Rosetta Utilities  2014.35
Namespaces | Functions | Variables
basic::options::OptionKeys::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")
 
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 outer_cycles ("loops: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")
 
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

BooleanOptionKey const loops
 
StringOptionKey const cen_weights
 
StringOptionKey const cen_patch
 
FileOptionKey const input_pdb
 
StringVectorOptionKey const loop_file
 
FileOptionKey const extended_loop_file
 
FileOptionKey const mm_loop_file
 
BooleanOptionKey const fix_natsc
 
BooleanOptionKey const refine_only
 
BooleanOptionKey const fast
 
FileOptionKey const vall_file
 
IntegerVectorOptionKey const frag_sizes
 
FileVectorOptionKey const frag_files
 
FileOptionKey const output_pdb
 
BooleanOptionKey const debug
 
BooleanOptionKey const build_initial
 
BooleanOptionKey const extended
 
BooleanOptionKey const remove_extended_loops
 
BooleanOptionKey const idealize_after_loop_close
 
BooleanOptionKey const idealize_before_loop_close
 
IntegerOptionKey const select_best_loop_from
 
IntegerOptionKey const build_attempts
 
IntegerOptionKey const grow_attempts
 
RealOptionKey const random_grow_loops_by
 
BooleanOptionKey const accept_aborted_loops
 
BooleanOptionKey const strict_loops
 
BooleanOptionKey const superimpose_native
 
IntegerVectorOptionKey const build_specific_loops
 
BooleanOptionKey const random_order
 
BooleanOptionKey const build_all_loops
 
BooleanOptionKey const fa_closure_protocol
 
RealOptionKey const combine_rate
 
StringOptionKey const remodel
 
StringOptionKey const intermedrelax
 
StringOptionKey const refine
 
StringOptionKey const relax
 
BooleanOptionKey const final_clean_fastrelax
 
BooleanOptionKey const relax_with_foldtree
 
RealOptionKey const constrain_rigid_segments
 
StringOptionKey const loopscores
 
BooleanOptionKey const timer
 
BooleanOptionKey const vicinity_sampling
 
RealOptionKey const vicinity_degree
 
RealOptionKey const neighbor_dist
 
IntegerOptionKey const kic_max_seglen
 
BooleanOptionKey const kic_recover_last
 
BooleanOptionKey const kic_min_after_repack
 
BooleanOptionKey const optimize_only_kic_region_sidechains_after_move
 
IntegerOptionKey const max_kic_build_attempts
 
IntegerOptionKey const remodel_kic_attempts
 
IntegerOptionKey const max_kic_perturber_samples
 
BooleanOptionKey const nonpivot_torsion_sampling
 
BooleanOptionKey const fix_ca_bond_angles
 
BooleanOptionKey const kic_use_linear_chainbreak
 
BooleanOptionKey const sample_omega_at_pre_prolines
 
BooleanOptionKey const allow_omega_move
 
BooleanOptionKey const kic_with_cartmin
 
BooleanOptionKey const allow_takeoff_torsion_move
 
IntegerOptionKey const extend_length
 
IntegerOptionKey const outer_cycles
 
IntegerOptionKey const max_inner_cycles
 
IntegerOptionKey const repack_period
 
RealOptionKey const remodel_init_temp
 
RealOptionKey const remodel_final_temp
 
RealOptionKey const refine_init_temp
 
RealOptionKey const refine_final_temp
 
IntegerOptionKey const gapspan
 
IntegerOptionKey const spread
 
IntegerOptionKey const kinematic_wrapper_cycles
 
IntegerOptionKey const kic_num_rotamer_trials
 
BooleanOptionKey const kic_omega_sampling
 
RealOptionKey const kic_bump_overlap_factor
 
StringOptionKey const restrict_kic_sampling_to_torsion_string
 
BooleanOptionKey const derive_torsion_string_from_native_pose
 
