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	paraBBMB_positions
BooleanOptionKey const	use_paraBBMB_filters
RealOptionKey const	paraBBMB_sidechain_distance_filter_multiplier
RealOptionKey const	paraBBMB_constraints_energy_filter_multiplier
BooleanOptionKey const	link_all_cys_with_paraBBMB
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_7().

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_7().

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_7().

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_7().

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_paraBBMB

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().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::paraBBMB_constraints_energy_filter_multiplier

Referenced by add_rosetta_options_7().

IntegerVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::paraBBMB_positions

Referenced by add_rosetta_options_7().

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::paraBBMB_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_7().

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(), and main().

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_paraBBMB_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().