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deleted a tracer in SSMotifFinderFilter
Updating PyRosetta dependency calculation algorithm
Fixing Linux PyRosetta build
fix to RDAT.cc to compile on linux!
Add a set of simple_movers for grafting, make all and GraftMovers and utility movers available to RS
This commit adds a set of simple movers to protocols/grafting, which are basically wrappers to some grafting utility functions.
Combined with SavePoseMover and the main GraftMovers, both CCDEndsGraftMover and AnchoredGraftMover, one can create a grafting protocol within RS.
Adds unit tests for all the simple movers
No integration test changes expected.
Here is an example RS for grafting CDRS from one renumbered antibody into another:
<ROSETTASCRIPTS>
<MOVERS>
<SavePoseMover name=save_current reference_name=current/>
<SavePoseMover name=save_CDR reference_name=CDR/>
<SavePoseMover name=restore_current restore_pose=1 reference_name=current/>
<SavePoseMover name=restore_ab restore_pose=1 reference_name=ab pdb_file=%%from%%/>
<ParsedProtocol name=save_cdr_restore >
<Add mover=save_CDR />
<Add mover=restore_current />
</ParsedProtocol>
<ParsedProtocol name=save_current_restore_ab >
<Add mover=save_current />
<Add mover=restore_ab />
</ParsedProtocol>
<KeepRegionMover name=k_L1 start_pdb_num=24L end_pdb_num=42L nter_overhang=2 cter_overhang=2/>
<KeepRegionMover name=k_L2 start_pdb_num=57L end_pdb_num=72L nter_overhang=2 cter_overhang=2/>
<KeepRegionMover name=k_L3 start_pdb_num=107L end_pdb_num=138L nter_overhang=2 cter_overhang=2/>
<KeepRegionMover name=k_H1 start_pdb_num=24H end_pdb_num=42H nter_overhang=2 cter_overhang=2/>
<KeepRegionMover name=k_H2 start_pdb_num=57H end_pdb_num=69H nter_overhang=2 cter_overhang=2/>
<KeepRegionMover name=k_H3 start_pdb_num=107H end_pdb_num=138H nter_overhang=2 cter_overhang=2/>
<CCDEndsGraftMover name=graft_L1 start_pdb_num=23L end_pdb_num=43L spm_reference_name=CDR copy_pdbinfo=1/>
<CCDEndsGraftMover name=graft_L2 start_pdb_num=56L end_pdb_num=73L spm_reference_name=CDR copy_pdbinfo=1/>
<CCDEndsGraftMover name=graft_L3 start_pdb_num=106L end_pdb_num=139L spm_reference_name=CDR copy_pdbinfo=1/>
<CCDEndsGraftMover name=graft_H1 start_pdb_num=23H end_pdb_num=43H spm_reference_name=CDR copy_pdbinfo=1/>
<CCDEndsGraftMover name=graft_H2 start_pdb_num=56H end_pdb_num=70H spm_reference_name=CDR copy_pdbinfo=1/>
<CCDEndsGraftMover name=graft_H3 start_pdb_num=106H end_pdb_num=139H spm_reference_name=CDR copy_pdbinfo=1/>
</MOVERS>
<PROTOCOLS>
<Add mover_name=save_current />
<Add mover_name=restore_ab/>
<Add mover_name=k_L1 />
<Add mover_name=save_cdr_restore/>
<Add mover_name=graft_L1/>
<Add mover_name=save_current_restore_ab/>
<Add mover_name=k_L2/>
<Add mover_name=save_cdr_restore/>
<Add mover_name=graft_L2/>
<Add mover_name=save_current_restore_ab/>
<Add mover_name=k_L3/>
<Add mover_name=save_cdr_restore/>
<Add mover_name=graft_L3/>
<Add mover_name=save_current_restore_ab/>
<Add mover_name=k_H1/>
<Add mover_name=save_cdr_restore/>
<Add mover_name=graft_H1/>
<Add mover_name=save_current_restore_ab/>
<Add mover_name=k_H2/>
<Add mover_name=save_cdr_restore/>
<Add mover_name=graft_H2/>
<Add mover_name=save_current_restore_ab/>
<Add mover_name=k_H3/>
<Add mover_name=save_cdr_restore/>
<Add mover_name=graft_H3/>
<Add mover_name=save_current/>
</PROTOCOLS>
</ROSETTASCRIPTS>
small fixes to get rna puzzle 12 jobs to run
Reenable warnings-as-errors in scons.
Also fix warnings-as-errors issues with gcc and clang under linux.
Hopefully the test server doesn't pick up any additional ones.
fix to unit tests for hbond_type_manager.
Move packaged binding generation scripts into packaged_bindings submodule.
Moving egg-packaged binding generation scripts into standalone
packaged_bindings submodule to support independant modification of
package-oriented bindings. Updating packaged binding script to support
unix-like platforms.
Fixing PyRosetta monolith build
PyRosetta. Minor fix to Windows build.
adding protocols_b.4 to protocols_b.5.src.settings file. This should fix the build
Added a bond length creator for small molecules. Bond length sizes were determined from an averaging of the CSD. Works with gasteiger atom types. Added unit test.
Switching Benchmark PyRosetta builds to monolith mode. Removing some undefined functions.
Fix app_exception_handling integration test.
fixing FastRelax default options should also be used in parse_my_tags
some integration changes expected
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