BooleanOptionKey const always_remodel_full_loop
 
BooleanOptionKey const taboo_sampling
 
BooleanOptionKey const taboo_in_fa
 
BooleanOptionKey const ramp_fa_rep
 
BooleanOptionKey const ramp_rama
 
BooleanOptionKey const kic_rama2b
 
BooleanOptionKey const kic_leave_centroid_after_initial_closure
 
BooleanOptionKey const legacy_kic
 
BooleanOptionKey const alternative_closure_protocol
 
RealOptionKey const chainbreak_max_accept
 
BooleanOptionKey const debug_loop_closure
 
BooleanOptionKey const non_ideal_loop_closing
 
RealOptionKey const scored_frag_cycles
 
RealOptionKey const short_frag_cycles
 
RealOptionKey const rmsd_tol
 
RealOptionKey const chain_break_tol
 
BooleanOptionKey const random_loop
 
FileVectorOptionKey const stealfrags
 
IntegerOptionKey const stealfrags_times
 
RealOptionKey const coord_cst
 
RealOptionKey const skip_1mers
 
RealOptionKey const skip_3mers
 
RealOptionKey const skip_9mers
 
BooleanOptionKey const loop_model
 
RealOptionKey const score_filter_cutoff
 
BooleanOptionKey const ccd_closure
 
BooleanOptionKey const skip_ccd_moves
 
BooleanOptionKey const no_randomize_loop
 
BooleanOptionKey const loops_subset
 
IntegerOptionKey const num_desired_loops
 
RealOptionKey const loop_combine_rate
 
RealOptionKey const final_score_filter
 
BooleanOptionKey const no_combine_if_fail
 
BooleanOptionKey const shorten_long_terminal_loop
 
IntegerOptionKey const backrub_trials
 
RealOptionKey const looprlx_cycle_ratio
 
RealOptionKey const extended_beta
 
BooleanOptionKey const no_looprebuild
 
BooleanOptionKey const allow_lig_move
 
FileOptionKey const keep_natro
 
IntegerOptionKey const refine_design_iterations
 

Function Documentation

BooleanOptionKey const basic::options::OptionKeys::loops::accept_aborted_loops ( "loops:accept_aborted_loops"  )
BooleanOptionKey const basic::options::OptionKeys::loops::allow_lig_move ( "loops:allow_lig_move"  )
BooleanOptionKey const basic::options::OptionKeys::loops::allow_omega_move ( "loops:allow_omega_move"  )
BooleanOptionKey const basic::options::OptionKeys::loops::allow_takeoff_torsion_move ( "loops:allow_takeoff_torsion_move"  )
BooleanOptionKey const basic::options::OptionKeys::loops::alternative_closure_protocol ( "loops:alternative_closure_protocol"  )
BooleanOptionKey const basic::options::OptionKeys::loops::always_remodel_full_loop ( "loops:always_remodel_full_loop"  )
IntegerOptionKey const basic::options::OptionKeys::loops::backrub_trials ( "loops:backrub_trials"  )
BooleanOptionKey const basic::options::OptionKeys::loops::build_all_loops ( "loops:build_all_loops"  )
IntegerOptionKey const basic::options::OptionKeys::loops::build_attempts ( "loops:build_attempts"  )
BooleanOptionKey const basic::options::OptionKeys::loops::build_initial ( "loops:build_initial"  )
IntegerVectorOptionKey const basic::options::OptionKeys::loops::build_specific_loops ( "loops:build_specific_loops"  )
BooleanOptionKey const basic::options::OptionKeys::loops::ccd_closure ( "loops:ccd_closure"  )
StringOptionKey const basic::options::OptionKeys::loops::cen_patch ( "loops:cen_patch"  )
StringOptionKey const basic::options::OptionKeys::loops::cen_weights ( "loops:cen_weights"  )
RealOptionKey const basic::options::OptionKeys::loops::chain_break_tol ( "loops:chain_break_tol"  )
RealOptionKey const basic::options::OptionKeys::loops::chainbreak_max_accept ( "loops:chainbreak_max_accept"  )
