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	lanthionine_positions
BooleanOptionKey const	lariat_sample_cis
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

allowed_residues_by_position

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

extern

angle_length_relax_rounds

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

extern

angle_relax_rounds

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

extern

bondangle_perturbation_magnitude

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

extern

bondlength_perturbation_magnitude

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

extern

cartesian_relax_rounds

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

extern

checkpoint_file

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

extern

checkpoint_job_identifier

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

extern

compute_ensemble_sasa_metrics

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

extern

compute_pnear_to_this_fract

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

extern

compute_rmsd_to_lowest

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

extern

Referenced by main().

count_sc_hbonds

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

extern

cyclic_peptide

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

extern

cyclic_permutations

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

extern

cyclization_type

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

extern

D_alpha_comp_file

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

extern

D_beta_comp_file

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

extern

default_rama_sampling_table

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

extern

design_peptide

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

extern

disulf_cutoff_postrelax

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

extern

disulf_cutoff_prerelax

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

extern

do_not_count_adjacent_res_hbonds

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

extern

exclude_residues_from_rms

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

extern

fast_relax_rounds

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

extern

filter_oversaturated_hbond_acceptors

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

extern

genkic_closure_attempts

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

extern

genkic_min_solution_count

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

extern

hbond_acceptor_energy_cutoff

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

extern

hbond_energy_cutoff

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

extern

high_hbond_weight_multiplier

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

extern

L_alpha_comp_file

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

extern

L_beta_comp_file

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

extern

lanthionine_positions

IntegerVectorOptionKey const basic::options::OptionKeys::cyclic_peptide::lanthionine_positions

extern

lariat_sample_cis

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

extern

lariat_sidechain_index

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

extern

link_all_cys_with_paraBBMB

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

extern

link_all_cys_with_TBMB

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

extern

min_final_hbonds

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

extern

min_genkic_hbonds

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

extern

MPI_auto_2level_distribution

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

extern

MPI_batchsize_by_level

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

extern

MPI_choose_highest

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

extern

MPI_output_fraction

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

extern

MPI_pnear_kbt

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

extern

MPI_pnear_lambda

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

extern

MPI_processes_by_level

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

extern

MPI_sort_by

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

extern

MPI_stop_after_time

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

extern

n_methyl_positions

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

extern

octahedral_metal_constraints_energy_filter_multiplier

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

extern

octahedral_metal_positions

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

extern

octahedral_metal_sidechain_distance_filter_multiplier

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

extern

paraBBMB_constraints_energy_filter_multiplier

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

extern

paraBBMB_positions

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

extern

paraBBMB_sidechain_distance_filter_multiplier

RealOptionKey const basic::options::OptionKeys::cyclic_peptide::paraBBMB_sidechain_distance_filter_multiplier

extern

prohibit_D_at_negative_phi

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

extern

prohibit_L_at_positive_phi

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

extern

rama_cutoff

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

extern

rama_sampling_table_by_res

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

extern

rand_checkpoint_file

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

extern

require_disulfides

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

extern

require_symmetry_angle_threshold

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

extern

require_symmetry_mirroring

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

extern

require_symmetry_perturbation

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

extern

require_symmetry_repeats

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

extern

sample_cis_pro_frequency

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

extern

sequence_file

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

extern

Referenced by LoopHashRelax_Sampler::apply(), and main().

sidechain_isopeptide_indices

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

extern

square_planar_metal_constraints_energy_filter_multiplier

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

extern

square_planar_metal_positions

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

extern

square_planar_metal_sidechain_distance_filter_multiplier

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

extern

square_pyramidal_metal_constraints_energy_filter_multiplier

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

extern

square_pyramidal_metal_positions

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

extern

square_pyramidal_metal_sidechain_distance_filter_multiplier

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

extern

TBMB_constraints_energy_filter_multiplier

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

extern

TBMB_positions

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

extern

TBMB_sidechain_distance_filter_multiplier

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

extern

tetrahedral_metal_constraints_energy_filter_multiplier

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

extern

tetrahedral_metal_positions

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

extern

tetrahedral_metal_sidechain_distance_filter_multiplier

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

extern

threads_per_worker

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

extern

Referenced by main().

TMA_constraints_energy_filter_multiplier

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

extern

TMA_positions

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

extern

TMA_sidechain_distance_filter_multiplier

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

extern

total_energy_cutoff

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

extern

trigonal_planar_metal_constraints_energy_filter_multiplier

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

extern

trigonal_planar_metal_positions

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

extern

trigonal_planar_metal_sidechain_distance_filter_multiplier

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

extern

trigonal_pyramidal_metal_constraints_energy_filter_multiplier

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

extern

trigonal_pyramidal_metal_positions

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

extern

trigonal_pyramidal_metal_sidechain_distance_filter_multiplier

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

extern

use_chainbreak_energy

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

extern

use_classic_rama_for_sampling

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

extern

use_octahedral_metal_filters

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

extern

use_paraBBMB_filters

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

extern

use_rama_filter

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

extern

use_square_planar_metal_filters

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

extern

use_square_pyramidal_metal_filters

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

extern

use_TBMB_filters

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

extern

use_tetrahedral_metal_filters

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

extern

use_TMA_filters

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

extern

use_trigonal_planar_metal_filters

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

extern

use_trigonal_pyramidal_metal_filters

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

extern

user_set_alpha_dihedral_perturbation

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

extern

user_set_alpha_dihedrals

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

extern