cyclic_peptide Namespace Reference

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

Function Documentation

FileOptionKey const cyclic_peptide::allowed_residues_by_position

(

"cyclic_peptide:allowed_residues_by_position"

)

IntegerOptionKey const cyclic_peptide::angle_length_relax_rounds

(

"cyclic_peptide:angle_length_relax_rounds"

)

IntegerOptionKey const cyclic_peptide::angle_relax_rounds

(

"cyclic_peptide:angle_relax_rounds"

)

IntegerOptionKey const cyclic_peptide::cartesian_relax_rounds

(

"cyclic_peptide:cartesian_relax_rounds"

)

StringOptionKey const cyclic_peptide::checkpoint_file

(

"cyclic_peptide:checkpoint_file"

)

StringOptionKey const cyclic_peptide::checkpoint_job_identifier

(

"cyclic_peptide:checkpoint_job_identifier"

)

BooleanOptionKey const cyclic_peptide::count_sc_hbonds

(

"cyclic_peptide:count_sc_hbonds"

)

BooleanOptionKey const cyclic_peptide::cyclic_peptide

(

"cyclic_peptide"

)

BooleanOptionKey const cyclic_peptide::cyclic_permutations

(

"cyclic_peptide:cyclic_permutations"

)

StringOptionKey const cyclic_peptide::cyclization_type

(

"cyclic_peptide:cyclization_type"

)

FileOptionKey const cyclic_peptide::D_alpha_comp_file

(

"cyclic_peptide:D_alpha_comp_file"

)

FileOptionKey const cyclic_peptide::D_beta_comp_file

(

"cyclic_peptide:D_beta_comp_file"

)

StringOptionKey const cyclic_peptide::default_rama_sampling_table

(

"cyclic_peptide:default_rama_sampling_table"

)

BooleanOptionKey const cyclic_peptide::design_peptide

(

"cyclic_peptide:design_peptide"

)

RealOptionKey const cyclic_peptide::disulf_cutoff_postrelax

(

"cyclic_peptide:disulf_cutoff_postrelax"

)

RealOptionKey const cyclic_peptide::disulf_cutoff_prerelax

(

"cyclic_peptide:disulf_cutoff_prerelax"

)

BooleanOptionKey const cyclic_peptide::do_not_count_adjacent_res_hbonds

(

"cyclic_peptide:do_not_count_adjacent_res_hbonds"

)

IntegerVectorOptionKey const cyclic_peptide::exclude_residues_from_rms

(

"cyclic_peptide:exclude_residues_from_rms"

)

IntegerOptionKey const cyclic_peptide::fast_relax_rounds

(

"cyclic_peptide:fast_relax_rounds"

)

BooleanOptionKey const cyclic_peptide::filter_oversaturated_hbond_acceptors

(

"cyclic_peptide:filter_oversaturated_hbond_acceptors"

)

IntegerOptionKey const cyclic_peptide::genkic_closure_attempts

(

"cyclic_peptide:genkic_closure_attempts"

)

IntegerOptionKey const cyclic_peptide::genkic_min_solution_count

(

"cyclic_peptide:genkic_min_solution_count"

)

RealOptionKey const cyclic_peptide::hbond_acceptor_energy_cutoff

(

"cyclic_peptide:hbond_acceptor_energy_cutoff"

)

RealOptionKey const cyclic_peptide::hbond_energy_cutoff

(

"cyclic_peptide:hbond_energy_cutoff"

)

RealOptionKey const cyclic_peptide::high_hbond_weight_multiplier

(

"cyclic_peptide:high_hbond_weight_multiplier"

)

FileOptionKey const cyclic_peptide::L_alpha_comp_file

(

"cyclic_peptide:L_alpha_comp_file"

)

FileOptionKey const cyclic_peptide::L_beta_comp_file

(

"cyclic_peptide:L_beta_comp_file"

)

IntegerOptionKey const cyclic_peptide::lariat_sidechain_index

(

"cyclic_peptide:lariat_sidechain_index"

)

BooleanOptionKey const cyclic_peptide::link_all_cys_with_TBMB

(

"cyclic_peptide:link_all_cys_with_TBMB"

)

RealOptionKey const cyclic_peptide::min_final_hbonds

(

"cyclic_peptide:min_final_hbonds"

)

RealOptionKey const cyclic_peptide::min_genkic_hbonds

(

"cyclic_peptide:min_genkic_hbonds"

)

IntegerVectorOptionKey const cyclic_peptide::MPI_batchsize_by_level

(

"cyclic_peptide:MPI_batchsize_by_level"

)

BooleanOptionKey const cyclic_peptide::MPI_choose_highest

(

"cyclic_peptide:MPI_choose_highest"

)