RealOptionKey const basic::options::OptionKeys::loops::combine_rate ( "loops:combine_rate"  )
RealOptionKey const basic::options::OptionKeys::loops::constrain_rigid_segments ( "loops:constrain_rigid_segments"  )
RealOptionKey const basic::options::OptionKeys::loops::coord_cst ( "loops:coord_cst"  )
BooleanOptionKey const basic::options::OptionKeys::loops::debug ( "loops:debug"  )
BooleanOptionKey const basic::options::OptionKeys::loops::debug_loop_closure ( "loops:debug_loop_closure"  )
BooleanOptionKey const basic::options::OptionKeys::loops::derive_torsion_string_from_native_pose ( "loops:derive_torsion_string_from_native_pose"  )
IntegerOptionKey const basic::options::OptionKeys::loops::extend_length ( "loops:extend_length"  )
BooleanOptionKey const basic::options::OptionKeys::loops::extended ( "loops:extended"  )
RealOptionKey const basic::options::OptionKeys::loops::extended_beta ( "loops:extended_beta"  )
FileOptionKey const basic::options::OptionKeys::loops::extended_loop_file ( "loops:extended_loop_file"  )
BooleanOptionKey const basic::options::OptionKeys::loops::fa_closure_protocol ( "loops:fa_closure_protocol"  )
BooleanOptionKey const basic::options::OptionKeys::loops::fast ( "loops:fast"  )
BooleanOptionKey const basic::options::OptionKeys::loops::final_clean_fastrelax ( "loops:final_clean_fastrelax"  )
RealOptionKey const basic::options::OptionKeys::loops::final_score_filter ( "loops:final_score_filter"  )
BooleanOptionKey const basic::options::OptionKeys::loops::fix_ca_bond_angles ( "loops:fix_ca_bond_angles"  )
BooleanOptionKey const basic::options::OptionKeys::loops::fix_natsc ( "loops:fix_natsc"  )
FileVectorOptionKey const basic::options::OptionKeys::loops::frag_files ( "loops:frag_files"  )
IntegerVectorOptionKey const basic::options::OptionKeys::loops::frag_sizes ( "loops:frag_sizes"  )
IntegerOptionKey const basic::options::OptionKeys::loops::gapspan ( "loops:gapspan"  )
IntegerOptionKey const basic::options::OptionKeys::loops::grow_attempts ( "loops:grow_attempts"  )
BooleanOptionKey const basic::options::OptionKeys::loops::idealize_after_loop_close ( "loops:idealize_after_loop_close"  )
BooleanOptionKey const basic::options::OptionKeys::loops::idealize_before_loop_close ( "loops:idealize_before_loop_close"  )
FileOptionKey const basic::options::OptionKeys::loops::input_pdb ( "loops:input_pdb"  )
StringOptionKey const basic::options::OptionKeys::loops::intermedrelax ( "loops:intermedrelax"  )
FileOptionKey const basic::options::OptionKeys::loops::keep_natro ( "loops:keep_natro"  )
RealOptionKey const basic::options::OptionKeys::loops::kic_bump_overlap_factor ( "loops:kic_bump_overlap_factor"  )
BooleanOptionKey const basic::options::OptionKeys::loops::kic_leave_centroid_after_initial_closure ( "loops:kic_leave_centroid_after_initial_closure"  )
IntegerOptionKey const basic::options::OptionKeys::loops::kic_max_seglen ( "loops:kic_max_seglen"  )
BooleanOptionKey const basic::options::OptionKeys::loops::kic_min_after_repack ( "loops:kic_min_after_repack"  )
IntegerOptionKey const basic::options::OptionKeys::loops::kic_num_rotamer_trials ( "loops:kic_num_rotamer_trials"  )
BooleanOptionKey const basic::options::OptionKeys::loops::kic_omega_sampling ( "loops:kic_omega_sampling"  )
BooleanOptionKey const basic::options::OptionKeys::loops::kic_rama2b ( "loops:kic_rama2b"  )
BooleanOptionKey const basic::options::OptionKeys::loops::kic_recover_last ( "loops:kic_recover_last"  )
