Rosetta  2020.37
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Variables
basic::options::OptionKeys::cyclic_peptide Namespace Reference

Variables

BooleanOptionKey const cyclic_peptide
 
StringOptionKey const cyclization_type
 
BooleanOptionKey const use_chainbreak_energy
 
StringOptionKey const rand_checkpoint_file
 
StringOptionKey const checkpoint_file
 
StringOptionKey const checkpoint_job_identifier
 
IntegerVectorOptionKey const exclude_residues_from_rms
 
StringOptionKey const default_rama_sampling_table
 
StringVectorOptionKey const rama_sampling_table_by_res
 
StringOptionKey const sequence_file
 
IntegerOptionKey const genkic_closure_attempts
 
IntegerOptionKey const genkic_min_solution_count
 
BooleanOptionKey const cyclic_permutations
 
BooleanOptionKey const use_rama_filter
 
RealOptionKey const rama_cutoff
 
RealOptionKey const high_hbond_weight_multiplier
 
RealOptionKey const min_genkic_hbonds
 
RealOptionKey const min_final_hbonds
 
RealOptionKey const total_energy_cutoff
 
RealOptionKey const hbond_energy_cutoff
 
BooleanOptionKey const do_not_count_adjacent_res_hbonds
 
IntegerOptionKey const fast_relax_rounds
 
BooleanOptionKey const count_sc_hbonds
 
BooleanOptionKey const require_disulfides
 
RealOptionKey const disulf_cutoff_prerelax
 
RealOptionKey const disulf_cutoff_postrelax
 
RealVectorOptionKey const user_set_alpha_dihedrals
 
RealOptionKey const user_set_alpha_dihedral_perturbation
 
RealOptionKey const bondlength_perturbation_magnitude
 
RealOptionKey const bondangle_perturbation_magnitude
 
BooleanOptionKey const filter_oversaturated_hbond_acceptors
 
RealOptionKey const hbond_acceptor_energy_cutoff
 
RealOptionKey const sample_cis_pro_frequency
 
BooleanOptionKey const design_peptide
 
FileOptionKey const allowed_residues_by_position
 
BooleanOptionKey const prohibit_D_at_negative_phi
 
BooleanOptionKey const prohibit_L_at_positive_phi
 
FileOptionKey const L_alpha_comp_file
 
FileOptionKey const D_alpha_comp_file
 
FileOptionKey const L_beta_comp_file
 
FileOptionKey const D_beta_comp_file
 
IntegerOptionKey const angle_relax_rounds
 
IntegerOptionKey const angle_length_relax_rounds
 
IntegerOptionKey const cartesian_relax_rounds
 
BooleanOptionKey const use_classic_rama_for_sampling
 
IntegerVectorOptionKey const n_methyl_positions
 
IntegerOptionKey const lariat_sidechain_index
 
IntegerVectorOptionKey const sidechain_isopeptide_indices
 
IntegerVectorOptionKey const TBMB_positions
 
BooleanOptionKey const use_TBMB_filters
 
RealOptionKey const TBMB_sidechain_distance_filter_multiplier
 
RealOptionKey const TBMB_constraints_energy_filter_multiplier
 
BooleanOptionKey const link_all_cys_with_TBMB
 
IntegerVectorOptionKey const TMA_positions
 
BooleanOptionKey const use_TMA_filters
 
RealOptionKey const TMA_sidechain_distance_filter_multiplier
 
RealOptionKey const TMA_constraints_energy_filter_multiplier
 
StringVectorOptionKey const square_pyramidal_metal_positions
 
BooleanOptionKey const use_square_pyramidal_metal_filters
 
RealOptionKey const square_pyramidal_metal_sidechain_distance_filter_multiplier
 
RealOptionKey const square_pyramidal_metal_constraints_energy_filter_multiplier
 
StringVectorOptionKey const square_planar_metal_positions
 
BooleanOptionKey const use_square_planar_metal_filters
 
RealOptionKey const square_planar_metal_sidechain_distance_filter_multiplier
 
RealOptionKey const square_planar_metal_constraints_energy_filter_multiplier
 
StringVectorOptionKey const trigonal_pyramidal_metal_positions
 
BooleanOptionKey const use_trigonal_pyramidal_metal_filters
 
RealOptionKey const trigonal_pyramidal_metal_sidechain_distance_filter_multiplier
 
RealOptionKey const trigonal_pyramidal_metal_constraints_energy_filter_multiplier
 
