Rosetta 3.3
Functions | Variables
loops Namespace Reference

Functions

BooleanOptionKey const loops ("loops")
StringOptionKey const cen_weights ("loops:cen_weights")
StringOptionKey const cen_patch ("loops:cen_patch")
FileOptionKey const input_pdb ("loops:input_pdb")
StringVectorOptionKey const loop_file ("loops:loop_file")
FileOptionKey const extended_loop_file ("loops:extended_loop_file")
FileOptionKey const mm_loop_file ("loops:mm_loop_file")
BooleanOptionKey const fix_natsc ("loops:fix_natsc")
BooleanOptionKey const refine_only ("loops:refine_only")
BooleanOptionKey const fa_input ("loops:fa_input")
BooleanOptionKey const fast ("loops:fast")
FileOptionKey const vall_file ("loops:vall_file")
IntegerVectorOptionKey const frag_sizes ("loops:frag_sizes")
FileVectorOptionKey const frag_files ("loops:frag_files")
FileOptionKey const output_pdb ("loops:output_pdb")
BooleanOptionKey const debug ("loops:debug")
BooleanOptionKey const build_initial ("loops:build_initial")
BooleanOptionKey const extended ("loops:extended")
BooleanOptionKey const remove_extended_loops ("loops:remove_extended_loops")
BooleanOptionKey const idealize_after_loop_close ("loops:idealize_after_loop_close")
BooleanOptionKey const idealize_before_loop_close ("loops:idealize_before_loop_close")
IntegerOptionKey const select_best_loop_from ("loops:select_best_loop_from")
IntegerOptionKey const build_attempts ("loops:build_attempts")
IntegerOptionKey const grow_attempts ("loops:grow_attempts")
RealOptionKey const random_grow_loops_by ("loops:random_grow_loops_by")
BooleanOptionKey const accept_aborted_loops ("loops:accept_aborted_loops")
BooleanOptionKey const strict_loops ("loops:strict_loops")
BooleanOptionKey const superimpose_native ("loops:superimpose_native")
IntegerVectorOptionKey const build_specific_loops ("loops:build_specific_loops")
BooleanOptionKey const random_order ("loops:random_order")
BooleanOptionKey const build_all_loops ("loops:build_all_loops")
BooleanOptionKey const fa_closure_protocol ("loops:fa_closure_protocol")
RealOptionKey const combine_rate ("loops:combine_rate")
StringOptionKey const remodel ("loops:remodel")
StringOptionKey const intermedrelax ("loops:intermedrelax")
StringOptionKey const refine ("loops:refine")
StringOptionKey const relax ("loops:relax")
IntegerOptionKey const n_rebuild_tries ("loops:n_rebuild_tries")
BooleanOptionKey const final_clean_fastrelax ("loops:final_clean_fastrelax")
BooleanOptionKey const relax_with_foldtree ("loops:relax_with_foldtree")
RealOptionKey const constrain_rigid_segments ("loops:constrain_rigid_segments")
StringOptionKey const loopscores ("loops:loopscores")
BooleanOptionKey const timer ("loops:timer")
BooleanOptionKey const vicinity_sampling ("loops:vicinity_sampling")
RealOptionKey const vicinity_degree ("loops:vicinity_degree")
RealOptionKey const neighbor_dist ("loops:neighbor_dist")
IntegerOptionKey const kic_max_seglen ("loops:kic_max_seglen")
BooleanOptionKey const kic_recover_last ("loops:kic_recover_last")
BooleanOptionKey const kic_min_after_repack ("loops:kic_min_after_repack")
BooleanOptionKey const optimize_only_kic_region_sidechains_after_move ("loops:optimize_only_kic_region_sidechains_after_move")
IntegerOptionKey const max_kic_build_attempts ("loops:max_kic_build_attempts")
IntegerOptionKey const remodel_kic_attempts ("loops:remodel_kic_attempts")
IntegerOptionKey const max_kic_perturber_samples ("loops:max_kic_perturber_samples")
BooleanOptionKey const nonpivot_torsion_sampling ("loops:nonpivot_torsion_sampling")
IntegerOptionKey const extend_length ("loops:extend_length")
IntegerOptionKey const outer_cycles ("loops:outer_cycles")
IntegerOptionKey const max_inner_cycles ("loops:max_inner_cycles")
IntegerOptionKey const repack_period ("loops:repack_period")
BooleanOptionKey const repack_never ("loops:repack_never")
RealOptionKey const remodel_init_temp ("loops:remodel_init_temp")
RealOptionKey const remodel_final_temp ("loops:remodel_final_temp")
RealOptionKey const refine_init_temp ("loops:refine_init_temp")
RealOptionKey const refine_final_temp ("loops:refine_final_temp")
IntegerOptionKey const gapspan ("loops:gapspan")
IntegerOptionKey const spread ("loops:spread")
IntegerOptionKey const kinematic_wrapper_cycles ("loops:kinematic_wrapper_cycles")
BooleanOptionKey const alternative_closure_protocol ("loops:alternative_closure_protocol")
RealOptionKey const chainbreak_max_accept ("loops:chainbreak_max_accept")
BooleanOptionKey const debug_loop_closure ("loops:debug_loop_closure")
BooleanOptionKey const non_ideal_loop_closing ("loops:non_ideal_loop_closing")
RealOptionKey const scored_frag_cycles ("loops:scored_frag_cycles")
RealOptionKey const short_frag_cycles ("loops:short_frag_cycles")
RealOptionKey const rmsd_tol ("loops:rmsd_tol")
RealOptionKey const chain_break_tol ("loops:chain_break_tol")
BooleanOptionKey const random_loop ("loops:random_loop")
FileVectorOptionKey const stealfrags ("loops:stealfrags")
IntegerOptionKey const stealfrags_times ("loops:stealfrags_times")
RealOptionKey const coord_cst ("loops:coord_cst")
RealOptionKey const skip_1mers ("loops:skip_1mers")
RealOptionKey const skip_3mers ("loops:skip_3mers")
RealOptionKey const skip_9mers ("loops:skip_9mers")
BooleanOptionKey const loop_model ("loops:loop_model")
RealOptionKey const score_filter_cutoff ("loops:score_filter_cutoff")
BooleanOptionKey const loop_farlx ("loops:loop_farlx")
BooleanOptionKey const ccd_closure ("loops:ccd_closure")
BooleanOptionKey const skip_ccd_moves ("loops:skip_ccd_moves")
BooleanOptionKey const no_randomize_loop ("loops:no_randomize_loop")
BooleanOptionKey const loops_subset ("loops:loops_subset")
IntegerOptionKey const num_desired_loops ("loops:num_desired_loops")
RealOptionKey const loop_combine_rate ("loops:loop_combine_rate")
RealOptionKey const final_score_filter ("loops:final_score_filter")
BooleanOptionKey const no_combine_if_fail ("loops:no_combine_if_fail")
BooleanOptionKey const shorten_long_terminal_loop ("loops:shorten_long_terminal_loop")
IntegerOptionKey const backrub_trials ("loops:backrub_trials")
RealOptionKey const looprlx_cycle_ratio ("loops:looprlx_cycle_ratio")
RealOptionKey const extended_beta ("loops:extended_beta")
BooleanOptionKey const shortrelax ("loops:shortrelax")
BooleanOptionKey const fastrelax ("loops:fastrelax")
BooleanOptionKey const no_looprebuild ("loops:no_looprebuild")
BooleanOptionKey const allow_lig_move ("loops:allow_lig_move")
FileOptionKey const keep_natro ("loops:keep_natro")
IntegerOptionKey const refine_design_iterations ("loops:refine_design_iterations")