BooleanOptionKey const basic::options::OptionKeys::loops::kic_use_linear_chainbreak ( "loops:kic_use_linear_chainbreak"  )
BooleanOptionKey const basic::options::OptionKeys::loops::kic_with_cartmin ( "loops:kic_with_cartmin"  )
IntegerOptionKey const basic::options::OptionKeys::loops::kinematic_wrapper_cycles ( "loops:kinematic_wrapper_cycles"  )
BooleanOptionKey const basic::options::OptionKeys::loops::legacy_kic ( "loops:legacy_kic"  )
RealOptionKey const basic::options::OptionKeys::loops::loop_combine_rate ( "loops:loop_combine_rate"  )
StringVectorOptionKey const basic::options::OptionKeys::loops::loop_file ( "loops:loop_file"  )
BooleanOptionKey const basic::options::OptionKeys::loops::loop_model ( "loops:loop_model"  )
RealOptionKey const basic::options::OptionKeys::loops::looprlx_cycle_ratio ( "loops:looprlx_cycle_ratio"  )
BooleanOptionKey const basic::options::OptionKeys::loops::loops ( "loops"  )
BooleanOptionKey const basic::options::OptionKeys::loops::loops_subset ( "loops:loops_subset"  )
StringOptionKey const basic::options::OptionKeys::loops::loopscores ( "loops:loopscores"  )
IntegerOptionKey const basic::options::OptionKeys::loops::max_inner_cycles ( "loops:max_inner_cycles"  )
IntegerOptionKey const basic::options::OptionKeys::loops::max_kic_build_attempts ( "loops:max_kic_build_attempts"  )
IntegerOptionKey const basic::options::OptionKeys::loops::max_kic_perturber_samples ( "loops:max_kic_perturber_samples"  )
FileOptionKey const basic::options::OptionKeys::loops::mm_loop_file ( "loops:mm_loop_file"  )
RealOptionKey const basic::options::OptionKeys::loops::neighbor_dist ( "loops:neighbor_dist"  )
BooleanOptionKey const basic::options::OptionKeys::loops::no_combine_if_fail ( "loops:no_combine_if_fail"  )
BooleanOptionKey const basic::options::OptionKeys::loops::no_looprebuild ( "loops:no_looprebuild"  )
BooleanOptionKey const basic::options::OptionKeys::loops::no_randomize_loop ( "loops:no_randomize_loop"  )
BooleanOptionKey const basic::options::OptionKeys::loops::non_ideal_loop_closing ( "loops:non_ideal_loop_closing"  )
BooleanOptionKey const basic::options::OptionKeys::loops::nonpivot_torsion_sampling ( "loops:nonpivot_torsion_sampling"  )
IntegerOptionKey const basic::options::OptionKeys::loops::num_desired_loops ( "loops:num_desired_loops"  )
BooleanOptionKey const basic::options::OptionKeys::loops::optimize_only_kic_region_sidechains_after_move ( "loops:optimize_only_kic_region_sidechains_after_move"  )
IntegerOptionKey const basic::options::OptionKeys::loops::outer_cycles ( "loops:outer_cycles"  )
FileOptionKey const basic::options::OptionKeys::loops::output_pdb ( "loops:output_pdb"  )
BooleanOptionKey const basic::options::OptionKeys::loops::ramp_fa_rep ( "loops:ramp_fa_rep"  )
BooleanOptionKey const basic::options::OptionKeys::loops::ramp_rama ( "loops:ramp_rama"  )
RealOptionKey const basic::options::OptionKeys::loops::random_grow_loops_by ( "loops:random_grow_loops_by"  )
BooleanOptionKey const basic::options::OptionKeys::loops::random_loop ( "loops:random_loop"  )
BooleanOptionKey const basic::options::OptionKeys::loops::random_order ( "loops:random_order"  )
StringOptionKey const basic::options::OptionKeys::loops::refine ( "loops:refine"  )
IntegerOptionKey const basic::options::OptionKeys::loops::refine_design_iterations ( "loops:refine_design_iterations"  )
RealOptionKey const basic::options::OptionKeys::loops::refine_final_temp ( "loops:refine_final_temp"  )