StringVectorOptionKey const trigonal_planar_metal_positions
 
BooleanOptionKey const use_trigonal_planar_metal_filters
 
RealOptionKey const trigonal_planar_metal_sidechain_distance_filter_multiplier
 
RealOptionKey const trigonal_planar_metal_constraints_energy_filter_multiplier
 
StringVectorOptionKey const tetrahedral_metal_positions
 
BooleanOptionKey const use_tetrahedral_metal_filters
 
RealOptionKey const tetrahedral_metal_sidechain_distance_filter_multiplier
 
RealOptionKey const tetrahedral_metal_constraints_energy_filter_multiplier
 
StringVectorOptionKey const octahedral_metal_positions
 
BooleanOptionKey const use_octahedral_metal_filters
 
RealOptionKey const octahedral_metal_sidechain_distance_filter_multiplier
 
RealOptionKey const octahedral_metal_constraints_energy_filter_multiplier
 
IntegerOptionKey const require_symmetry_repeats
 
BooleanOptionKey const require_symmetry_mirroring
 
RealOptionKey const require_symmetry_angle_threshold
 
RealOptionKey const require_symmetry_perturbation
 
BooleanOptionKey const MPI_auto_2level_distribution
 
IntegerVectorOptionKey const MPI_processes_by_level
 
IntegerVectorOptionKey const MPI_batchsize_by_level
 
StringOptionKey const MPI_sort_by
 
BooleanOptionKey const MPI_choose_highest
 
RealOptionKey const MPI_output_fraction
 
IntegerOptionKey const MPI_stop_after_time
 
RealOptionKey const MPI_pnear_lambda
 
RealOptionKey const MPI_pnear_kbt
 
IntegerOptionKey const threads_per_worker
 
BooleanOptionKey const compute_rmsd_to_lowest
 
RealOptionKey const compute_pnear_to_this_fract
 
BooleanOptionKey const compute_ensemble_sasa_metrics
 

Variable Documentation

FileOptionKey const basic::options::OptionKeys::cyclic_peptide::allowed_residues_by_position

Referenced by add_rosetta_options_7().

IntegerOptionKey const basic::options::OptionKeys::cyclic_peptide::angle_length_relax_rounds

Referenced by add_rosetta_options_7().

IntegerOptionKey const basic::options::OptionKeys::cyclic_peptide::angle_relax_rounds

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::bondangle_perturbation_magnitude

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::bondlength_perturbation_magnitude

Referenced by add_rosetta_options_7().

IntegerOptionKey const basic::options::OptionKeys::cyclic_peptide::cartesian_relax_rounds

Referenced by add_rosetta_options_7().

StringOptionKey const basic::options::OptionKeys::cyclic_peptide::checkpoint_file

Referenced by add_rosetta_options_6().

StringOptionKey const basic::options::OptionKeys::cyclic_peptide::checkpoint_job_identifier

Referenced by add_rosetta_options_6().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::compute_ensemble_sasa_metrics

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::compute_pnear_to_this_fract

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::compute_rmsd_to_lowest

Referenced by add_rosetta_options_7(), and main().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::count_sc_hbonds

Referenced by add_rosetta_options_6().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::cyclic_peptide

Referenced by add_rosetta_options_6().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::cyclic_permutations

Referenced by add_rosetta_options_6().

StringOptionKey const basic::options::OptionKeys::cyclic_peptide::cyclization_type

Referenced by add_rosetta_options_6().

FileOptionKey const basic::options::OptionKeys::cyclic_peptide::D_alpha_comp_file

Referenced by add_rosetta_options_7().

FileOptionKey const basic::options::OptionKeys::cyclic_peptide::D_beta_comp_file

Referenced by add_rosetta_options_7().

StringOptionKey const basic::options::OptionKeys::cyclic_peptide::default_rama_sampling_table

Referenced by add_rosetta_options_6().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::design_peptide

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::disulf_cutoff_postrelax

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::disulf_cutoff_prerelax

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::do_not_count_adjacent_res_hbonds

Referenced by add_rosetta_options_6().

IntegerVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::exclude_residues_from_rms

Referenced by add_rosetta_options_6().

IntegerOptionKey const basic::options::OptionKeys::cyclic_peptide::fast_relax_rounds

Referenced by add_rosetta_options_6().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::filter_oversaturated_hbond_acceptors

Referenced by add_rosetta_options_7().

IntegerOptionKey const basic::options::OptionKeys::cyclic_peptide::genkic_closure_attempts

Referenced by add_rosetta_options_6().

IntegerOptionKey const basic::options::OptionKeys::cyclic_peptide::genkic_min_solution_count

Referenced by add_rosetta_options_6().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::hbond_acceptor_energy_cutoff

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::hbond_energy_cutoff

Referenced by add_rosetta_options_6().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::high_hbond_weight_multiplier

Referenced by add_rosetta_options_6().

FileOptionKey const basic::options::OptionKeys::cyclic_peptide::L_alpha_comp_file

Referenced by add_rosetta_options_7().

FileOptionKey const basic::options::OptionKeys::cyclic_peptide::L_beta_comp_file

Referenced by add_rosetta_options_7().