Variables

tuple p = Pose()
tuple starting_p = Pose()
tuple scorefxn_low = create_score_function('cen_std')
tuple scorefxn_high = create_score_function_ws_patch('standard', 'score12')
int loop_begin = 77
int loop_end = 85
int cutpoint = 81
tuple my_loop = Loop( loop_begin, loop_end, cutpoint)
tuple movemap = MoveMap()
tuple fragset3mer = ConstantLengthFragSet(3, "test_in3_fragments")
tuple mover_3mer = ClassicFragmentMover(fragset3mer,movemap)
tuple ccd_closure = CcdLoopClosureMover(my_loop, movemap)
tuple to_centroid = SwitchResidueTypeSetMover('centroid')
tuple to_fullatom = SwitchResidueTypeSetMover('fa_standard')
tuple recover_sidechains = ReturnSidechainMover(starting_p)
tuple task_pack = TaskFactory.create_packer_task(starting_p)
tuple pack = PackRotamersMover( scorefxn_high, task_pack )
tuple starting_p_centroid = Pose()
tuple jd = Job_dist("loop_output", 100, scorefxn_high)
int outer_cycles = 10
int inner_cycles = 30
float init_temp = 2.0
float final_temp = 0.8
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 my_loops = Loops()
tuple loop_refine = LoopMover_Refine_CCD(my_loops)
tuple Lrms = loop_rmsd(p, starting_p, my_loops, True)