RealOptionKey const basic::options::OptionKeys::loops::refine_init_temp ( "loops:refine_init_temp"  )
BooleanOptionKey const basic::options::OptionKeys::loops::refine_only ( "loops:refine_only"  )
StringOptionKey const basic::options::OptionKeys::loops::relax ( "loops:relax"  )
BooleanOptionKey const basic::options::OptionKeys::loops::relax_with_foldtree ( "loops:relax_with_foldtree"  )
StringOptionKey const basic::options::OptionKeys::loops::remodel ( "loops:remodel"  )
RealOptionKey const basic::options::OptionKeys::loops::remodel_final_temp ( "loops:remodel_final_temp"  )
RealOptionKey const basic::options::OptionKeys::loops::remodel_init_temp ( "loops:remodel_init_temp"  )
IntegerOptionKey const basic::options::OptionKeys::loops::remodel_kic_attempts ( "loops:remodel_kic_attempts"  )
BooleanOptionKey const basic::options::OptionKeys::loops::remove_extended_loops ( "loops:remove_extended_loops"  )
IntegerOptionKey const basic::options::OptionKeys::loops::repack_period ( "loops:repack_period"  )
StringOptionKey const basic::options::OptionKeys::loops::restrict_kic_sampling_to_torsion_string ( "loops:restrict_kic_sampling_to_torsion_string"  )
RealOptionKey const basic::options::OptionKeys::loops::rmsd_tol ( "loops:rmsd_tol"  )
BooleanOptionKey const basic::options::OptionKeys::loops::sample_omega_at_pre_prolines ( "loops:sample_omega_at_pre_prolines"  )
RealOptionKey const basic::options::OptionKeys::loops::score_filter_cutoff ( "loops:score_filter_cutoff"  )
RealOptionKey const basic::options::OptionKeys::loops::scored_frag_cycles ( "loops:scored_frag_cycles"  )
IntegerOptionKey const basic::options::OptionKeys::loops::select_best_loop_from ( "loops:select_best_loop_from"  )
RealOptionKey const basic::options::OptionKeys::loops::short_frag_cycles ( "loops:short_frag_cycles"  )
BooleanOptionKey const basic::options::OptionKeys::loops::shorten_long_terminal_loop ( "loops:shorten_long_terminal_loop"  )
RealOptionKey const basic::options::OptionKeys::loops::skip_1mers ( "loops:skip_1mers"  )
RealOptionKey const basic::options::OptionKeys::loops::skip_3mers ( "loops:skip_3mers"  )
RealOptionKey const basic::options::OptionKeys::loops::skip_9mers ( "loops:skip_9mers"  )
BooleanOptionKey const basic::options::OptionKeys::loops::skip_ccd_moves ( "loops:skip_ccd_moves"  )
IntegerOptionKey const basic::options::OptionKeys::loops::spread ( "loops:spread"  )
FileVectorOptionKey const basic::options::OptionKeys::loops::stealfrags ( "loops:stealfrags"  )
IntegerOptionKey const basic::options::OptionKeys::loops::stealfrags_times ( "loops:stealfrags_times"  )
BooleanOptionKey const basic::options::OptionKeys::loops::strict_loops ( "loops:strict_loops"  )
BooleanOptionKey const basic::options::OptionKeys::loops::superimpose_native ( "loops:superimpose_native"  )
BooleanOptionKey const basic::options::OptionKeys::loops::taboo_in_fa ( "loops:taboo_in_fa"  )
BooleanOptionKey const basic::options::OptionKeys::loops::taboo_sampling ( "loops:taboo_sampling"  )
BooleanOptionKey const basic::options::OptionKeys::loops::timer ( "loops:timer"  )
FileOptionKey const basic::options::OptionKeys::loops::vall_file ( "loops:vall_file"  )
RealOptionKey const basic::options::OptionKeys::loops::vicinity_degree ( "loops:vicinity_degree"  )
BooleanOptionKey const basic::options::OptionKeys::loops::vicinity_sampling ( "loops:vicinity_sampling"  )

