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loops Namespace Reference

Namespaces

 ccd
 

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 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")
 
BooleanOptionKey const skip_initial_loop_build ("loops:skip_initial_loop_build")
 
StringOptionKey const remodel ("loops:remodel")
 
StringOptionKey const intermedrelax ("loops:intermedrelax")
 
StringOptionKey const refine ("loops:refine")
 
StringOptionKey const relax ("loops:relax")
 
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")
 
BooleanOptionKey const fix_ca_bond_angles ("loops:fix_ca_bond_angles")
 
BooleanOptionKey const kic_use_linear_chainbreak ("loops:kic_use_linear_chainbreak")
 
BooleanOptionKey const sample_omega_at_pre_prolines ("loops:sample_omega_at_pre_prolines")
 
BooleanOptionKey const allow_omega_move ("loops:allow_omega_move")
 
BooleanOptionKey const kic_with_cartmin ("loops:kic_with_cartmin")
 
BooleanOptionKey const allow_takeoff_torsion_move ("loops:allow_takeoff_torsion_move")
 
IntegerOptionKey const extend_length ("loops:extend_length")
 
IntegerOptionKey const perturb_outer_cycles ("loops:perturb_outer_cycles")
 
IntegerOptionKey const refine_outer_cycles ("loops:refine_outer_cycles")
 
IntegerOptionKey const max_inner_cycles ("loops:max_inner_cycles")
 
IntegerOptionKey const repack_period ("loops:repack_period")
 
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")
 
IntegerOptionKey const kic_num_rotamer_trials ("loops:kic_num_rotamer_trials")
 
BooleanOptionKey const kic_omega_sampling ("loops:kic_omega_sampling")
 
RealOptionKey const kic_bump_overlap_factor ("loops:kic_bump_overlap_factor")
 
IntegerOptionKey const minimize_max_iter ("loops:minimize_max_iter")
 
StringOptionKey const restrict_kic_sampling_to_torsion_string ("loops:restrict_kic_sampling_to_torsion_string")
 
BooleanOptionKey const derive_torsion_string_from_native_pose ("loops:derive_torsion_string_from_native_pose")
 
BooleanOptionKey const always_remodel_full_loop ("loops:always_remodel_full_loop")
 
BooleanOptionKey const taboo_sampling ("loops:taboo_sampling")
 
BooleanOptionKey const taboo_in_fa ("loops:taboo_in_fa")
 
BooleanOptionKey const ramp_fa_rep ("loops:ramp_fa_rep")
 
BooleanOptionKey const ramp_rama ("loops:ramp_rama")
 
BooleanOptionKey const kic_rama2b ("loops:kic_rama2b")
 
BooleanOptionKey const kic_leave_centroid_after_initial_closure ("loops:kic_leave_centroid_after_initial_closure")
 
BooleanOptionKey const legacy_kic ("loops:legacy_kic")
 
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 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 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('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 = 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 = TaskFactory.create_packer_task(starting_p)
 