IntegerOptionKey const basic::options::OptionKeys::cyclic_peptide::lariat_sidechain_index

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::link_all_cys_with_TBMB

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::min_final_hbonds

Referenced by add_rosetta_options_6().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::min_genkic_hbonds

Referenced by add_rosetta_options_6().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::MPI_auto_2level_distribution

Referenced by add_rosetta_options_7().

IntegerVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::MPI_batchsize_by_level

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::MPI_choose_highest

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::MPI_output_fraction

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::MPI_pnear_kbt

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::MPI_pnear_lambda

Referenced by add_rosetta_options_7().

IntegerVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::MPI_processes_by_level

Referenced by add_rosetta_options_7().

StringOptionKey const basic::options::OptionKeys::cyclic_peptide::MPI_sort_by

Referenced by add_rosetta_options_7().

IntegerOptionKey const basic::options::OptionKeys::cyclic_peptide::MPI_stop_after_time

Referenced by add_rosetta_options_7().

IntegerVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::n_methyl_positions

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::octahedral_metal_constraints_energy_filter_multiplier

Referenced by add_rosetta_options_7().

StringVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::octahedral_metal_positions

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::octahedral_metal_sidechain_distance_filter_multiplier

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::prohibit_D_at_negative_phi

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::prohibit_L_at_positive_phi

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::rama_cutoff

Referenced by add_rosetta_options_6().

StringVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::rama_sampling_table_by_res

Referenced by add_rosetta_options_6().

StringOptionKey const basic::options::OptionKeys::cyclic_peptide::rand_checkpoint_file

Referenced by add_rosetta_options_6().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::require_disulfides

Referenced by add_rosetta_options_6().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::require_symmetry_angle_threshold

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::require_symmetry_mirroring

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::require_symmetry_perturbation

Referenced by add_rosetta_options_7().

IntegerOptionKey const basic::options::OptionKeys::cyclic_peptide::require_symmetry_repeats

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::sample_cis_pro_frequency

Referenced by add_rosetta_options_7().

StringOptionKey const basic::options::OptionKeys::cyclic_peptide::sequence_file

Referenced by add_rosetta_options_6().

IntegerVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::sidechain_isopeptide_indices

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::square_planar_metal_constraints_energy_filter_multiplier

Referenced by add_rosetta_options_7().

StringVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::square_planar_metal_positions

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::square_planar_metal_sidechain_distance_filter_multiplier

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::square_pyramidal_metal_constraints_energy_filter_multiplier

Referenced by add_rosetta_options_7().

StringVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::square_pyramidal_metal_positions

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::square_pyramidal_metal_sidechain_distance_filter_multiplier

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::TBMB_constraints_energy_filter_multiplier

Referenced by add_rosetta_options_7().

IntegerVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::TBMB_positions

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::TBMB_sidechain_distance_filter_multiplier

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::tetrahedral_metal_constraints_energy_filter_multiplier

Referenced by add_rosetta_options_7().

StringVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::tetrahedral_metal_positions

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::tetrahedral_metal_sidechain_distance_filter_multiplier

Referenced by add_rosetta_options_7().

IntegerOptionKey const basic::options::OptionKeys::cyclic_peptide::threads_per_worker

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::TMA_constraints_energy_filter_multiplier

Referenced by add_rosetta_options_7().

IntegerVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::TMA_positions

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::TMA_sidechain_distance_filter_multiplier

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::total_energy_cutoff

Referenced by add_rosetta_options_6().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::trigonal_planar_metal_constraints_energy_filter_multiplier

Referenced by add_rosetta_options_7().

StringVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::trigonal_planar_metal_positions

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::trigonal_planar_metal_sidechain_distance_filter_multiplier

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::trigonal_pyramidal_metal_constraints_energy_filter_multiplier

Referenced by add_rosetta_options_7().

StringVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::trigonal_pyramidal_metal_positions

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::trigonal_pyramidal_metal_sidechain_distance_filter_multiplier

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::use_chainbreak_energy

Referenced by add_rosetta_options_6().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::use_classic_rama_for_sampling

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::use_octahedral_metal_filters

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::use_rama_filter

Referenced by add_rosetta_options_6().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::use_square_planar_metal_filters

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::use_square_pyramidal_metal_filters

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::use_TBMB_filters

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::use_tetrahedral_metal_filters

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::use_TMA_filters

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::use_trigonal_planar_metal_filters

Referenced by add_rosetta_options_7().

BooleanOptionKey const basic::options::OptionKeys::cyclic_peptide::use_trigonal_pyramidal_metal_filters

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::user_set_alpha_dihedral_perturbation

Referenced by add_rosetta_options_7().

RealVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::user_set_alpha_dihedrals

Referenced by add_rosetta_options_7().