Variable Documentation

BooleanOptionKey const basic::options::OptionKeys::loops::accept_aborted_loops("loops:accept_aborted_loops")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::allow_lig_move("loops:allow_lig_move")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::allow_omega_move("loops:allow_omega_move")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::allow_takeoff_torsion_move("loops:allow_takeoff_torsion_move")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::alternative_closure_protocol("loops:alternative_closure_protocol")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::always_remodel_full_loop("loops:always_remodel_full_loop")

Referenced by add_rosetta_options_1().

IntegerOptionKey const basic::options::OptionKeys::loops::backrub_trials("loops:backrub_trials")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::build_all_loops("loops:build_all_loops")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::loops::build_attempts("loops:build_attempts")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::build_initial("loops:build_initial")

Referenced by add_rosetta_options_0().

IntegerVectorOptionKey const basic::options::OptionKeys::loops::build_specific_loops("loops:build_specific_loops")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::ccd_closure("loops:ccd_closure")

Referenced by add_rosetta_options_1().

StringOptionKey const basic::options::OptionKeys::loops::cen_patch("loops:cen_patch")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::loops::cen_weights("loops:cen_weights")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::loops::chain_break_tol("loops:chain_break_tol")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::loops::chainbreak_max_accept("loops:chainbreak_max_accept")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::loops::combine_rate("loops:combine_rate")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::loops::constrain_rigid_segments("loops:constrain_rigid_segments")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::loops::coord_cst("loops:coord_cst")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::debug("loops:debug")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::debug_loop_closure("loops:debug_loop_closure")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::derive_torsion_string_from_native_pose("loops:derive_torsion_string_from_native_pose")

Referenced by add_rosetta_options_1().

IntegerOptionKey const basic::options::OptionKeys::loops::extend_length("loops:extend_length")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::extended("loops:extended")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::loops::extended_beta("loops:extended_beta")

Referenced by add_rosetta_options_1().

FileOptionKey const basic::options::OptionKeys::loops::extended_loop_file("loops:extended_loop_file")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::fa_closure_protocol("loops:fa_closure_protocol")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::fast("loops:fast")
BooleanOptionKey const basic::options::OptionKeys::loops::final_clean_fastrelax("loops:final_clean_fastrelax")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::loops::final_score_filter("loops:final_score_filter")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::fix_ca_bond_angles("loops:fix_ca_bond_angles")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::fix_natsc("loops:fix_natsc")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::loops::frag_files("loops:frag_files")
IntegerVectorOptionKey const basic::options::OptionKeys::loops::frag_sizes("loops:frag_sizes")
IntegerOptionKey const basic::options::OptionKeys::loops::gapspan("loops:gapspan")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::loops::grow_attempts("loops:grow_attempts")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::idealize_after_loop_close("loops:idealize_after_loop_close")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::idealize_before_loop_close("loops:idealize_before_loop_close")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::loops::input_pdb("loops:input_pdb")
StringOptionKey const basic::options::OptionKeys::loops::intermedrelax("loops:intermedrelax")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::loops::keep_natro("loops:keep_natro")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::loops::kic_bump_overlap_factor("loops:kic_bump_overlap_factor")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_leave_centroid_after_initial_closure("loops:kic_leave_centroid_after_initial_closure")

Referenced by add_rosetta_options_1().

IntegerOptionKey const basic::options::OptionKeys::loops::kic_max_seglen("loops:kic_max_seglen")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_min_after_repack("loops:kic_min_after_repack")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::loops::kic_num_rotamer_trials("loops:kic_num_rotamer_trials")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_omega_sampling("loops:kic_omega_sampling")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_rama2b("loops:kic_rama2b")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_recover_last("loops:kic_recover_last")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_use_linear_chainbreak("loops:kic_use_linear_chainbreak")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_with_cartmin("loops:kic_with_cartmin")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::loops::kinematic_wrapper_cycles("loops:kinematic_wrapper_cycles")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::legacy_kic("loops:legacy_kic")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::loops::loop_combine_rate("loops:loop_combine_rate")

Referenced by add_rosetta_options_1().

StringVectorOptionKey const basic::options::OptionKeys::loops::loop_file("loops:loop_file")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::loop_model("loops:loop_model")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::loops::looprlx_cycle_ratio("loops:looprlx_cycle_ratio")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::loops("loops")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::loops_subset("loops:loops_subset")

Referenced by add_rosetta_options_1().

