basic::options::OptionKeys::dna::specificity Namespace Reference

Variables
BooleanOptionKey const	specificity
BooleanOptionKey const	exclude_dna_dna
RealVectorOptionKey const	params
FileVectorOptionKey const	frag_files
BooleanOptionKey const	only_repack
BooleanOptionKey const	design_DNA
BooleanOptionKey const	soft_rep
BooleanOptionKey const	dump_pdbs
BooleanOptionKey const	fast
BooleanOptionKey const	randomize_motif
RealOptionKey const	Wfa_elec
RealOptionKey const	Wdna_bs
RealOptionKey const	Wdna_bp
RealOptionKey const	minimize_tolerance
StringOptionKey const	weights_tag
StringOptionKey const	weights_tag_list
StringOptionKey const	min_type
StringOptionKey const	mode
StringOptionKey const	score_function
BooleanOptionKey const	pre_minimize
BooleanOptionKey const	post_minimize
BooleanOptionKey const	pre_pack
IntegerOptionKey const	nloop
IntegerOptionKey const	n_inner
IntegerOptionKey const	n_outer
IntegerOptionKey const	nstep_water
IntegerOptionKey const	moving_jump
IntegerOptionKey const	motif_begin
IntegerOptionKey const	motif_size
StringVectorOptionKey const	pdb_pos
StringVectorOptionKey const	methylate
RealVectorOptionKey const	dna_backbone_torsion_sdevs
RealOptionKey const	dna_sugar_torsion_sdev
RealOptionKey const	dna_chi_torsion_sdev
StringOptionKey const	lk_ball_wtd_tag
BooleanOptionKey const	lk_ball_for_bb
RealOptionKey const	lk_ball_ramp_width_A2
RealOptionKey const	lk_ball_overlap_gap
RealOptionKey const	lk_ball_overlap_width_A2
RealOptionKey const	lk_ball_water_fade
RealVectorOptionKey const	lk_ball_wtd_prefactors
RealVectorOptionKey const	lk_ball_waters_sp2
RealVectorOptionKey const	lk_ball_waters_sp3
RealVectorOptionKey const	lk_ball_waters_ring
RealOptionKey const	lk_ball_waters_donor
RealOptionKey const	lk_ball_bridge_angle_widthscale
RealOptionKey const	lk_dome_max_angle
RealOptionKey const	lk_dome_min_angle
RealOptionKey const	lk_dome_occlusion_min
RealOptionKey const	lk_dome_occlusion_max
RealOptionKey const	lk_dome_h2o_radius
RealOptionKey const	lk_dome_ramp_width_A2
RealOptionKey const	lk_dome_overlap_width_A2
RealOptionKey const	lk_dome_ball_overlap_width_A2
RealOptionKey const	lk_dome_water_dist
RealOptionKey const	lk_dome_water_adjust

Variable Documentation

design_DNA

BooleanOptionKey const basic::options::OptionKeys::dna::specificity::design_DNA

extern

Referenced by design_test().

dna_backbone_torsion_sdevs

RealVectorOptionKey const basic::options::OptionKeys::dna::specificity::dna_backbone_torsion_sdevs

extern

dna_chi_torsion_sdev

RealOptionKey const basic::options::OptionKeys::dna::specificity::dna_chi_torsion_sdev

extern

dna_sugar_torsion_sdev

RealOptionKey const basic::options::OptionKeys::dna::specificity::dna_sugar_torsion_sdev

extern

dump_pdbs

BooleanOptionKey const basic::options::OptionKeys::dna::specificity::dump_pdbs

extern

exclude_dna_dna

BooleanOptionKey const basic::options::OptionKeys::dna::specificity::exclude_dna_dna

extern

fast

BooleanOptionKey const basic::options::OptionKeys::dna::specificity::fast

extern

Referenced by dna_specificity_test(), main(), my_main(), register_options(), rna_resample_test(), DomainAssemblerNDocker::run(), zf_test(), and zif268_test().

frag_files

FileVectorOptionKey const basic::options::OptionKeys::dna::specificity::frag_files

extern

Referenced by dna_stats(), main(), my_main(), read_pdbs(), and zf_relax_test().

