local Namespace Reference

Classes
struct	HbondInfo

Variables
basic::options::RealOptionKey const	hsasa_residue_cutoff ("hsasa_residue_cutoff")
basic::options::BooleanOptionKey const	zn_minimize ("zn_minimize")
basic::options::BooleanOptionKey const	bb_min ("bb_min")
basic::options::BooleanOptionKey const	zn_min_pack ("zn_min_pack")
basic::options::IntegerOptionKey const	zn_min_pack_cycles ("zn_min_pack_cycles")
basic::options::RealOptionKey const	zn_constraint_weight ("zn_constraint_weight")
basic::options::BooleanOptionKey const	evaluate_coordinating_res_types ("evaluate_coordinating_res_types")
basic::options::BooleanOptionKey const	evaluate_coordinating_res_energies ("evaluate_coordinating_res_energies")
basic::options::BooleanOptionKey const	evaluate_zinc_geometry ("evaluate_zinc_geometry")
basic::options::BooleanOptionKey const	evaluate_zinc_neighbors ("evaluate_zinc_neighbors")
basic::options::BooleanOptionKey const	evaluate_ligand_sasa ("evaluate_ligand_sasa")
basic::options::BooleanOptionKey const	evaluate_zinc_second_shell ("evaluate_zinc_second_shell")
basic::options::BooleanOptionKey const	evaluate_mutations_native ("evaluate_mutations_native")
basic::options::FileOptionKey const	evaluate_mutations_native_pdb ("evaluate_mutations_native_pdb")
basic::options::StringOptionKey const	ligand_3_letter_code ("ligand_3_letter_code")
basic::options::IntegerOptionKey const	zinc_resnum ("zinc_resnum")
basic::options::IntegerOptionKey const	n_ligands ("n_ligands")
basic::options::IntegerOptionKey const	num_iterations ("num_iterations")
basic::options::RealOptionKey const	prob_br_move ("prob_br_move")
basic::options::BooleanOptionKey const	add_ligand_constraints ("add_ligand_constraints")
basic::options::StringVectorOptionKey const	ligand_cst_atoms ("ligand_cst_atoms")
basic::options::RealOptionKey const	dist_cst_weight ("dist_cst_weight")
basic::options::RealOptionKey const	dihedral_cst_weight ("dihedral_cst_weight")
basic::options::RealOptionKey const	mc_temperature ("mc_temperature")
basic::options::FileOptionKey const	heme_conformation ("heme_conformation")
basic::options::BooleanOptionKey const	no_relax ("no_relax")
basic::options::IntegerOptionKey const	num_trials ("num_trials")
basic::options::RealOptionKey const	repacking_distance ("repacking_distance")
basic::options::IntegerOptionKey const	nbr_residue ("local::nbr_residue")
basic::options::StringOptionKey const	master ("local::master")
basic::options::IntegerOptionKey const	surface_residue ("surface_residue")
basic::options::BooleanOptionKey const	use_pdb_numbering ("use_pdb_numbering")
basic::options::IntegerOptionKey const	chain1 ("local::chain1")
basic::options::IntegerOptionKey const	chain2 ("local::chain2")
basic::options::BooleanOptionKey const	AvNAPSA_positive ("AvNAPSA_positive")
basic::options::BooleanOptionKey const	AvNAPSA_negative ("AvNAPSA_negative")
basic::options::BooleanOptionKey const	target_net_charge_active ("target_net_charge_active")
basic::options::IntegerOptionKey const	target_net_charge ("target_net_charge")
basic::options::IntegerOptionKey const	surface_atom_cutoff ("surface_atom_cutoff")
basic::options::IntegerOptionKey const	surface_residue_cutoff ("surface_residue_cutoff")
basic::options::BooleanOptionKey const	include_arg ("include_arg")
basic::options::BooleanOptionKey const	include_lys ("include_lys")
basic::options::BooleanOptionKey const	include_asp ("include_asp")
basic::options::BooleanOptionKey const	include_glu ("include_glu")