StringOptionKey const basic::options::OptionKeys::loops::loopscores("loops:loopscores")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::loops::max_inner_cycles("loops:max_inner_cycles")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::loops::max_kic_build_attempts("loops:max_kic_build_attempts")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::loops::max_kic_perturber_samples("loops:max_kic_perturber_samples")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::loops::mm_loop_file("loops:mm_loop_file")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::loops::neighbor_dist("loops:neighbor_dist")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::no_combine_if_fail("loops:no_combine_if_fail")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::no_looprebuild("loops:no_looprebuild")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::no_randomize_loop("loops:no_randomize_loop")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::non_ideal_loop_closing("loops:non_ideal_loop_closing")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::nonpivot_torsion_sampling("loops:nonpivot_torsion_sampling")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::loops::num_desired_loops("loops:num_desired_loops")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::optimize_only_kic_region_sidechains_after_move("loops:optimize_only_kic_region_sidechains_after_move")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::loops::outer_cycles("loops:outer_cycles")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::loops::output_pdb("loops:output_pdb")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::ramp_fa_rep("loops:ramp_fa_rep")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::ramp_rama("loops:ramp_rama")
RealOptionKey const basic::options::OptionKeys::loops::random_grow_loops_by("loops:random_grow_loops_by")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::random_loop("loops:random_loop")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::random_order("loops:random_order")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::loops::refine("loops:refine")
IntegerOptionKey const basic::options::OptionKeys::loops::refine_design_iterations("loops:refine_design_iterations")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::loops::refine_final_temp("loops:refine_final_temp")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::loops::refine_init_temp("loops:refine_init_temp")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::refine_only("loops:refine_only")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::loops::relax("loops:relax")
BooleanOptionKey const basic::options::OptionKeys::loops::relax_with_foldtree("loops:relax_with_foldtree")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::loops::remodel("loops:remodel")
RealOptionKey const basic::options::OptionKeys::loops::remodel_final_temp("loops:remodel_final_temp")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::loops::remodel_init_temp("loops:remodel_init_temp")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::loops::remodel_kic_attempts("loops:remodel_kic_attempts")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::remove_extended_loops("loops:remove_extended_loops")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::loops::repack_period("loops:repack_period")

Referenced by add_rosetta_options_0().

StringOptionKey const basic::options::OptionKeys::loops::restrict_kic_sampling_to_torsion_string("loops:restrict_kic_sampling_to_torsion_string")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::loops::rmsd_tol("loops:rmsd_tol")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::sample_omega_at_pre_prolines("loops:sample_omega_at_pre_prolines")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::loops::score_filter_cutoff("loops:score_filter_cutoff")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::loops::scored_frag_cycles("loops:scored_frag_cycles")

Referenced by add_rosetta_options_1().

IntegerOptionKey const basic::options::OptionKeys::loops::select_best_loop_from("loops:select_best_loop_from")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::loops::short_frag_cycles("loops:short_frag_cycles")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::shorten_long_terminal_loop("loops:shorten_long_terminal_loop")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::loops::skip_1mers("loops:skip_1mers")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::loops::skip_3mers("loops:skip_3mers")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::loops::skip_9mers("loops:skip_9mers")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::skip_ccd_moves("loops:skip_ccd_moves")

Referenced by add_rosetta_options_1().

IntegerOptionKey const basic::options::OptionKeys::loops::spread("loops:spread")

Referenced by add_rosetta_options_0().

FileVectorOptionKey const basic::options::OptionKeys::loops::stealfrags("loops:stealfrags")

Referenced by add_rosetta_options_1().

IntegerOptionKey const basic::options::OptionKeys::loops::stealfrags_times("loops:stealfrags_times")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::strict_loops("loops:strict_loops")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::superimpose_native("loops:superimpose_native")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::taboo_in_fa("loops:taboo_in_fa")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::taboo_sampling("loops:taboo_sampling")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::loops::timer("loops:timer")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::loops::vall_file("loops:vall_file")
RealOptionKey const basic::options::OptionKeys::loops::vicinity_degree("loops:vicinity_degree")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::loops::vicinity_sampling("loops:vicinity_sampling")

Referenced by add_rosetta_options_0().