
Merge: 3768aa6 eeff495
Date: Fri Mar 4 02:15:41 2016 +0200
Merge pull request #1067 from RosettaCommons/orlypolo/peptiderive-report-reformat
This adds / fixes some features in `PeptideDeriverFilter` and `DisulfideInsertionMover`
- change PeptideDeriver report file format
- information of peptides with cyclization potential now appears in a table of its own.
- If best linear peptide has cyclization potential but is not the best cyclic peptide, will be added to the (new) cyclic peptides table
- add Rosetta version info
- fix a few bugs:
- far away chains cause segfault
- specifying partner chain which appears before a receptor chain would reverse the order
- remove internal energy filtering of cyclized peptide
- add `peptiderive` integration test
- `DisulfideIntersionMover` unit test coverage: test `determine_cyclization_viability`
- `PeptideDeriverFilter` unit test coverage: edge case of far away chains
Expected integration test changes: `peptiderive` (new integration test!)
commit 3768aa6a3638623d8f4fed7d1e589e674c00e038
Merge: 38f32b9 b5939a9
Date: Thu Mar 3 13:43:50 2016 -0800
Merge pull request #1145 from RosettaCommons/vmullig/add_betanov15_tests
Add beta_nov15 tests to the sfxn_fingerprint test suite.
If I'm going to start fixing problems in the beta_nov15 scorefunction, I need to be sure that I'm not introducing scorefunction changes by accident. This adds a test for the beta_nov15 scorefunction to the sfxn_fingerprint test suite.
commit 38f32b96f2d77126078263189f61ed21c9fe9fdd
Merge: 5f9235f f5a9dab
Date: Thu Mar 3 13:04:55 2016 -0600
Merge pull request #1147 from RosettaCommons/roccomoretti/cmake_linker
Make CMake builds slightly faster
This cherry picks two efficiency improvements from pull request #958
1. Convert from using the python script smart_symlink.py to using the CMake-internal symlinking facility.
2. Adjust version.py not to re-write the version header if it hasn't changed.
On my machine, these improvements speed up a no-change rebuild by about a factor of 3 or so. (Symlinking now takes less than a second.) The speedups also (slightly) help with normal rebuilds.
commit 5f9235fe5569b4569c635212cafcd616093629c5
Merge: 112d1cd 9ff8e25
Date: Thu Mar 3 02:32:12 2016 -0800
Merge pull request #1144 from RosettaCommons/vmullig/add_betanov15_tests
Add symmetric gly, symmetric scoring, and cyclic permutation unit tests for the beta_nov15 energy function
**Note: this deliberately adds unit tests that fail. This is to illustrate current scorefunction failures that need to be addressed.**
Talaris is now fully symmetric (i.e. mirror-image poses consisting of L- and D-amino acids score identically), fully consistent with cyclic permutations (i.e. cyclic peptides core identically no matter where residue 1 is), and has a mode in which glycine behaves perfectly symmetrically (favouring left- and right-handed conformations equally). Unit tests already enforce this for talaris and for whatever the default scorefunction is at any given time. However, the beta_nov15 scorefunction is seeing increasing use, and these unit tests do not cover this scorefunction.
This pull request adds these unit tests for this scorefunction. Since the beta_nov15 scorefunction has introduced asymmetries, they currently FAIL, and will continue to do so until this is fixed. (That is, they are illustrating a current failure of Rosetta, not introducing a new one.)
commit 112d1cdb210d44b210f44e954f0bc545569b42fd
Date: Wed Mar 2 15:59:02 2016 -0800
Fixing the Mac PyRosetta build.
commit 090baad10470f20b85882933a111bbb1d4242ba8
Merge: 5ab9dd8 86f3b6a
Date: Wed Mar 2 13:52:29 2016 -0600
Merge pull request #1139 from RosettaCommons/roccomoretti/reb_pdbnum
Add PDB numbering to residue_energy_breakdown and per_residue_energies output
Integration test changes to residue_energy_breakdown and per_residue_energies expected (extra columns in output).
commit 5ab9dd8d8a4a3643d64d01e4dd556d5687690075
Merge: 427a08c 1605193
Date: Wed Mar 2 10:37:49 2016 -0800
Merge pull request #1134 from RosettaCommons/jadolfbr/sugars/debug_valgrind
Fix issues identified by valgrind for (de)glycosylation
Fix issue identified in carbohydrate util Unit Test
Fix issue identified in simple glycosylate mover integration test
commit 427a08cf2eb021257a79b55208164496e77dd567
Merge: 5f29cd7 16c35de
Date: Wed Mar 2 08:45:58 2016 -0800
Merge pull request #1022 from RosettaCommons/tjbrunette/fast_forward_folding
Tjbrunette/fast forward folding this code introduces code to: A. Generate a structural profile fast. B. Fix the structure of short loops. C. Score centroid models with Will's motif score term.