RealOptionKey const cyclic_peptide::MPI_output_fraction

(

"cyclic_peptide:MPI_output_fraction"

)

RealOptionKey const cyclic_peptide::MPI_pnear_kbt

(

"cyclic_peptide:MPI_pnear_kbt"

)

RealOptionKey const cyclic_peptide::MPI_pnear_lambda

(

"cyclic_peptide:MPI_pnear_lambda"

)

IntegerVectorOptionKey const cyclic_peptide::MPI_processes_by_level

(

"cyclic_peptide:MPI_processes_by_level"

)

StringOptionKey const cyclic_peptide::MPI_sort_by

(

"cyclic_peptide:MPI_sort_by"

)

IntegerOptionKey const cyclic_peptide::MPI_stop_after_time

(

"cyclic_peptide:MPI_stop_after_time"

)

IntegerVectorOptionKey const cyclic_peptide::n_methyl_positions

(

"cyclic_peptide:n_methyl_positions"

)

RealOptionKey const cyclic_peptide::octahedral_metal_constraints_energy_filter_multiplier

(

"cyclic_peptide:octahedral_metal_constraints_energy_filter_multiplier"

)

StringVectorOptionKey const cyclic_peptide::octahedral_metal_positions

(

"cyclic_peptide:octahedral_metal_positions"

)

RealOptionKey const cyclic_peptide::octahedral_metal_sidechain_distance_filter_multiplier

(

"cyclic_peptide:octahedral_metal_sidechain_distance_filter_multiplier"

)

BooleanOptionKey const cyclic_peptide::prohibit_D_at_negative_phi

(

"cyclic_peptide:prohibit_D_at_negative_phi"

)

BooleanOptionKey const cyclic_peptide::prohibit_L_at_positive_phi

(

"cyclic_peptide:prohibit_L_at_positive_phi"

)

RealOptionKey const cyclic_peptide::rama_cutoff

(

"cyclic_peptide:rama_cutoff"

)

StringVectorOptionKey const cyclic_peptide::rama_sampling_table_by_res

(

"cyclic_peptide:rama_sampling_table_by_res"

)

StringOptionKey const cyclic_peptide::rand_checkpoint_file

(

"cyclic_peptide:rand_checkpoint_file"

)

BooleanOptionKey const cyclic_peptide::require_disulfides

(

"cyclic_peptide:require_disulfides"

)

RealOptionKey const cyclic_peptide::require_symmetry_angle_threshold

(

"cyclic_peptide:require_symmetry_angle_threshold"

)

BooleanOptionKey const cyclic_peptide::require_symmetry_mirroring

(

"cyclic_peptide:require_symmetry_mirroring"

)

RealOptionKey const cyclic_peptide::require_symmetry_perturbation

(

"cyclic_peptide:require_symmetry_perturbation"

)

IntegerOptionKey const cyclic_peptide::require_symmetry_repeats

(

"cyclic_peptide:require_symmetry_repeats"

)

RealOptionKey const cyclic_peptide::sample_cis_pro_frequency

(

"cyclic_peptide:sample_cis_pro_frequency"

)

StringOptionKey const cyclic_peptide::sequence_file

(

"cyclic_peptide:sequence_file"

)

IntegerVectorOptionKey const cyclic_peptide::sidechain_isopeptide_indices

(

"cyclic_peptide:sidechain_isopeptide_indices"

)

RealOptionKey const cyclic_peptide::square_planar_metal_constraints_energy_filter_multiplier

(

"cyclic_peptide:square_planar_metal_constraints_energy_filter_multiplier"

)

StringVectorOptionKey const cyclic_peptide::square_planar_metal_positions

(

"cyclic_peptide:square_planar_metal_positions"

)

RealOptionKey const cyclic_peptide::square_planar_metal_sidechain_distance_filter_multiplier

(

"cyclic_peptide:square_planar_metal_sidechain_distance_filter_multiplier"

)

RealOptionKey const cyclic_peptide::square_pyramidal_metal_constraints_energy_filter_multiplier

(

"cyclic_peptide:square_pyramidal_metal_constraints_energy_filter_multiplier"

)

StringVectorOptionKey const cyclic_peptide::square_pyramidal_metal_positions

(

"cyclic_peptide:square_pyramidal_metal_positions"

)

RealOptionKey const cyclic_peptide::square_pyramidal_metal_sidechain_distance_filter_multiplier

(

"cyclic_peptide:square_pyramidal_metal_sidechain_distance_filter_multiplier"

)

RealOptionKey const cyclic_peptide::TBMB_constraints_energy_filter_multiplier

(

"cyclic_peptide:TBMB_constraints_energy_filter_multiplier"

)

IntegerVectorOptionKey const cyclic_peptide::TBMB_positions

(

"cyclic_peptide:TBMB_positions"

