Rosetta  2020.28
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Namespaces | Variables
basic::options::OptionKeys::loops Namespace Reference

Namespaces

 ccd
 

Variables

BooleanOptionKey const loops
 
StringOptionKey const cen_weights
 
StringOptionKey const cen_patch
 
FileOptionKey const input_pdb
 Input options#####################################. More...
 
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
 
BooleanOptionKey const skip_initial_loop_build
 
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 perturb_outer_cycles
 
IntegerOptionKey const refine_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
 
IntegerOptionKey const minimize_max_iter
 
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
 

Variable Documentation

BooleanOptionKey const basic::options::OptionKeys::loops::accept_aborted_loops

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::allow_lig_move

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::allow_omega_move

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::allow_takeoff_torsion_move

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::alternative_closure_protocol

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::always_remodel_full_loop

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::backrub_trials

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::build_all_loops

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::build_attempts

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::build_initial

Referenced by add_rosetta_options_3().

IntegerVectorOptionKey const basic::options::OptionKeys::loops::build_specific_loops

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::ccd_closure

Referenced by add_rosetta_options_4().

StringOptionKey const basic::options::OptionKeys::loops::cen_patch

Referenced by add_rosetta_options_3().

StringOptionKey const basic::options::OptionKeys::loops::cen_weights

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::chain_break_tol

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::chainbreak_max_accept

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::combine_rate

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::constrain_rigid_segments

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::coord_cst

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::debug

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::debug_loop_closure

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::derive_torsion_string_from_native_pose

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::extend_length

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::extended

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::extended_beta

Referenced by add_rosetta_options_4().

FileOptionKey const basic::options::OptionKeys::loops::extended_loop_file

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::fa_closure_protocol

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::fast

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::final_clean_fastrelax

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::final_score_filter

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::fix_ca_bond_angles

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::fix_natsc

Referenced by add_rosetta_options_3().

FileVectorOptionKey const basic::options::OptionKeys::loops::frag_files
IntegerVectorOptionKey const basic::options::OptionKeys::loops::frag_sizes

Referenced by add_rosetta_options_3(), and my_main().

IntegerOptionKey const basic::options::OptionKeys::loops::gapspan

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::grow_attempts

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::idealize_after_loop_close

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::idealize_before_loop_close

Referenced by add_rosetta_options_3().

FileOptionKey const basic::options::OptionKeys::loops::input_pdb

Input options#####################################.

Referenced by add_rosetta_options_3(), and main().

StringOptionKey const basic::options::OptionKeys::loops::intermedrelax

Referenced by add_rosetta_options_3().

FileOptionKey const basic::options::OptionKeys::loops::keep_natro

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::kic_bump_overlap_factor

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_leave_centroid_after_initial_closure

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::kic_max_seglen

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_min_after_repack

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::kic_num_rotamer_trials

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_omega_sampling

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_rama2b

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_recover_last

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_use_linear_chainbreak

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::kic_with_cartmin

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::kinematic_wrapper_cycles

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::legacy_kic

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::loop_combine_rate

Referenced by add_rosetta_options_4().

StringVectorOptionKey const basic::options::OptionKeys::loops::loop_file
BooleanOptionKey const basic::options::OptionKeys::loops::loop_model

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::looprlx_cycle_ratio

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::loops

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::loops_subset

Referenced by add_rosetta_options_4().

StringOptionKey const basic::options::OptionKeys::loops::loopscores

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::max_inner_cycles

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::max_kic_build_attempts

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::max_kic_perturber_samples

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::minimize_max_iter

Referenced by add_rosetta_options_4().

FileOptionKey const basic::options::OptionKeys::loops::mm_loop_file

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::neighbor_dist

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::no_combine_if_fail

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::no_looprebuild

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::no_randomize_loop

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::non_ideal_loop_closing

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::nonpivot_torsion_sampling

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::num_desired_loops

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::optimize_only_kic_region_sidechains_after_move

Referenced by add_rosetta_options_4().

FileOptionKey const basic::options::OptionKeys::loops::output_pdb

Referenced by add_rosetta_options_3(), and main().

IntegerOptionKey const basic::options::OptionKeys::loops::perturb_outer_cycles

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::ramp_fa_rep

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::ramp_rama

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::random_grow_loops_by

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::random_loop

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::random_order

Referenced by add_rosetta_options_3().

StringOptionKey const basic::options::OptionKeys::loops::refine

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::refine_design_iterations

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::refine_final_temp

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::refine_init_temp

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::refine_only

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::refine_outer_cycles

Referenced by add_rosetta_options_4().

StringOptionKey const basic::options::OptionKeys::loops::relax

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::relax_with_foldtree

Referenced by add_rosetta_options_3().

StringOptionKey const basic::options::OptionKeys::loops::remodel

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::remodel_final_temp

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::remodel_init_temp

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::remodel_kic_attempts

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::remove_extended_loops

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::repack_period

Referenced by add_rosetta_options_4().

StringOptionKey const basic::options::OptionKeys::loops::restrict_kic_sampling_to_torsion_string

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::rmsd_tol

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::sample_omega_at_pre_prolines

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::score_filter_cutoff

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::scored_frag_cycles

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::select_best_loop_from

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::short_frag_cycles

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::shorten_long_terminal_loop

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::skip_1mers

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::skip_3mers

Referenced by add_rosetta_options_4().

RealOptionKey const basic::options::OptionKeys::loops::skip_9mers

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::skip_ccd_moves

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::skip_initial_loop_build

Referenced by add_rosetta_options_3().

IntegerOptionKey const basic::options::OptionKeys::loops::spread

Referenced by add_rosetta_options_4().

FileVectorOptionKey const basic::options::OptionKeys::loops::stealfrags

Referenced by add_rosetta_options_4().

IntegerOptionKey const basic::options::OptionKeys::loops::stealfrags_times

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::strict_loops

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::superimpose_native

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::taboo_in_fa

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::taboo_sampling

Referenced by add_rosetta_options_4().

BooleanOptionKey const basic::options::OptionKeys::loops::timer

Referenced by add_rosetta_options_3().

FileOptionKey const basic::options::OptionKeys::loops::vall_file

Referenced by add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::loops::vicinity_degree

Referenced by add_rosetta_options_3().

BooleanOptionKey const basic::options::OptionKeys::loops::vicinity_sampling

Referenced by add_rosetta_options_3().