Merge pull request #929 from RosettaCommons/dimaio/rama_prepro
This checkin adds the latest version of the beta energy function. It is enabled with the flag -beta_nov15. Also adding the flag -beta which will always point to the most recent energy function version.
Details of the energy function are available on the doc wiki at https://www.rosettacommons.org/docs/wiki/Overview-of-Seattle-Group-energy-function-optimization-project (overview) and https://www.rosettacommons.org/docs/wiki/Updates-beta-nov15 (this specific update).
29 integration tests fail. Most are related to:
a) cart_bonded scores changing due to typo being fixed in the default set (e.g. hybridization)
b) cart_bonded tracer change (e.g. antibody_designer)
c) the addition of new scoreterms cause the database_* and features* tests to fail
d) debug output removed from code (fuzzy)
e) bugfix to symmetric disulfidize (symm_disulfidize)
The following integration tests change for other reasons:
ddG_of_mutation
enzdes
flexpepdock
inv_kin_lig_loop_design
membrane_relax
mp_relax
mp_relax_w_ligand
next_generation_KIC
pocket_relax
splice_*
On closer inspection, all of them look to have very small score changes in their logs, which then propagate (perhaps the new score terms introduced changes the order in which scores are summed?)
Additionally, there are changes to sweep_respair_energies that are difficult to trace (since its just a binary diff) but I suspect they are related to the above.
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Merge pull request #927 from RosettaCommons/jadolfbr/ab_graft_mover
Add AntibodyCDRGrafter mover
Overview
------------
This PR adds a mover for antibody grafting with settings I've used for antibody design with a RosettaScript implementation that can graft from file or save_pose_mover reference name. It is usually quite fast, and using both graft movers (the default) results in 100% graft closure as measured by bond lengths and angles at the connection points. Unit tests and Docs added.
Documentation:
---------------------
https://www.rosettacommons.org/docs/wiki/scripting_documentation/RosettaScripts/Movers/movers_pages/AntibodyCDRGrafter
Test Changes:
-------------------
No integration test changes expected other than cosmetic changes to antibody designer due to name change of AntibodyDesignModeler.
Sample Script
-------------------
```
<ROSETTASCRIPTS>
<MOVERS>
<AntibodyCDRGrafter name=grafter cdrs=L2,L1,H4 cdr_definition=North numbering_scheme=AHO_Scheme donor_structure_from_pdb=mis_start.pdb use_secondary_graft_mover=1 optimize_cdrs=1 optimize_cdr4_if_neighbor=1/>
</MOVERS>
<PROTOCOLS>
<Add mover_name=grafter/>
</PROTOCOLS>
</ROSETTASCRIPTS>
```
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Merge pull request #923 from RosettaCommons/rhiju/seg_id_update
Rhiju/seg id update
In tests, removes SEGMENT_ID lines from the stepwise silent files, as expected.
There are still the ~10 tests that always change due to numerical instabilities
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Merge pull request #928 from RosettaCommons/vmullig/shuffle_libraries
Move ResidueSelectors to core.3 from core.4, and to a new directory
This is in anticipation of development work that will allow ResidueSelectors to be used as input to Constraints (and other things). I think it makes sense for ResidueSelectors to be moved away from the PackerTask machinery: though they can be used as input into a TaskOperation, they really should become the standard way of selecting residues for anything in Rosetta that takes a residue selection.
Tasks:
-- Move ResidueSelectors to core/select/residue_selectors. Everything associated with just selecting residues (or atoms, or anything else that we might one day be able to select), independent of the packer, will now live in core/select (core.3); packer-associated stuff will remain in core/pack (core.4).
-- Keep the ClashBasedRepackShellSelector in core/pack/task/residue_selector, since it has core.4 dependencies. Create a Creator for this, since its base class (and the Creators list associated with the base class) is now in a different namespace.
-- Move interface_vector_calculate from core/pack/task/operation/util to core/select/util, and from core.4 to core.3. This resolves library dependency issues and keeps selection logic separate from packer-specific logic.
-- Move SelectResiduesByLayer from core/util to core/select/util, and from core.4 to core.3. This also resolves library dependency issues and helps to group selection logic in core/select.
-- Ensure that all namespaces, all tracer names, and all unit tests are updated to reflect the new directory and namespace organization.
All of this should result in cosmetic integration test changes resulting from changed namespaces (which is why I want it to be a separate pull request from the other stuff that I'm doing in pull request #926), but no actual functionality changes.