lk_ball_bridge_angle_widthscale

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_ball_bridge_angle_widthscale

extern

lk_ball_for_bb

BooleanOptionKey const basic::options::OptionKeys::dna::specificity::lk_ball_for_bb

extern

lk_ball_overlap_gap

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_ball_overlap_gap

extern

lk_ball_overlap_width_A2

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_ball_overlap_width_A2

extern

lk_ball_ramp_width_A2

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_ball_ramp_width_A2

extern

lk_ball_water_fade

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_ball_water_fade

extern

lk_ball_waters_donor

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_ball_waters_donor

extern

lk_ball_waters_ring

RealVectorOptionKey const basic::options::OptionKeys::dna::specificity::lk_ball_waters_ring

extern

lk_ball_waters_sp2

RealVectorOptionKey const basic::options::OptionKeys::dna::specificity::lk_ball_waters_sp2

extern

lk_ball_waters_sp3

RealVectorOptionKey const basic::options::OptionKeys::dna::specificity::lk_ball_waters_sp3

extern

lk_ball_wtd_prefactors

RealVectorOptionKey const basic::options::OptionKeys::dna::specificity::lk_ball_wtd_prefactors

extern

lk_ball_wtd_tag

StringOptionKey const basic::options::OptionKeys::dna::specificity::lk_ball_wtd_tag

extern

lk_dome_ball_overlap_width_A2

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_dome_ball_overlap_width_A2

extern

lk_dome_h2o_radius

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_dome_h2o_radius

extern

lk_dome_max_angle

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_dome_max_angle

extern

lk_dome_min_angle

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_dome_min_angle

extern

lk_dome_occlusion_max

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_dome_occlusion_max

extern

lk_dome_occlusion_min

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_dome_occlusion_min

extern

lk_dome_overlap_width_A2

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_dome_overlap_width_A2

extern

lk_dome_ramp_width_A2

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_dome_ramp_width_A2

extern

lk_dome_water_adjust

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_dome_water_adjust

extern

lk_dome_water_dist

RealOptionKey const basic::options::OptionKeys::dna::specificity::lk_dome_water_dist

extern

methylate

StringVectorOptionKey const basic::options::OptionKeys::dna::specificity::methylate

extern

Referenced by not1_loop_test().

min_type

StringOptionKey const basic::options::OptionKeys::dna::specificity::min_type

extern

Referenced by DougsDockDesignMinimizeMagicMover::apply(), InteractionDistMinimizer::apply(), ElecDensMinPackMinMover::apply(), PepMinMover::apply(), SymFixbbMover::apply(), A3BHbsCreatorMover::apply(), A3BHbsDockDesignMinimizeMover::apply(), TrizaolamerDockDesignMinimizeMover::apply(), LDConverterMover::apply(), MinPackMinMover::apply(), HbsDesignMover::apply(), OopDesignMover::apply(), PeptoidDesignMover::apply(), HDdesignMover::apply(), Minimize::apply(), NCMinimize::apply(), dna_specificity_test(), A3BHbsCreatorMover::do_mc(), endo_test(), main(), place_waters_and_minimize(), register_options(), apps::pilot::momeara::HBondConformation::relax_pose_around_hbond(), saxs_energy(), A3BHbsCreatorMover::scan(), simple_opte_test(), HDdesignMover::sym_repack_minimize(), and tf_specificity_test().

minimize_tolerance

RealOptionKey const basic::options::OptionKeys::dna::specificity::minimize_tolerance

extern

Referenced by dna_specificity_test(), endo_test(), and tf_specificity_test().

mode

StringOptionKey const basic::options::OptionKeys::dna::specificity::mode

extern

motif_begin

IntegerOptionKey const basic::options::OptionKeys::dna::specificity::motif_begin

extern

Referenced by bzip_test(), dna_specificity_test(), endo_test(), luxr_test(), not1_test(), and zif268_test().

motif_size

IntegerOptionKey const basic::options::OptionKeys::dna::specificity::motif_size

extern

Referenced by bzip_test(), dna_specificity_test(), endo_test(), luxr_test(), zf_test(), and zif268_test().

moving_jump

IntegerOptionKey const basic::options::OptionKeys::dna::specificity::moving_jump

extern

Referenced by analyze_interface_test(), and luxr_test().

n_inner

IntegerOptionKey const basic::options::OptionKeys::dna::specificity::n_inner

extern

Referenced by capri15_relax(), dna_stats(), and zf_relax_test().

n_outer

IntegerOptionKey const basic::options::OptionKeys::dna::specificity::n_outer

extern

Referenced by capri15_relax(), capri_t033_centroid_trim_dock_test(), dna_stats(), and zf_relax_test().