-The integration test errors are expected and due to the new energy functions
-Most of the new code uses an hdf5 database so there are no integration tests to protect it because hdf5 needs a different compile then is currently being done.
commit 5f29cd737e2948d4669e707b4b5398901709616b
Merge: da03a45 ec517a4
Date: Wed Mar 2 09:15:10 2016 -0500
Merge pull request #1073 from RosettaCommons/aleaverfay/pose_builder_tests
Rosetta will now read ACE and NME residues without needing any special flags.
Changing the variant types given to the AcetylatedProteinNterm and MethylatedProteinCterm patches so that they register as LOWER_TERMINUS and UPPER_TERMINUS variants, which they are.
The effect is to enable some code in the PoseFromSFRBuilder that has been laying in wait. Now, when Rosetta encounters an ACE residue on the Nterm of a chain, it will take the atoms for that residue and append them to the next residue, which will end up patched with the AcetylatedProteinNterm patch.
NOTE: we have two ACE patches in rosetta when we should really only have one. "N_acetylated" and "AcetylatedProteinNterm". The more commonly used patch is "N_acetylated". It, however, has a different set of backbone torsion angles than the one defined by "AcetylatedProteinNterm". The same applies for the "C_methylamidated" and "MethylatedProteinCterm" pair.
We should rapidly decide how we are going to eliminate one of the two ACE patches and one of the two methylamidadtion patches, as duplication is the devil.
commit da03a457ca426aa909c1f3e4c4060d95fe049c36
Merge: c7374cd 355898b
Date: Wed Mar 2 08:52:16 2016 -0500
Merge pull request #1112 from RosettaCommons/aleaverfay/fix_sp3acc_discontinuity
Reformulating the chi penalty for sp3 acceptors to fix a discontinuity.
The "chi" dihedral for sp3 acceptors is defined by the four atoms:
Hdon -- Acc -- Acc Base -- Hacc
where "Hacc" is the hydrogen chemically boudn to the acceptor
(but which is not participating in the hydrogen bond). On serine,
for example, Acc would be "OG", Acc Base would be "CB" and Hacc would
be "HG".
With the Talaris2013 score function, we added a penalty based on
chi for sp3 hybridized acceptors that had not been present in score12.
In score12, the "BAH" angle was measured with respect to Hacc, and it
was assumed that the lennard-jones term would push the Hdon atom away
from the Acc Base atom. This resulted, however, in rather funky
geometries if you looked at the Acc Base--Acc--Hdon angle. What
measuring the BAH angle wrt the Hacc atom did accomplish, however,
was avoiding geometries where Hdon and Hacc were very close.
In the Talaris2013 score function, we define the BAH angle wrt the
Acc Base atom. To make sure that Hdon and Hacc did not get too close,
I also added in a penalty that dependend on chi and only chi. Of
course this penalty had a discontinuity when the BAH angle hit 180;
I was aware of the discontinuity, but thought it would not be
disruptive. After Talaris2013 became the default score function, the
degree of its disruptiveness became apparent.
To remedy this problem, I worked with Frank off and on with a "soft-max"
function to take the worse of two scores: one defined by the
BAH angle and one defined by the Hdon -- Acc -- Acc Base angle, but we have
not smoothed out all of the edges on this formulation.
The fix in this commit defines the "chi" penalty for sp3 hybridized acceptors
to also respect the BAH angle in order to avoid a discontinuity at BAH=180.
It is not necessarily the best formulation, but it does fix the discontinuity
and the derivative discontinuity, and thus should fix the common cases of
"inaccurate G!" that shut down minimization.
This is a stopgap. The softmax potential will be much more useful and smooth and generally better than this ugly thing. It's a work in progress, however, and this is easy to bring online.