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Merge pull request #932 from RosettaCommons/vmullig/small_aacomp_bug
Fixing a minor bug in AACompositionEnergySetup
Fixing a minor bug in AACompositionEnergySetup that would affect the copying of PROPERTIES and NOT_PROPERTIES definitions when using the aa_composition score term. This will likely affect the bundlegridsampler_composition_energy integration test. This is minor enough that I'm going to merge it without testing it first.
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Merge pull request #925 from RosettaCommons/fsee/roleMoverInt
Adding features to RollMover
Merged Will's RollMover with master by adding a few features.
Modify the RollMover
Integration test
Merge latest master into branch
Beautify code
Update documentation
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Merge pull request #916 from RosettaCommons/vmullig/layerselect
Create a LayerSelect ResidueSelector (like LayerDesign)
ResidueSelectors were initially created because of frustrations involving LayerDesign, a TaskOperation used both to define selections of residue (core, boundary, surface, based on burial) and also to configure packer behaviour. However, LayerDesign has never properly been replaced by ResidueSelectors because there is no selector to select based on layer. This pull request is intended to rectify this. It also:
Partially solves the headaches of mixed canonical/noncanonical design. (LayerDesign is a pain for that, since it can only define layers -- not regions based on linear sequence -- and can only turn canonicals off and non-canonicals on).
Sets up the infrastructure for letting the aa_composition score term count residue types in different sub-regions of a pose (a common request from users being layer-based scoring).
Tasks:
- Move the layer selection logic from protocols to core so that it can be called by core classes. (This is useful, fundamental code that really should be in core in any case.)
- Correct dependencies in LayerDesign.
- Correct dependencies in RotamerBoltzmannWeight.
- Correct various other dependencies.
- Give the user control over sidechain neighbour parameters (cone width, cone length, sigmoid falloff, etc.)
- Distance falloff.
- Factor by which overall residue count is divided.
- Angular factor. (Note that this is calculated poorly, currently. This needs to be refactored, albeit in a way that preserves the current functionality.)
- Document these in LayerDesign.
- Implement a LayerSelect ResidueSelector.
- parse_my_tag()
- apply()
- Documentation.
- Integration test.
- Tweak the ReadResfile TaskOperation to accept a ResidueSelector as a mask.
- Documentation.
- Integration test.
- While I'm at it, fix the irritating behaviour of the ReadResfile TaskOperation that has it read the resfile repeatedly, at apply time, rather than at parse time. (I'm sure the Blue Gene people are a bit sick of this.)
- Track down and fix current issues:
- dna_interface_design integration test failure to run.
- sequence_profile_constraints integration test failure to run.
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Merge pull request #920 from RosettaCommons/sergey/colors
- Adding channel_color and channel_name_color variables to Tracer so now it is possible to specify default colors for particular Tracer object
- Adding extra constructor which allows to specify colors
- Making Tracer to send color ’Reset’ before each new line
- Updating ColorsDemo app
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Merge pull request #736 from RosettaCommons/antibody
Adding antibody/grafting which is a C++ port of antibody.py script. Right now the following parts is ported/implemented:
- regex-based CDR detection
- Chothia Numberer
- SCS with NCBI B+ template selection implementation
- some grafting code
Also: fixes to CSI code (proper detection of TTY) and various other small fixes.
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Merge pull request #915 from RosettaCommons/sergey/eigen
Upgrading Eigen lib so Rosetta could now be build with GCC-4.9+. Some regression tests is expected due to changes in linear algebra code.
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Merge pull request #918 from RosettaCommons/kimdn/dn
- Minor updates of sewing
1) Update of ModelTrimmer
* From now on, ModelTrimmer mandatorily removes any models with L
terminal segment
* Do 'leave_models_with_E_terminal_ss' mandatorily when
'leave_antiparallel_way_H_bonded_models_by_terminal_strands_only' turned on
2) Update of MonteCarloAssemblyMover
* User can turn remove_cut_off_assembly option on/off for MonteCarloAssemblyMover
3) Update of sewing_hasher
* Added comment "Only terminal Es are hash bool true to be merged with other nodes
later (but as of 2015/11/14, later model assembly has 'ERROR:
alignment_scores.size() == 1')"
4) Integration test
continuous_sewing_hasher and discontinuous_sewing_hasher changed as expected
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