basic::options::OptionKeys::stepwise Namespace Reference

Namespaces
	monte_carlo
	polar_hydrogens
	protein
	rna

Variables
BooleanOptionKey const	stepwise
StringVectorOptionKey const	s1
StringVectorOptionKey const	s2
StringVectorOptionKey const	silent1
StringVectorOptionKey const	silent2
StringVectorOptionKey const	tags1
StringVectorOptionKey const	tags2
IntegerVectorOptionKey const	slice_res1
IntegerVectorOptionKey const	slice_res2
IntegerVectorOptionKey const	input_res1
IntegerVectorOptionKey const	input_res2
BooleanOptionKey const	backbone_only1
BooleanOptionKey const	backbone_only2
IntegerVectorOptionKey const	fixed_res
BooleanOptionKey const	test_encapsulation
BooleanOptionKey const	choose_random
IntegerOptionKey const	num_random_samples
IntegerOptionKey const	max_tries_multiplier_for_ccd
IntegerOptionKey const	num_pose_minimize
BooleanOptionKey const	atr_rep_screen
BooleanOptionKey const	atr_rep_screen_for_docking
StringOptionKey const	align_pdb
StringOptionKey const	new_align_pdb
BooleanOptionKey const	enumerate
BooleanOptionKey const	preminimize
BooleanOptionKey const	skip_preminimize
BooleanOptionKey const	minimize_waters
BooleanOptionKey const	test_all_moves
BooleanOptionKey const	new_move_selector
BooleanOptionKey const	dump
BooleanOptionKey const	VERBOSE
BooleanOptionKey const	use_green_packer
RealOptionKey const	rmsd_screen
BooleanOptionKey const	skip_minimize
BooleanOptionKey const	virtualize_packable_moieties_in_screening_pose
StringOptionKey const	minimizer_mode
StringOptionKey const	sampler_silent_file
BooleanOptionKey const	superimpose_over_all
ResidueChainVectorOptionKey const	alignment_anchor_res
StringVectorOptionKey const	move
StringOptionKey const	min_type
RealOptionKey const	min_tolerance
BooleanOptionKey const	output_minimized_pose_list
BooleanOptionKey const	virtualize_free_moieties_in_native
BooleanOptionKey const	output_cluster_size
BooleanOptionKey const	lores
BooleanOptionKey const	verbose_sampler
BooleanOptionKey const	pack_protein_side_chains
IntegerVectorOptionKey const	definitely_virtualize
BooleanOptionKey const	force_moving_res_for_erraser
BooleanOptionKey const	boltzmann_choice_post_enumerated_minimize

Variable Documentation

align_pdb

StringOptionKey const basic::options::OptionKeys::stepwise::align_pdb

extern

Referenced by main(), rebuild_test(), and stepwise_template_test().

alignment_anchor_res

ResidueChainVectorOptionKey const basic::options::OptionKeys::stepwise::alignment_anchor_res

extern

atr_rep_screen

BooleanOptionKey const basic::options::OptionKeys::stepwise::atr_rep_screen

extern

Referenced by main(), and rebuild_test().

atr_rep_screen_for_docking

BooleanOptionKey const basic::options::OptionKeys::stepwise::atr_rep_screen_for_docking

extern

backbone_only1

BooleanOptionKey const basic::options::OptionKeys::stepwise::backbone_only1

extern

backbone_only2

BooleanOptionKey const basic::options::OptionKeys::stepwise::backbone_only2

extern

boltzmann_choice_post_enumerated_minimize

BooleanOptionKey const basic::options::OptionKeys::stepwise::boltzmann_choice_post_enumerated_minimize

extern

choose_random

BooleanOptionKey const basic::options::OptionKeys::stepwise::choose_random

extern

Referenced by main(), and rna_sample_virtual_sugar().

definitely_virtualize

IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::definitely_virtualize

extern

dump

BooleanOptionKey const basic::options::OptionKeys::stepwise::dump

extern

Referenced by initialize_native_pose(), post_rebuild_bulge_assembly(), and swa_rna_cluster().

