Rosetta
2019.07
|
Variables | |
int | MAX_KIC_BUILD_ATTEMPTS = 10000 |
tuple | p = core.import_pose.pose_from_file( "../test/data/2cpl_min.pdb" ) |
tuple | starting_p = Pose() |
tuple | scorefxn_low = protocols.loops.get_cen_scorefxn() |
tuple | scorefxn_high = protocols.loops.get_fa_scorefxn() |
tuple | pymol = PyMOLMover() |
int | loop_begin = 145 |
int | loop_end = 155 |
int | loop_cut = 150 |
tuple | my_loop = protocols.loops.Loop( loop_begin, loop_end, loop_cut ) |
tuple | my_loops = protocols.loops.Loops() |
tuple | movemap = MoveMap() |
tuple | kic_mover = KinematicMover() |
tuple | to_centroid = protocols.simple_moves.SwitchResidueTypeSetMover( 'centroid' ) |
tuple | to_fullatom = protocols.simple_moves.SwitchResidueTypeSetMover( 'fa_standard' ) |
tuple | recover_sidechains = protocols.simple_moves.ReturnSidechainMover( starting_p ) |
tuple | task_pack = core.pack.task.TaskFactory.create_packer_task( starting_p ) |
tuple | pack = protocols.minimization_packing.PackRotamersMover( scorefxn_high, task_pack ) |
tuple | mm = MoveMap() |
float | tol = 0.001 |
string | min_type = "linmin" |
tuple | linmin_mover = protocols.minimization_packing.MinMover( mm, scorefxn_low, min_type, tol, True ) |
tuple | starting_p_centroid = Pose() |
success = False | |
int | outer_cycles = 1 |
int | inner_cycles = 1 |
float | init_temp = 2.0 |
float | final_temp = 1.0 |
tuple | gamma = math.pow( ( final_temp/init_temp ),( 1.0/( outer_cycles*inner_cycles ) ) ) |
kT = init_temp | |
tuple | mc = MonteCarlo( p, scorefxn_low, kT ) |
tuple | kic_start = randrange( loop_begin, loop_end - 1 ) |
tuple | kic_end = randrange( kic_start+2, loop_end+1 ) |
tuple | middle_offset = ( kic_end - kic_start ) |
kic_middle = kic_start+middle_offset | |
tuple | rms = protocols.loops.loop_rmsd( p, starting_p, my_loops ) |
tuple | loop_refine = rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC( my_loops ) |
float test.T650_LoopsKIC.final_temp = 1.0 |
tuple test.T650_LoopsKIC.gamma = math.pow( ( final_temp/init_temp ),( 1.0/( outer_cycles*inner_cycles ) ) ) |
float test.T650_LoopsKIC.init_temp = 2.0 |
int test.T650_LoopsKIC.inner_cycles = 1 |
test.T650_LoopsKIC.kic_middle = kic_start+middle_offset |
tuple test.T650_LoopsKIC.kic_mover = KinematicMover() |
tuple test.T650_LoopsKIC.kic_start = randrange( loop_begin, loop_end - 1 ) |
test.T650_LoopsKIC.kT = init_temp |
tuple test.T650_LoopsKIC.linmin_mover = protocols.minimization_packing.MinMover( mm, scorefxn_low, min_type, tol, True ) |
int test.T650_LoopsKIC.loop_begin = 145 |
int test.T650_LoopsKIC.loop_cut = 150 |
int test.T650_LoopsKIC.loop_end = 155 |
tuple test.T650_LoopsKIC.loop_refine = rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC( my_loops ) |
int test.T650_LoopsKIC.MAX_KIC_BUILD_ATTEMPTS = 10000 |
tuple test.T650_LoopsKIC.mc = MonteCarlo( p, scorefxn_low, kT ) |
string test.T650_LoopsKIC.min_type = "linmin" |
Referenced by add_rosetta_options_1(), add_rosetta_options_12(), add_rosetta_options_13(), add_rosetta_options_14(), add_rosetta_options_7(), Minimize.apply(), NCMinimize.apply(), HDdesignMover.apply(), HbsDesignMover.apply(), PeptoidDesignMover.apply(), OopDesignMover.apply(), DougsDockDesignMinimizeMagicMover.apply(), UBQ_GTPase_disulfide_Mover.apply(), UBQ_E2Mover.apply(), main(), and HDdesignMover.sym_repack_minimize().
tuple test.T650_LoopsKIC.mm = MoveMap() |
tuple test.T650_LoopsKIC.movemap = MoveMap() |
tuple test.T650_LoopsKIC.my_loop = protocols.loops.Loop( loop_begin, loop_end, loop_cut ) |
tuple test.T650_LoopsKIC.my_loops = protocols.loops.Loops() |
int test.T650_LoopsKIC.outer_cycles = 1 |
tuple test.T650_LoopsKIC.p = core.import_pose.pose_from_file( "../test/data/2cpl_min.pdb" ) |
tuple test.T650_LoopsKIC.pack = protocols.minimization_packing.PackRotamersMover( scorefxn_high, task_pack ) |
tuple test.T650_LoopsKIC.pymol = PyMOLMover() |
tuple test.T650_LoopsKIC.recover_sidechains = protocols.simple_moves.ReturnSidechainMover( starting_p ) |
tuple test.T650_LoopsKIC.rms = protocols.loops.loop_rmsd( p, starting_p, my_loops ) |
tuple test.T650_LoopsKIC.scorefxn_high = protocols.loops.get_fa_scorefxn() |
tuple test.T650_LoopsKIC.scorefxn_low = protocols.loops.get_cen_scorefxn() |
tuple test.T650_LoopsKIC.starting_p = Pose() |
tuple test.T650_LoopsKIC.starting_p_centroid = Pose() |
test.T650_LoopsKIC.success = False |
tuple test.T650_LoopsKIC.task_pack = core.pack.task.TaskFactory.create_packer_task( starting_p ) |
tuple test.T650_LoopsKIC.to_centroid = protocols.simple_moves.SwitchResidueTypeSetMover( 'centroid' ) |
tuple test.T650_LoopsKIC.to_fullatom = protocols.simple_moves.SwitchResidueTypeSetMover( 'fa_standard' ) |
float test.T650_LoopsKIC.tol = 0.001 |