This will effect everyone who is using talaris2013 and talaris2014. I am bumping the score function revision ID so the "score function fingerprint" test will change. You should note that the score function in master is changing.
commit c7374cd9a951e1311288596d6c5de326a5593d1f
Merge: dc6a037 8c0b1c2
Date: Wed Mar 2 03:30:50 2016 -0800
Merge pull request #1140 from RosettaCommons/vmullig/fix_macrocycles
Trying to fix the macrocycles integration test
The app has a while( !closed ) loop that can potentially loop forever. I think that my changes didn't actually break the app -- they just altered the trajectory so that it no longer converges in the time limit for the integration test. This is a temporary workaround that causes the app to break out from that loop if a maximum number of iterations for loop closure is passed.
(Incidentally, please don't ever close a loop like this in a real instance! Use GenKIC, CCD, or anything else -- it'll definitely be faster!)
@everyday847
commit dc6a03730235641c4027baf43862ea1fdf8572c5
Merge: f5f5fdd b431915
Date: Tue Mar 1 16:41:22 2016 -0800
Merge pull request #1137 from RosettaCommons/vmullig/fix_resarrayannealeval
Adding an escape check to the initialize() function of the ResidueArrayAnnealingEvaluator so that it doesn't try to do expensive rotamer setup steps if nothing is going to use them.
commit f5f5fdd470b43e3a64763a24e0d73e2a41c9c611
Merge: d26fd52 d594607
Date: Tue Mar 1 10:47:14 2016 -0600
Merge pull request #1115 from RosettaCommons/bazzoli/water-gensp3-hbeval
Changed HBEvalType for tuple (hbdon_H2O, hbacc_GENERIC_SP3SC, seq_sep_other)
commit d26fd5296f75136bfa16af9d307090e8fe3cfee8
Merge: 4ea1e91 c38c05a
Date: Mon Feb 29 16:41:20 2016 -0800
Merge pull request #1136 from RosettaCommons/jadolfbr/remove_extra_pdb_reader_tracers
Remove some extra output on pdb reading
Right now, each unknown record is printing to std::cout on PDB reading if -pdb_comments is passed. I'm not sure I agree with reading pdb_comments or other things at all, but this simple PR will change the cout printing to a TR.Debug.
commit 4ea1e91327c0f88e0543ed8991de5b686dbc3788
Merge: 9a2d27e 02e4e79
Date: Mon Feb 29 15:40:16 2016 -0600
Merge pull request #1135 from RosettaCommons/roccomoretti/cppcheck_ignore_forward
Add suppression of unnecessaryForwardDeclaration to cppcheck.
This test looks to be unnaturally sensitive, and has been removed from recent versions of cppcheck.
commit 9a2d27e0034f02760875cbb966ae97cbe04b152c
Date: Mon Feb 29 13:50:49 2016 +0200
Added a flag for building the public docs.
By default, doxygen is built with doxygen_devel.*
commit eaa8ca1c4d5888ca911075c86cf5419f345cdbc9
Date: Mon Feb 29 12:51:43 2016 +0200
Update doxyfile_release.00
commit a4e5ab926c6cf67646781c12cf0f2965bcbfbe8a
Date: Mon Feb 29 12:50:33 2016 +0200
Update doxyfile_release.01
commit dfc47c6c586fc5cf1d4626b72c0a4e54f3deeb41
Date: Sat Feb 27 21:26:28 2016 -0800
Remove extra output I added while debugging
I forgot to remove it before pushing to master. This will result in disulfidize integration test changes
commit 3cf3e910e5a267dc6ea0dbe15580a34aa9892296
Merge: 3b13f35 8dc1ac5
Date: Sat Feb 27 17:29:45 2016 -0800
Merge pull request #1132 from RosettaCommons/tlinsky/sequence_recovery_scorefxn
Add scorefxn option to SequenceRecoveryFilter
commit 3b13f357c1aa5f13d97b11e6215c4a67500abb88
Merge: d24db99 7d51c15
Date: Sat Feb 27 17:27:18 2016 -0800
Merge pull request #1131 from RosettaCommons/tlinsky/fix_disulfidize
Fix issue where PDB additional data didn't print out
commit d24db999d1c3aaae0427a066f9f8ee1ea4c88e06
Merge: 3b485b0 755b19e
Date: Fri Feb 26 17:44:34 2016 -0800
Merge pull request #1093 from RosettaCommons/vmullig/fix_cycpep_issues
Make RamaPrePro work with D-amino acids and noncanonicals
Currently, RamaPrePro segfaults if you try to use it with noncanonicals. This pull request allows it to score canonical D-amino acids (using inverted Ramachandran tables, as the vanilla rama term does) and anything with a BACKBONE_AA line in its params file, and to return zero for any other noncanonical (which is nicer than crashing). It also allows it to work properly with cyclic geometry.