Function Documentation

BooleanOptionKey const loops::accept_aborted_loops ( "loops:accept_aborted_loops"  )
BooleanOptionKey const loops::allow_lig_move ( "loops:allow_lig_move"  )
BooleanOptionKey const loops::alternative_closure_protocol ( "loops:alternative_closure_protocol"  )
IntegerOptionKey const loops::backrub_trials ( "loops:backrub_trials"  )
BooleanOptionKey const loops::build_all_loops ( "loops:build_all_loops"  )
IntegerOptionKey const loops::build_attempts ( "loops:build_attempts"  )
BooleanOptionKey const loops::build_initial ( "loops:build_initial"  )
IntegerVectorOptionKey const loops::build_specific_loops ( "loops:build_specific_loops"  )
BooleanOptionKey const loops::ccd_closure ( "loops:ccd_closure"  )
StringOptionKey const loops::cen_patch ( "loops:cen_patch"  )
StringOptionKey const loops::cen_weights ( "loops:cen_weights"  )
RealOptionKey const loops::chain_break_tol ( "loops:chain_break_tol"  )
RealOptionKey const loops::chainbreak_max_accept ( "loops:chainbreak_max_accept"  )
RealOptionKey const loops::combine_rate ( "loops:combine_rate"  )
RealOptionKey const loops::constrain_rigid_segments ( "loops:constrain_rigid_segments"  )
RealOptionKey const loops::coord_cst ( "loops:coord_cst"  )
BooleanOptionKey const loops::debug ( "loops:debug"  )
BooleanOptionKey const loops::debug_loop_closure ( "loops:debug_loop_closure"  )
IntegerOptionKey const loops::extend_length ( "loops:extend_length"  )
BooleanOptionKey const loops::extended ( "loops:extended"  )
RealOptionKey const loops::extended_beta ( "loops:extended_beta"  )
FileOptionKey const loops::extended_loop_file ( "loops:extended_loop_file"  )
BooleanOptionKey const loops::fa_closure_protocol ( "loops:fa_closure_protocol"  )
BooleanOptionKey const loops::fa_input ( "loops:fa_input"  )
BooleanOptionKey const loops::fast ( "loops:fast"  )
BooleanOptionKey const loops::fastrelax ( "loops:fastrelax"  )
BooleanOptionKey const loops::final_clean_fastrelax ( "loops:final_clean_fastrelax"  )
RealOptionKey const loops::final_score_filter ( "loops:final_score_filter"  )
BooleanOptionKey const loops::fix_natsc ( "loops:fix_natsc"  )
FileVectorOptionKey const loops::frag_files ( "loops:frag_files"  )
IntegerVectorOptionKey const loops::frag_sizes ( "loops:frag_sizes"  )
IntegerOptionKey const loops::gapspan ( "loops:gapspan"  )
IntegerOptionKey const loops::grow_attempts ( "loops:grow_attempts"  )
BooleanOptionKey const loops::idealize_after_loop_close ( "loops:idealize_after_loop_close"  )
BooleanOptionKey const loops::idealize_before_loop_close ( "loops:idealize_before_loop_close"  )
FileOptionKey const loops::input_pdb ( "loops:input_pdb"  )
StringOptionKey const loops::intermedrelax ( "loops:intermedrelax"  )
FileOptionKey const loops::keep_natro ( "loops:keep_natro"  )
IntegerOptionKey const loops::kic_max_seglen ( "loops:kic_max_seglen"  )
BooleanOptionKey const loops::kic_min_after_repack ( "loops:kic_min_after_repack"  )
BooleanOptionKey const loops::kic_recover_last ( "loops:kic_recover_last"  )
IntegerOptionKey const loops::kinematic_wrapper_cycles ( "loops:kinematic_wrapper_cycles"  )
RealOptionKey const loops::loop_combine_rate ( "loops:loop_combine_rate"  )
BooleanOptionKey const loops::loop_farlx ( "loops:loop_farlx"  )
StringVectorOptionKey const loops::loop_file ( "loops:loop_file"  )
BooleanOptionKey const loops::loop_model ( "loops:loop_model"  )
RealOptionKey const loops::looprlx_cycle_ratio ( "loops:looprlx_cycle_ratio"  )
BooleanOptionKey const loops::loops ( "loops"  )
BooleanOptionKey const loops::loops_subset ( "loops:loops_subset"  )
StringOptionKey const loops::loopscores ( "loops:loopscores"  )
IntegerOptionKey const loops::max_inner_cycles ( "loops:max_inner_cycles"  )
IntegerOptionKey const loops::max_kic_build_attempts ( "loops:max_kic_build_attempts"  )