)

RealOptionKey const cyclic_peptide::TBMB_sidechain_distance_filter_multiplier

(

"cyclic_peptide:TBMB_sidechain_distance_filter_multiplier"

)

RealOptionKey const cyclic_peptide::tetrahedral_metal_constraints_energy_filter_multiplier

(

"cyclic_peptide:tetrahedral_metal_constraints_energy_filter_multiplier"

)

StringVectorOptionKey const cyclic_peptide::tetrahedral_metal_positions

(

"cyclic_peptide:tetrahedral_metal_positions"

)

RealOptionKey const cyclic_peptide::tetrahedral_metal_sidechain_distance_filter_multiplier

(

"cyclic_peptide:tetrahedral_metal_sidechain_distance_filter_multiplier"

)

IntegerOptionKey const cyclic_peptide::threads_per_slave

(

"cyclic_peptide:threads_per_slave"

)

RealOptionKey const cyclic_peptide::TMA_constraints_energy_filter_multiplier

(

"cyclic_peptide:TMA_constraints_energy_filter_multiplier"

)

IntegerVectorOptionKey const cyclic_peptide::TMA_positions

(

"cyclic_peptide:TMA_positions"

)

RealOptionKey const cyclic_peptide::TMA_sidechain_distance_filter_multiplier

(

"cyclic_peptide:TMA_sidechain_distance_filter_multiplier"

)

RealOptionKey const cyclic_peptide::total_energy_cutoff

(

"cyclic_peptide:total_energy_cutoff"

)

RealOptionKey const cyclic_peptide::trigonal_planar_metal_constraints_energy_filter_multiplier

(

"cyclic_peptide:trigonal_planar_metal_constraints_energy_filter_multiplier"

)

StringVectorOptionKey const cyclic_peptide::trigonal_planar_metal_positions

(

"cyclic_peptide:trigonal_planar_metal_positions"

)

RealOptionKey const cyclic_peptide::trigonal_planar_metal_sidechain_distance_filter_multiplier

(

"cyclic_peptide:trigonal_planar_metal_sidechain_distance_filter_multiplier"

)

RealOptionKey const cyclic_peptide::trigonal_pyramidal_metal_constraints_energy_filter_multiplier

(

"cyclic_peptide:trigonal_pyramidal_metal_constraints_energy_filter_multiplier"

)

StringVectorOptionKey const cyclic_peptide::trigonal_pyramidal_metal_positions

(

"cyclic_peptide:trigonal_pyramidal_metal_positions"

)

RealOptionKey const cyclic_peptide::trigonal_pyramidal_metal_sidechain_distance_filter_multiplier

(

"cyclic_peptide:trigonal_pyramidal_metal_sidechain_distance_filter_multiplier"

)

BooleanOptionKey const cyclic_peptide::use_chainbreak_energy

(

"cyclic_peptide:use_chainbreak_energy"

)

BooleanOptionKey const cyclic_peptide::use_classic_rama_for_sampling

(

"cyclic_peptide:use_classic_rama_for_sampling"

)

BooleanOptionKey const cyclic_peptide::use_octahedral_metal_filters

(

"cyclic_peptide:use_octahedral_metal_filters"

)

BooleanOptionKey const cyclic_peptide::use_rama_filter

(

"cyclic_peptide:use_rama_filter"

)

BooleanOptionKey const cyclic_peptide::use_square_planar_metal_filters

(

"cyclic_peptide:use_square_planar_metal_filters"

)

BooleanOptionKey const cyclic_peptide::use_square_pyramidal_metal_filters

(

"cyclic_peptide:use_square_pyramidal_metal_filters"

)

BooleanOptionKey const cyclic_peptide::use_TBMB_filters

(

"cyclic_peptide:use_TBMB_filters"

)

BooleanOptionKey const cyclic_peptide::use_tetrahedral_metal_filters

(

"cyclic_peptide:use_tetrahedral_metal_filters"

)

BooleanOptionKey const cyclic_peptide::use_TMA_filters

(

"cyclic_peptide:use_TMA_filters"

)

BooleanOptionKey const cyclic_peptide::use_trigonal_planar_metal_filters

(

"cyclic_peptide:use_trigonal_planar_metal_filters"

)

BooleanOptionKey const cyclic_peptide::use_trigonal_pyramidal_metal_filters

(

"cyclic_peptide:use_trigonal_pyramidal_metal_filters"

)

RealOptionKey const cyclic_peptide::user_set_alpha_dihedral_perturbation

(

"cyclic_peptide:user_set_alpha_dihedral_perturbation"

)

RealVectorOptionKey const cyclic_peptide::user_set_alpha_dihedrals

(

"cyclic_peptide:user_set_alpha_dihedrals"

)