basic::options::RealOptionKey const	refweight_arg ("refweight_arg")
basic::options::RealOptionKey const	refweight_lys ("refweight_lys")
basic::options::RealOptionKey const	refweight_asp ("refweight_asp")
basic::options::RealOptionKey const	refweight_glu ("refweight_glu")
basic::options::BooleanOptionKey const	dont_mutate_glyprocys ("dont_mutate_glyprocys")
basic::options::BooleanOptionKey const	dont_mutate_correct_charge ("dont_mutate_correct_charge")
basic::options::BooleanOptionKey const	dont_mutate_hbonded_sidechains ("dont_mutate_hbonded_sidechains")
basic::options::BooleanOptionKey const	pre_packminpack ("pre_packminpack")
basic::options::IntegerOptionKey const	nstruct ("nstruct")
basic::options::BooleanOptionKey const	compare_residue_energies_all ("compare_residue_energies_all")
basic::options::BooleanOptionKey const	compare_residue_energies_mut ("compare_residue_energies_mut")
basic::options::FileOptionKey const	partner1 ("partner1")
basic::options::FileOptionKey const	partner2 ("partner2")
basic::options::FileOptionKey const	match_pdb ("match_pdb")
basic::options::IntegerOptionKey const	partner2_residue ("partner2_residue")
basic::options::BooleanOptionKey const	skip_sitegraft_repack ("skip_sitegraft_repack")
basic::options::RealOptionKey const	atom_sasa_cutoff ("atom_sasa_cutoff")
basic::options::RealOptionKey const	neighbor_distance_cutoff ("neighbor_distance_cutoff")
basic::options::IntegerOptionKey const	window_width ("window_width")
basic::options::IntegerOptionKey const	helix_length ("helix_length")
basic::options::StringOptionKey const	reference_zinc_site ("reference_zinc_site")
basic::options::IntegerOptionKey const	first_ref_his ("first_ref_his")
basic::options::IntegerOptionKey const	ref_zinc ("ref_zinc")
basic::options::RealOptionKey const	temperature ("temperature")
basic::options::IntegerOptionKey const	n_moves ("n_moves")
basic::options::RealOptionKey const	constraint_weight ("constraint_weight")
basic::options::RealOptionKey const	max_angle ("max_angle")
basic::options::IntegerOptionKey const	small_moves ("small_moves")
basic::options::IntegerOptionKey const	shear_moves ("shear_moves")
basic::options::StringOptionKey const	metal_type ("metal_type")
basic::options::RealOptionKey const	metal_ligand_distance_cutoff ("metal_ligand_distance_cutoff")
basic::options::IntegerOptionKey const	min_total_coord_atoms ("min_total_coord_atoms")
basic::options::IntegerOptionKey const	min_local_coord_atoms ("min_local_coord_atoms")
basic::options::IntegerOptionKey const	min_coord_res ("min_coord_res")
basic::options::IntegerOptionKey const	max_res_span ("max_res_span")
basic::options::BooleanOptionKey const	require_bordering_ss ("require_bordering_ss")
basic::options::IntegerOptionKey const	max_loop_size ("max_loop_size")
basic::options::BooleanOptionKey const	helices_only ("helices_only")
basic::options::BooleanOptionKey const	strict_ss_changes ("strict_ss_changes")
basic::options::BooleanOptionKey const	append_nonlocal_residues ("append_nonlocal_residues")
basic::options::StringOptionKey const	allowed_elements ("allowed_elements")
basic::options::BooleanOptionKey const	allow_his ("allow_his")
basic::options::BooleanOptionKey const	allow_de ("allow_de")
basic::options::StringOptionKey const	secstruct ("secstruct")
basic::options::RealOptionKey const	sampling_range ("sampling_range")
basic::options::RealOptionKey const	sampling_increment ("sampling_increment")
basic::options::StringOptionKey const	output_name ("output_name")