IntegerOptionKey const loops::max_kic_perturber_samples ( "loops:max_kic_perturber_samples"  )
FileOptionKey const loops::mm_loop_file ( "loops:mm_loop_file"  )
IntegerOptionKey const loops::n_rebuild_tries ( "loops:n_rebuild_tries"  )
RealOptionKey const loops::neighbor_dist ( "loops:neighbor_dist"  )
BooleanOptionKey const loops::no_combine_if_fail ( "loops:no_combine_if_fail"  )
BooleanOptionKey const loops::no_looprebuild ( "loops:no_looprebuild"  )
BooleanOptionKey const loops::no_randomize_loop ( "loops:no_randomize_loop"  )
BooleanOptionKey const loops::non_ideal_loop_closing ( "loops:non_ideal_loop_closing"  )
BooleanOptionKey const loops::nonpivot_torsion_sampling ( "loops:nonpivot_torsion_sampling"  )
IntegerOptionKey const loops::num_desired_loops ( "loops:num_desired_loops"  )
BooleanOptionKey const loops::optimize_only_kic_region_sidechains_after_move ( "loops:optimize_only_kic_region_sidechains_after_move"  )
IntegerOptionKey const loops::outer_cycles ( "loops:outer_cycles"  )
FileOptionKey const loops::output_pdb ( "loops:output_pdb"  )
RealOptionKey const loops::random_grow_loops_by ( "loops:random_grow_loops_by"  )
BooleanOptionKey const loops::random_loop ( "loops:random_loop"  )
BooleanOptionKey const loops::random_order ( "loops:random_order"  )
StringOptionKey const loops::refine ( "loops:refine"  )
IntegerOptionKey const loops::refine_design_iterations ( "loops:refine_design_iterations"  )
RealOptionKey const loops::refine_final_temp ( "loops:refine_final_temp"  )
RealOptionKey const loops::refine_init_temp ( "loops:refine_init_temp"  )
BooleanOptionKey const loops::refine_only ( "loops:refine_only"  )
StringOptionKey const loops::relax ( "loops:relax"  )
BooleanOptionKey const loops::relax_with_foldtree ( "loops:relax_with_foldtree"  )
StringOptionKey const loops::remodel ( "loops:remodel"  )
RealOptionKey const loops::remodel_final_temp ( "loops:remodel_final_temp"  )
RealOptionKey const loops::remodel_init_temp ( "loops:remodel_init_temp"  )
IntegerOptionKey const loops::remodel_kic_attempts ( "loops:remodel_kic_attempts"  )
BooleanOptionKey const loops::remove_extended_loops ( "loops:remove_extended_loops"  )
BooleanOptionKey const loops::repack_never ( "loops:repack_never"  )
IntegerOptionKey const loops::repack_period ( "loops:repack_period"  )
RealOptionKey const loops::rmsd_tol ( "loops:rmsd_tol"  )
RealOptionKey const loops::score_filter_cutoff ( "loops:score_filter_cutoff"  )
RealOptionKey const loops::scored_frag_cycles ( "loops:scored_frag_cycles"  )
IntegerOptionKey const loops::select_best_loop_from ( "loops:select_best_loop_from"  )
RealOptionKey const loops::short_frag_cycles ( "loops:short_frag_cycles"  )
BooleanOptionKey const loops::shorten_long_terminal_loop ( "loops:shorten_long_terminal_loop"  )
BooleanOptionKey const loops::shortrelax ( "loops:shortrelax"  )
RealOptionKey const loops::skip_1mers ( "loops:skip_1mers"  )
RealOptionKey const loops::skip_3mers ( "loops:skip_3mers"  )
RealOptionKey const loops::skip_9mers ( "loops:skip_9mers"  )
BooleanOptionKey const loops::skip_ccd_moves ( "loops:skip_ccd_moves"  )
IntegerOptionKey const loops::spread ( "loops:spread"  )
FileVectorOptionKey const loops::stealfrags ( "loops:stealfrags"  )
IntegerOptionKey const loops::stealfrags_times ( "loops:stealfrags_times"  )
BooleanOptionKey const loops::strict_loops ( "loops:strict_loops"  )
BooleanOptionKey const loops::superimpose_native ( "loops:superimpose_native"  )
BooleanOptionKey const loops::timer ( "loops:timer"  )
FileOptionKey const loops::vall_file ( "loops:vall_file"  )
RealOptionKey const loops::vicinity_degree ( "loops:vicinity_degree"  )
BooleanOptionKey const loops::vicinity_sampling ( "loops:vicinity_sampling"  )