Since my new unit tests also revealed problems with fa_rep, fa_atr, fa_sol, and pro_close with cyclic geometry (cyclic permutations of the same cyclic peptide pose were not scoring identically), I've fixed those problems, too.
Tasks:
- [x] Properly invert phi/psi when scoring a canonical D-residue.
- [x] Add unit tests for this.
- [x] Derivatives too.
- [x] Add unit tests for derivatives with L-residues.
- [x] Add unit tests for derivatives with D-residues.
- [x] Use a canonical residue's rama tables if BACKBONE_AA is specified in its params file.
- [x] Derivatives too.
- [x] Add unit tests for this.
- [x] Check that rama_prepro handles cyclization properly (as rama does).
- [x] Make rama_prepro no longer dependent on seqpos. (That is, have it check what a residue is actually connected to at its UPPER_CONNECT, rather than assuming that it's connected to residue n+1.)
- [x] Update the PeptideBondedEnergyContainer to handle cyclic/nonstandard geometry.
- [x] Add unit tests for this.
- [x] Fix errors in pro_close with cyclization revealed by the above unit test.
- [x] Fix errors in fa_sol with cyclization revealed by the above unit test.
- [x] Fix errors in fa_rep with cyclization revealed by the above unit test.
- [x] Fix errors in fa_atr with cyclization revealed by the above unit test.
- [x] Add unit test for symmetric scoring of cyclic peptides.
- [x] Return 0 as the score for anything noncanonical (derivatives, too) passed to rama_prepro.
- [x] Add support for symmetric rama_prepro tables for glycine if the -symmetric_gly_tables flag is passed.
- [x] Add unit test for this.
- [x] Add unit test for minimization, too.
- [x] Re-enable the unit test that was disabled for speed (REVERT d00db89d78cc97af7eb89d375c2f50e12d9fc98a).
- [x] Take out debug output in RamaPreProEnergy.cc (REVERT 8c84be7ac1431ffbfe0052f7caa62d16e2381a74).
- [x] Disable dump_scored_pdb() lines in cyclic_geometry unit test.
- [x] Document all of this somewhere.
- [x] Check effect of PeptideBondedEnergyContainer refactor on cart_bonded.
- [x] Beauty.
This pull request also:
- [x] Turns on fa_elec minimizer unit tests. (Some malicious soul had commented them out!)
@fdimaio , @hahnbeom : This should not affect anything related to the calibration of this score term, or its scoring of canonical L-amino acids.
@dabaker : Once this is done, it will no longer be necessary to revert back to the old rama score term when using the beta_nov15 scorefunction
The remaining integration test changes are as a result to small changes to what the CartesianBondedEnergy iterates over when ligands are present.
commit 3b485b0e49ea270b79ab489551f960edc49f7364
Merge: ca1020b 11bffcd
Date: Fri Feb 26 14:40:57 2016 -0800
Merge pull request #1130 from RosettaCommons/vmullig/add_back_grab_additional_pose_data
Add back PoseToStructFileRepConverter::grab_additional_pose_data() function call
Somehow, the call to the grab_additional_pose_data() function in the PoseToStructFileRepConverter was deleted during the XRW. This adds it back.
This should cause a bunch of integration test changes. All the data that weren't being written out to PDBs should be there, now.