Variable Documentation

add_ligand_constraints

basic::options::BooleanOptionKey const local::add_ligand_constraints("add_ligand_constraints")

(

"add_ligand_constraints"

)

Referenced by main().

allow_de

basic::options::BooleanOptionKey const local::allow_de("allow_de")

(

"allow_de"

)

Referenced by zinc_stats::ZincStatisticGenerator::initialize_from_options(), and main().

allow_his

basic::options::BooleanOptionKey const local::allow_his("allow_his")

(

"allow_his"

)

Referenced by zinc_stats::ZincStatisticGenerator::initialize_from_options(), and main().

allowed_elements

basic::options::StringOptionKey const local::allowed_elements("allowed_elements")

(

"allowed_elements"

)

Referenced by MetalSiteFinderMover::initialize_from_options(), and main().

append_nonlocal_residues

basic::options::BooleanOptionKey const local::append_nonlocal_residues("append_nonlocal_residues")

(

"append_nonlocal_residues"

)

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

atom_sasa_cutoff

basic::options::RealOptionKey const local::atom_sasa_cutoff("atom_sasa_cutoff")

(

"atom_sasa_cutoff"

)

Referenced by BacksideHbondFinderMover::BacksideHbondFinderMover(), and main().

AvNAPSA_negative

basic::options::BooleanOptionKey const local::AvNAPSA_negative("AvNAPSA_negative")

(

"AvNAPSA_negative"

)

Referenced by main().

AvNAPSA_positive

basic::options::BooleanOptionKey const local::AvNAPSA_positive("AvNAPSA_positive")

(

"AvNAPSA_positive"

)

Referenced by main().

bb_min

basic::options::BooleanOptionKey const local::bb_min("bb_min")

(

"bb_min"

)

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

chain1

basic::options::IntegerOptionKey const local::chain1("local::chain1")

(

"local::chain1"

)

Referenced by numeric::kinematic_closure::radians::bridge_objects(), numeric::kinematic_closure::bridgeObjects(), dna_deriv_test(), dna_deriv_test_old(), interface_between_chains(), main(), region_for_string(), HDdesignMover::register_calculators(), register_metrics(), and numeric::kinematic_closure::test_rotateX().

chain2

basic::options::IntegerOptionKey const local::chain2("local::chain2")

(

"local::chain2"

)

Referenced by numeric::kinematic_closure::radians::bridge_objects(), numeric::kinematic_closure::bridgeObjects(), interface_between_chains(), main(), region_for_string(), HDdesignMover::register_calculators(), and register_metrics().

compare_residue_energies_all

basic::options::BooleanOptionKey const local::compare_residue_energies_all("compare_residue_energies_all")

(

"compare_residue_energies_all"

)

Referenced by main().

compare_residue_energies_mut

basic::options::BooleanOptionKey const local::compare_residue_energies_mut("compare_residue_energies_mut")

(

"compare_residue_energies_mut"

)

Referenced by main().

constraint_weight

basic::options::RealOptionKey const local::constraint_weight("constraint_weight")

(

"constraint_weight"

)

Referenced by protocols::jd2::RECONMPIJobDistributor::apply_linking_constraints(), protocols::jd2::RECONMPIJobDistributor::design_this_nodes_pose(), main(), and setup_ca_constraints().

dihedral_cst_weight

basic::options::RealOptionKey const local::dihedral_cst_weight("dihedral_cst_weight")

(

"dihedral_cst_weight"

)

Referenced by main().

dist_cst_weight

basic::options::RealOptionKey const local::dist_cst_weight("dist_cst_weight")

(

"dist_cst_weight"

)

Referenced by main().

dont_mutate_correct_charge

basic::options::BooleanOptionKey const local::dont_mutate_correct_charge("dont_mutate_correct_charge")

(

"dont_mutate_correct_charge"

)

Referenced by main().

dont_mutate_glyprocys

basic::options::BooleanOptionKey const local::dont_mutate_glyprocys("dont_mutate_glyprocys")

(

"dont_mutate_glyprocys"

)

Referenced by main().

dont_mutate_hbonded_sidechains

basic::options::BooleanOptionKey const local::dont_mutate_hbonded_sidechains("dont_mutate_hbonded_sidechains")

(

"dont_mutate_hbonded_sidechains"

)

Referenced by main().

evaluate_coordinating_res_energies

basic::options::BooleanOptionKey const local::evaluate_coordinating_res_energies("evaluate_coordinating_res_energies")

(

"evaluate_coordinating_res_energies"

)

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

evaluate_coordinating_res_types

basic::options::BooleanOptionKey const local::evaluate_coordinating_res_types("evaluate_coordinating_res_types")

(

"evaluate_coordinating_res_types"

)

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

evaluate_ligand_sasa

basic::options::BooleanOptionKey const local::evaluate_ligand_sasa("evaluate_ligand_sasa")

(

"evaluate_ligand_sasa"

)

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

evaluate_mutations_native

basic::options::BooleanOptionKey const local::evaluate_mutations_native("evaluate_mutations_native")

(

"evaluate_mutations_native"

)

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

evaluate_mutations_native_pdb

basic::options::FileOptionKey const local::evaluate_mutations_native_pdb("evaluate_mutations_native_pdb")

(

"evaluate_mutations_native_pdb"

)

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

evaluate_zinc_geometry

basic::options::BooleanOptionKey const local::evaluate_zinc_geometry("evaluate_zinc_geometry")

(

"evaluate_zinc_geometry"

)

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

evaluate_zinc_neighbors

basic::options::BooleanOptionKey const local::evaluate_zinc_neighbors("evaluate_zinc_neighbors")