nloop

IntegerOptionKey const basic::options::OptionKeys::dna::specificity::nloop

extern

Referenced by capri_t033_centroid_trim_dock_test(), decompose(), design_test(), dna_specificity_test(), endo_test(), full_protein_repack(), interface_repack_test(), main(), make_rand_ss_hs(), scmove_residue(), small_min_test(), spec_test(), spinner_test(), and tf_specificity_test().

nstep_water

IntegerOptionKey const basic::options::OptionKeys::dna::specificity::nstep_water

extern

Referenced by water_test().

only_repack

BooleanOptionKey const basic::options::OptionKeys::dna::specificity::only_repack

extern

Referenced by design_test().

params

RealVectorOptionKey const basic::options::OptionKeys::dna::specificity::params

extern

Referenced by binder::bind_constructor(), utility::graph::depth_first_search_sort(), dna_design_test_old(), get_base_steps(), get_numeric_deriv(), numeric::interpolation::Histogram< X, Y >::Histogram(), MC_run(), numeric::interpolation::Histogram< X, Y >::read_from_db(), numeric::interpolation::Histogram< X, Y >::set_params(), test_deriv_pose(), test_gradient(), thermal_sampler(), and zf_relax_test().

pdb_pos

StringVectorOptionKey const basic::options::OptionKeys::dna::specificity::pdb_pos

extern

Referenced by motif_scan(), parse_pdb_pos(), and pose_pos_from_pdb_pos().

post_minimize

BooleanOptionKey const basic::options::OptionKeys::dna::specificity::post_minimize

extern

Referenced by dna_specificity_test(), endo_test(), and tf_specificity_test().

pre_minimize

BooleanOptionKey const basic::options::OptionKeys::dna::specificity::pre_minimize

extern

Referenced by motif_scan().

pre_pack

BooleanOptionKey const basic::options::OptionKeys::dna::specificity::pre_pack

extern

Referenced by motif_scan().

randomize_motif

BooleanOptionKey const basic::options::OptionKeys::dna::specificity::randomize_motif

extern

Referenced by luxr_test().

score_function

StringOptionKey const basic::options::OptionKeys::dna::specificity::score_function

extern

Referenced by CustomMover::apply(), NativeEnsemble::apply(), describe_move(), design_test(), dna_stats(), ga_main(), interface_repack_test(), luxr_test(), main(), motif_scan(), my_main(), not1_loop_test(), not1_test(), SamplingManager::SamplingManager(), sequence_tolerance_main(), sequence_tolerance_mf_main(), water_test(), and zf_relax_test().

soft_rep

BooleanOptionKey const basic::options::OptionKeys::dna::specificity::soft_rep

extern

Referenced by dna_specificity_test(), do_color_by_score(), main(), rna_protein_rb_test(), and tf_specificity_test().

specificity

BooleanOptionKey const basic::options::OptionKeys::dna::specificity::specificity

extern

Wdna_bp

RealOptionKey const basic::options::OptionKeys::dna::specificity::Wdna_bp

extern

Referenced by bzip_test(), dna_specificity_test(), endo_test(), luxr_test(), not1_test(), tf_specificity_test(), zf_test(), and zif268_test().

Wdna_bs

RealOptionKey const basic::options::OptionKeys::dna::specificity::Wdna_bs

extern

Referenced by bzip_test(), dna_specificity_test(), endo_test(), luxr_test(), not1_test(), tf_specificity_test(), zf_test(), and zif268_test().

weights_tag

StringOptionKey const basic::options::OptionKeys::dna::specificity::weights_tag

extern

Referenced by bzip_test(), dna_specificity_test(), endo_test(), ga_main(), rescore_test(), tf_specificity_test(), zf_test(), and zif268_test().

weights_tag_list

StringOptionKey const basic::options::OptionKeys::dna::specificity::weights_tag_list

extern

Referenced by bzip_test(), dna_specificity_test(), endo_test(), rescore_test(), tf_specificity_test(), zf_test(), and zif268_test().

Wfa_elec

RealOptionKey const basic::options::OptionKeys::dna::specificity::Wfa_elec

extern

Referenced by bzip_test(), dna_specificity_test(), endo_test(), luxr_test(), not1_test(), tf_specificity_test(), zf_test(), and zif268_test().