@jadolfbr @tlinsky
commit ca1020b5facec3d9dd734e61601a6378abe89b99
Date: Fri Feb 26 15:02:03 2016 -0500
fix merge conflict in apps.src.settings to fix build. Tested that it compiles, other tests belong to previous commit.
commit c9c96ae82bc57f5368be8b721074bd7f3245adc9
Merge: a15e526 4571793
Date: Fri Feb 26 12:17:05 2016 -0600
Merge pull request #1126 from RosettaCommons/olungu/basic_settings
Olungu/basic_settings
commit a15e526f1a02f2784ecc62a6d8f5eb4b13b4c930
Merge: a79b112 48054f1
Date: Fri Feb 26 10:58:01 2016 -0700
Merge pull request #1109 from RosettaCommons/PyRosetta
Updating show functions for ScoreFunction and Energies so they work correctly in Jupyter notebook (redirecting output to Tracer instead of std::cout)
commit a79b1125a02b045fde921e98238e2ff060b99609
Merge: 5c3a26f 900c48b
Date: Fri Feb 26 04:08:11 2016 -0800
Merge pull request #1128 from RosettaCommons/vmullig/update_pro_close
Adding support for cyclic geometry to the pro_close energy term.
This is a piece of pull request #1093 that I want to merge separately, so that I can see what's changing what in the integration tests.
The usual integration test instabilities are seen.
commit 5c3a26fa2f90011357721f04051696ef80467b3c
Merge: 6ec414a 6ad87f2
Date: Thu Feb 25 22:33:19 2016 -0800
Merge pull request #1113 from RosettaCommons/imv-uw/cache_layer_selection
enable LayerSelector selection caching as a non-default option
commit 6ec414ae58a5550132ed0c47e73a7329fce48bd7
Merge: a9b534a 23d6844
Date: Thu Feb 25 22:11:18 2016 -0800
Merge pull request #1087 from RosettaCommons/everyday847/a3b_idealization
Secondary structure minimization bugfixes, hooray! And a3b parameters for ideal Crick-ian helices.
commit a9b534afd72fed963882ccf5a8c844fe78f46262
Merge: 2223f3d a2d53c6
Date: Thu Feb 25 18:28:41 2016 -0800
Merge pull request #945 from RosettaCommons/jadolfbr/simple_threader
Jadolfbr/simple threader
Adds a SimpleThreadingMover to Rosetta and RosettaScripts in simple_moves.
This mover is exactly what the name suggests. Thread a sequence from start_position onto a pose. Sequence is 'threaded' together and packed. Optionally pack neighbors using loop machinery. If '-' is in the sequence will skip those positions.
Example with neighbor packing:
```
```
https://www.rosettacommons.org/docs/wiki/scripting_documentation/RosettaScripts/Movers/movers_pages/SimpleThreadingMover
commit 2223f3d527d7c9d8fe3334625ab2fb9d8700b65c
Merge: c034895 f7c4d47
Date: Thu Feb 25 14:02:06 2016 -0800
Merge pull request #1121 from RosettaCommons/vmullig/fix_irm_again
Trying to fix the inverse_rotamer_remodel integration test.
This was broken by a combination of recent XRW-related changes to PDB output. Attempting a simple fix.
commit c0348954e1c6330eb3d84359aca99625f88fde7e
Merge: 9af92c6 a9657f7
Date: Thu Feb 25 12:03:17 2016 -0800
Merge pull request #1125 from RosettaCommons/everyday847/beta_util
1. Adds a toy app for evaluating a few 3_14 helices and point mutations vs. a target.
2. Fixes a bug with annotated_sequence that would totally screw up creating noncanonical poses from sequence--it would create them by jumps every time.
3. Messes around with my macrocycles pilot app a bit.
4. Integration tests for macrocycles app, since it is compiled by default.
5. Activates metapatches for residues other than just the peptoid 101, as they were meant to be!
commit 9af92c682052714a8ba07ccd2b82c5b9acb4ec08
Merge: 4f131a5 7008514
Date: Thu Feb 25 14:41:07 2016 -0500
Merge pull request #1123 from RosettaCommons/nmarze/SnugDockTest
SnugDock integration test updates:
-Updating SnugDock integration test to include ensemble dock
-Making snugdock app public
-SnugDock integration test changes are expected
-All other integration test changes appear to be existing minor numeric instabilities
commit 4f131a5552e9b7d397f3b0c908385960328ea65b
Merge: fd41b7a 5a75b59
Date: Wed Feb 24 14:17:53 2016 -0600
Merge pull request #1122 from RosettaCommons/roccomoretti/branch_distances_public
Move batch_distances application to public.
Application was used in the publication doi:10.1073/pnas.1202485109, so should be public. (We had a request on the forums.)
This application already has an integration test.