(

"evaluate_zinc_neighbors"

)

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

evaluate_zinc_second_shell

basic::options::BooleanOptionKey const local::evaluate_zinc_second_shell("evaluate_zinc_second_shell")

(

"evaluate_zinc_second_shell"

)

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

first_ref_his

basic::options::IntegerOptionKey const local::first_ref_his("first_ref_his")

(

"first_ref_his"

)

Referenced by main().

helices_only

basic::options::BooleanOptionKey const local::helices_only("helices_only")

(

"helices_only"

)

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

helix_length

basic::options::IntegerOptionKey const local::helix_length("helix_length")

(

"helix_length"

)

Referenced by main().

heme_conformation

basic::options::FileOptionKey const local::heme_conformation("heme_conformation")

(

"heme_conformation"

)

Referenced by HemeReplace::HemeReplace(), and main().

hsasa_residue_cutoff

basic::options::RealOptionKey const local::hsasa_residue_cutoff("hsasa_residue_cutoff")

(

"hsasa_residue_cutoff"

)

Referenced by main().

include_arg

basic::options::BooleanOptionKey const local::include_arg("include_arg")

(

"include_arg"

)

Referenced by main().

include_asp

basic::options::BooleanOptionKey const local::include_asp("include_asp")

(

"include_asp"

)

Referenced by main().

include_glu

basic::options::BooleanOptionKey const local::include_glu("include_glu")

(

"include_glu"

)

Referenced by main().

include_lys

basic::options::BooleanOptionKey const local::include_lys("include_lys")

(

"include_lys"

)

Referenced by main().

ligand_3_letter_code

basic::options::StringOptionKey const local::ligand_3_letter_code("ligand_3_letter_code")

(

"ligand_3_letter_code"

)

Referenced by ZincSiteEvaluator::evaluate_ligand_sasa(), ZincSiteEvaluator::evaluate_zinc_neighbors(), and main().

ligand_cst_atoms

basic::options::StringVectorOptionKey const local::ligand_cst_atoms("ligand_cst_atoms")

(

"ligand_cst_atoms"

)

Referenced by main().

master

basic::options::StringOptionKey const local::master("local::master")

(

"local::master"

)

Referenced by main().

match_pdb

basic::options::FileOptionKey const local::match_pdb("match_pdb")

(

"match_pdb"

)

Referenced by main().

max_angle

basic::options::RealOptionKey const local::max_angle("max_angle")

(

"max_angle"

)

Referenced by HDmakerMover::apply(), calculate_theoretical_RNA_length(), calculate_theoretical_RNA_length_with_bond_angle_dependence(), and main().

max_loop_size

basic::options::IntegerOptionKey const local::max_loop_size("max_loop_size")

(

"max_loop_size"

)

Referenced by MetalSiteFinderMover::initialize_from_options(), and main().

max_res_span

basic::options::IntegerOptionKey const local::max_res_span("max_res_span")

(

"max_res_span"

)

Referenced by MetalSiteFinderMover::initialize_from_options(), and main().

mc_temperature

basic::options::RealOptionKey const local::mc_temperature("mc_temperature")

(

"mc_temperature"

)

Referenced by MyProtocol::apply(), HemeBindingMover::initialize_from_options(), and main().

metal_ligand_distance_cutoff

basic::options::RealOptionKey const local::metal_ligand_distance_cutoff("metal_ligand_distance_cutoff")

(

"metal_ligand_distance_cutoff"

)

Referenced by MetalSiteFinderMover::initialize_from_options(), and main().

metal_type

basic::options::StringOptionKey const local::metal_type("metal_type")

(

"metal_type"

)

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

min_coord_res

basic::options::IntegerOptionKey const local::min_coord_res("min_coord_res")

(

"min_coord_res"

)

Referenced by MetalSiteFinderMover::initialize_from_options(), and main().

min_local_coord_atoms

basic::options::IntegerOptionKey const local::min_local_coord_atoms("min_local_coord_atoms")

(

"min_local_coord_atoms"

)

Referenced by MetalSiteFinderMover::initialize_from_options(), and main().

min_total_coord_atoms

basic::options::IntegerOptionKey const local::min_total_coord_atoms("min_total_coord_atoms")

(

"min_total_coord_atoms"

)

Referenced by MetalSiteFinderMover::initialize_from_options(), and main().

n_ligands

basic::options::IntegerOptionKey const local::n_ligands("n_ligands")

(

"n_ligands"

)