tuple pack = protocols.minimization_packing.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::allow_omega_move ( "loops:allow_omega_move"  )
BooleanOptionKey const loops::allow_takeoff_torsion_move ( "loops:allow_takeoff_torsion_move"  )
BooleanOptionKey const loops::alternative_closure_protocol ( "loops:alternative_closure_protocol"  )
BooleanOptionKey const loops::always_remodel_full_loop ( "loops:always_remodel_full_loop"  )
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"  )
BooleanOptionKey const loops::derive_torsion_string_from_native_pose ( "loops:derive_torsion_string_from_native_pose"  )
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::fast ( "loops:fast"  )
BooleanOptionKey const loops::final_clean_fastrelax ( "loops:final_clean_fastrelax"  )
RealOptionKey const loops::final_score_filter ( "loops:final_score_filter"  )
BooleanOptionKey const loops::fix_ca_bond_angles ( "loops:fix_ca_bond_angles"  )
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"  )
RealOptionKey const loops::kic_bump_overlap_factor ( "loops:kic_bump_overlap_factor"  )
BooleanOptionKey const loops::kic_leave_centroid_after_initial_closure ( "loops:kic_leave_centroid_after_initial_closure"  )
IntegerOptionKey const loops::kic_max_seglen ( "loops:kic_max_seglen"  )
BooleanOptionKey const loops::kic_min_after_repack ( "loops:kic_min_after_repack"  )
IntegerOptionKey const loops::kic_num_rotamer_trials ( "loops:kic_num_rotamer_trials"  )
BooleanOptionKey const loops::kic_omega_sampling ( "loops:kic_omega_sampling"  )
BooleanOptionKey const loops::kic_rama2b ( "loops:kic_rama2b"  )
BooleanOptionKey const loops::kic_recover_last ( "loops:kic_recover_last"  )
BooleanOptionKey const loops::kic_use_linear_chainbreak ( "loops:kic_use_linear_chainbreak"  )
BooleanOptionKey const loops::kic_with_cartmin ( "loops:kic_with_cartmin"  )
IntegerOptionKey const loops::kinematic_wrapper_cycles ( "loops:kinematic_wrapper_cycles"  )
BooleanOptionKey const loops::legacy_kic ( "loops:legacy_kic"  )
RealOptionKey const loops::loop_combine_rate ( "loops:loop_combine_rate"  )
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"  )
IntegerOptionKey const loops::minimize_max_iter ( "loops:minimize_max_iter"  )
FileOptionKey const loops::mm_loop_file ( "loops:mm_loop_file"  )
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"  )
FileOptionKey const loops::output_pdb ( "loops:output_pdb"  )
IntegerOptionKey const loops::perturb_outer_cycles ( "loops:perturb_outer_cycles"  )
BooleanOptionKey const loops::ramp_fa_rep ( "loops:ramp_fa_rep"  )
BooleanOptionKey const loops::ramp_rama ( "loops:ramp_rama"  )
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"  )
IntegerOptionKey const loops::refine_outer_cycles ( "loops:refine_outer_cycles"  )
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"  )
IntegerOptionKey const loops::repack_period ( "loops:repack_period"  )
StringOptionKey const loops::restrict_kic_sampling_to_torsion_string ( "loops:restrict_kic_sampling_to_torsion_string"  )
RealOptionKey const loops::rmsd_tol ( "loops:rmsd_tol"  )
BooleanOptionKey const loops::sample_omega_at_pre_prolines ( "loops:sample_omega_at_pre_prolines"  )
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"  )
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"  )
BooleanOptionKey const loops::skip_initial_loop_build ( "loops:skip_initial_loop_build"  )
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::taboo_in_fa ( "loops:taboo_in_fa"  )
BooleanOptionKey const loops::taboo_sampling ( "loops:taboo_sampling"  )
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_4().

int loops.cutpoint = 81
float loops.final_temp = 0.8
tuple loops.fragset3mer = ConstantLengthFragSet(3, "test_in3_fragments")
tuple loops.gamma = math.pow((final_temp/init_temp),(1.0/(outer_cycles*inner_cycles)))
float loops.init_temp = 2.0
int loops.inner_cycles = 30
tuple loops.jd = Job_dist("loop_output", 100, scorefxn_high)
loops.kT = init_temp
int loops.loop_begin = 77
int loops.loop_end = 85
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_loop = Loop( loop_begin, loop_end, cutpoint)
tuple loops.my_loops = Loops()
int loops.outer_cycles = 10
tuple loops.p = Pose()
tuple loops.pack = protocols.minimization_packing.PackRotamersMover( scorefxn_high, task_pack )
tuple loops.recover_sidechains = protocols.simple_moves.ReturnSidechainMover(starting_p)
tuple loops.scorefxn_high = create_score_function('standard', 'score12')
tuple loops.scorefxn_low = create_score_function('cen_std')
tuple loops.starting_p = Pose()
tuple loops.starting_p_centroid = Pose()
tuple loops.task_pack = TaskFactory.create_packer_task(starting_p)
tuple loops.to_centroid = protocols.simple_moves.SwitchResidueTypeSetMover('centroid')
tuple loops.to_fullatom = protocols.simple_moves.SwitchResidueTypeSetMover('fa_standard')