Variable Documentation

tuple loops::ccd_closure = CcdLoopClosureMover(my_loop, movemap)

Referenced by add_rosetta_options_2().

float loops::final_temp = 0.8
tuple loops::fragset3mer = ConstantLengthFragSet(3, "test_in3_fragments")
float loops::init_temp = 2.0
tuple loops::jd = Job_dist("loop_output", 100, scorefxn_high)

Referenced by APDBCMover::apply(), and main().

tuple loops::loop_refine = LoopMover_Refine_CCD(my_loops)
tuple loops::Lrms = loop_rmsd(p, starting_p, my_loops, True)
tuple loops::mc = MonteCarlo(p, scorefxn_low, kT)
tuple loops::movemap = MoveMap()
tuple loops::mover_3mer = ClassicFragmentMover(fragset3mer,movemap)
tuple loops::my_loops = Loops()
tuple loops::p = Pose()
tuple loops::pack = PackRotamersMover( scorefxn_high, task_pack )

Referenced by main(), and packmin_unbound_pep().

tuple loops::recover_sidechains = ReturnSidechainMover(starting_p)
tuple loops::scorefxn_high = create_score_function_ws_patch('standard', 'score12')
tuple loops::scorefxn_low = create_score_function('cen_std')
tuple loops::starting_p = Pose()
tuple loops::task_pack = TaskFactory.create_packer_task(starting_p)
tuple loops::to_centroid = SwitchResidueTypeSetMover('centroid')
tuple loops::to_fullatom = SwitchResidueTypeSetMover('fa_standard')
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