Referenced by ZincSiteEvaluator::find_zinc_site(), and main().

n_moves

basic::options::IntegerOptionKey const local::n_moves("n_moves")

(

"n_moves"

)

Referenced by main().

nbr_residue

basic::options::IntegerOptionKey const local::nbr_residue("local::nbr_residue")

(

"local::nbr_residue"

)

Referenced by main().

neighbor_distance_cutoff

basic::options::RealOptionKey const local::neighbor_distance_cutoff("neighbor_distance_cutoff")

(

"neighbor_distance_cutoff"

)

Referenced by BacksideHbondFinderMover::BacksideHbondFinderMover(), and main().

no_relax

basic::options::BooleanOptionKey const local::no_relax("no_relax")

(

"no_relax"

)

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

nstruct

basic::options::IntegerOptionKey const local::nstruct("nstruct")

(

"nstruct"

)

Referenced by capri_t033_centroid_trim_dock_test(), capri_t033_loop_test(), capri_t033_trim_dock_test(), cst_relax_test(), diversify_sam_loop_test(), dna_stats(), protocols::abinitio::JumpSpecificAbrelax::do_distributed_rerun(), do_erraser2(), dock(), doit(), doit_refine(), erraser2_test(), fill_input_poses_based_on_possible_checkpoints(), InterfaceDDGBindJobInputter::fill_jobs(), first_preminimized_namer(), protocols::abinitio::JumpSpecificAbrelax::fold(), ligand_dock_main_jd1(), luxr_test(), main(), my_main(), not1_loop_test(), obtain_start_pose(), report_and_dump(), resample_full_model(), rna_build_helix_test(), rna_build_helix_test_OLD(), rna_design_gap_test(), rna_design_test(), rna_protein_rb_test(), round_minimized_namer(), round_resampled_namer(), FragmentAssemblyMover::run(), run_parallel_docking(), sample_rna_dofs_new(), second_preminimized_namer(), small_min_test(), myspace::test_bbgauss(), myspace::test_loophash(), myspace::test_MD(), myspace::test_recombine(), myspace::test_relax(), third_preminimized_namer(), trim_dock_rebuild_relax_test(), trim_dock_rebuild_relax_test_rhiju(), use_backrub(), and zf_relax_test().

num_iterations

basic::options::IntegerOptionKey const local::num_iterations("num_iterations")

(

"num_iterations"

)

Referenced by HemeBindingMover::initialize_from_options(), and main().

num_trials

basic::options::IntegerOptionKey const local::num_trials("num_trials")

(

"num_trials"

)

Referenced by HemeReplace::apply(), main(), ChallengeMover::sample(), NativeEnsemble::write_schema_to_db(), and NativeEnsemble::write_stats_to_db().

output_name

basic::options::StringOptionKey const local::output_name("output_name")

(

"output_name"

)

Referenced by zinc_stats::ZincStatisticGenerator::initialize_from_options(), and main().

partner1

basic::options::FileOptionKey const local::partner1("partner1")

(

"partner1"

)

Referenced by main().

partner2

basic::options::FileOptionKey const local::partner2("partner2")

(

"partner2"

)

Referenced by main().

partner2_residue

basic::options::IntegerOptionKey const local::partner2_residue("partner2_residue")

(

"partner2_residue"

)

Referenced by main().

pre_packminpack

basic::options::BooleanOptionKey const local::pre_packminpack("pre_packminpack")

(

"pre_packminpack"

)

Referenced by main().

prob_br_move

basic::options::RealOptionKey const local::prob_br_move("prob_br_move")

(

"prob_br_move"

)

Referenced by HemeBindingMover::initialize_from_options(), and main().

ref_zinc

basic::options::IntegerOptionKey const local::ref_zinc("ref_zinc")

(

"ref_zinc"

)

Referenced by main().

reference_zinc_site

basic::options::StringOptionKey const local::reference_zinc_site("reference_zinc_site")

(

"reference_zinc_site"

)

Referenced by main().

refweight_arg

basic::options::RealOptionKey const local::refweight_arg("refweight_arg")

(

"refweight_arg"

)

Referenced by main().

refweight_asp

basic::options::RealOptionKey const local::refweight_asp("refweight_asp")

(

"refweight_asp"

)

Referenced by main().

refweight_glu

basic::options::RealOptionKey const local::refweight_glu("refweight_glu")

(

"refweight_glu"

)

Referenced by main().

refweight_lys

basic::options::RealOptionKey const local::refweight_lys("refweight_lys")

(

"refweight_lys"

)

Referenced by main().

repacking_distance

basic::options::RealOptionKey const local::repacking_distance("repacking_distance")

(

"repacking_distance"

)

Referenced by main(), and HemeReplace::setup_task_factory().

require_bordering_ss

basic::options::BooleanOptionKey const local::require_bordering_ss("require_bordering_ss")

(

"require_bordering_ss"

)

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

sampling_increment

basic::options::RealOptionKey const local::sampling_increment("sampling_increment")

(

"sampling_increment"

)

Referenced by zinc_stats::ZincStatisticGenerator::initialize_from_options(), and main().

sampling_range

basic::options::RealOptionKey const local::sampling_range("sampling_range")

(

"sampling_range"

)

Referenced by double_helix_test(), helix_ST(), zinc_stats::ZincStatisticGenerator::initialize_from_options(), main(), and update_system().

secstruct

basic::options::StringOptionKey const local::secstruct("secstruct")

(

"secstruct"

)

Referenced by zinc_stats::ZincStatisticGenerator::initialize_from_options(), and main().

shear_moves

basic::options::IntegerOptionKey const local::shear_moves("shear_moves")

(

"shear_moves"

)

Referenced by main().

skip_sitegraft_repack

basic::options::BooleanOptionKey const local::skip_sitegraft_repack("skip_sitegraft_repack")

(

"skip_sitegraft_repack"

)

Referenced by main().

small_moves

basic::options::IntegerOptionKey const local::small_moves("small_moves")

(

"small_moves"

)

Referenced by main().

strict_ss_changes

basic::options::BooleanOptionKey const local::strict_ss_changes("strict_ss_changes")

(

"strict_ss_changes"

)

Referenced by MetalSiteFinderMover::initialize_from_options(), and main().

surface_atom_cutoff

basic::options::IntegerOptionKey const local::surface_atom_cutoff("surface_atom_cutoff")

(

"surface_atom_cutoff"

)

Referenced by main().

surface_residue

basic::options::IntegerOptionKey const local::surface_residue("surface_residue")

(

"surface_residue"

)

Referenced by main().

surface_residue_cutoff

basic::options::IntegerOptionKey const local::surface_residue_cutoff("surface_residue_cutoff")

(

"surface_residue_cutoff"

)

Referenced by main().

target_net_charge

basic::options::IntegerOptionKey const local::target_net_charge("target_net_charge")

(

"target_net_charge"

)

Referenced by main().

target_net_charge_active

basic::options::BooleanOptionKey const local::target_net_charge_active("target_net_charge_active")

(

"target_net_charge_active"

)

Referenced by main().

temperature

basic::options::RealOptionKey const local::temperature("temperature")

(

"temperature"

)

Referenced by SmoothFragRepackMover::apply(), numeric::boltzmann_accept_probability(), coarse_rna_denovo_test(), create_ensemble(), ChallengeMover::do_rigid_body_moves(), doit(), erraser_monte_carlo(), main(), register_options(), rna_design_gap_test(), core::pack::annealer::FixbbSimAnnealer::run(), run_mc(), SamplingManager::SamplingManager(), search_translations(), set_temp_based_on_ens_diversity(), sidechain_sample(), and NativeEnsemble::write_schema_to_db().

use_pdb_numbering

basic::options::BooleanOptionKey const local::use_pdb_numbering("use_pdb_numbering")

(

"use_pdb_numbering"

)

Referenced by main().

window_width

basic::options::IntegerOptionKey const local::window_width("window_width")

(

"window_width"

)

Referenced by main().

zinc_resnum

basic::options::IntegerOptionKey const local::zinc_resnum("zinc_resnum")

(

"zinc_resnum"

)

Referenced by ZincSiteEvaluator::find_zinc_site(), and main().

zn_constraint_weight

basic::options::RealOptionKey const local::zn_constraint_weight("zn_constraint_weight")

(

"zn_constraint_weight"

)

Referenced by main(), and ZincMinimize::set_scorefunction().

zn_min_pack

basic::options::BooleanOptionKey const local::zn_min_pack("zn_min_pack")

(

"zn_min_pack"

)

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

zn_min_pack_cycles

basic::options::IntegerOptionKey const local::zn_min_pack_cycles("zn_min_pack_cycles")

(

"zn_min_pack_cycles"

)

Referenced by main(), and ZincMinimize::zn_min_pack().

zn_minimize

basic::options::BooleanOptionKey const local::zn_minimize("zn_minimize")

(

"zn_minimize"

)

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