enumerate

BooleanOptionKey const basic::options::OptionKeys::stepwise::enumerate

extern

Referenced by pyrosetta.distributed.cluster.converters::_get_compressed_packed_pose_kwargs_pairs_list(), pyrosetta.distributed.cluster.core.PyRosettaCluster::_run(), pyrosetta.distributed.cluster.utilities.SchedulerManager::_setup_clients_dict(), pyrosetta.distributed.viewer.modules.setDisulfides::apply(), auto-DRRAFTER_setup::auto_setup_helices(), helpers::cache_trajectory(), percent_subangstrom::compare_benchmarks(), pyrosetta.bindings.pose::display_secstruct(), erraser_wrapper::erraser_single_res(), erraser_single_res_analysis::extract_info(), auto-DRRAFTER_setup_next_round::figure_out_next_round(), DRRAFTER_util::get_helix_stems(), util::get_surrounding_res(), auto-DRRAFTER_setup_next_round::get_top_ten_models_from_silent_files(), DRRAFTER_util::graph_from_ss(), pyrosetta.protocols.structure_search.alignment::length_blocks(), bin_torsions::load_torsions_from_dat(), get_lowest_scoring_relaxed_models::main(), options::main(), sidechain_cst_3::main(), main(), erraser_util::phenix_rna_validate(), bin_torsions::plot_score_function(), pyrosetta.tests.distributed.test_viewer.TestViewer::setUp(), DRRAFTER::setup_job(), drrafter_rna::setup_next_round(), pyrosetta.tests.bindings.core.test_pose.TestPoseIO::test_pose_io(), pyrosetta.tests.distributed.test_smoke.SmokeTestDistributed::test_poses_from_files_io(), pyrosetta.tests.protocols.indexed_structure_store.test_search.TestStructureSearch::test_rep_search(), pyrosetta.tests.distributed.cluster.test_smoke.RuntimeTest::test_timing_multi_instance(), pyrosetta.tests.distributed.cluster.test_smoke.RuntimeTest::test_timing_single_instance(), options_class::wrapCStrig(), and arls_impl::write_setup_script().

fixed_res

IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::fixed_res

extern

force_moving_res_for_erraser

BooleanOptionKey const basic::options::OptionKeys::stepwise::force_moving_res_for_erraser

extern

input_res1

IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::input_res1

extern

Referenced by main(), and stepwise_template_test().

input_res2

IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::input_res2

extern

Referenced by get_input_res(), main(), and stepwise_template_test().

lores

BooleanOptionKey const basic::options::OptionKeys::stepwise::lores

extern

Referenced by get_stepwise_score_function(), and StepWiseJobQueen::StepWiseJobQueen().

max_tries_multiplier_for_ccd

IntegerOptionKey const basic::options::OptionKeys::stepwise::max_tries_multiplier_for_ccd

extern

min_tolerance

RealOptionKey const basic::options::OptionKeys::stepwise::min_tolerance

extern

min_type

StringOptionKey const basic::options::OptionKeys::stepwise::min_type

extern

minimize_waters

BooleanOptionKey const basic::options::OptionKeys::stepwise::minimize_waters

extern

minimizer_mode

StringOptionKey const basic::options::OptionKeys::stepwise::minimizer_mode

extern

move

StringVectorOptionKey const basic::options::OptionKeys::stepwise::move

extern

Referenced by binder::bind_member_functions_for_call_back(), PyCallBack_Mammal_1_t::Breathe(), PyCallBack_Dog_1_t::Breathe(), StepWiseJobQueen::complete_larval_job_maturation(), MatchSet::cross(), MatchSet::cross_homodimer(), cyclic_superimpose(), PyCallBack_Animal_1_t::Eat(), PyCallBack_Mammal_1_t::Eat(), PyCallBack_Dog_1_t::Eat(), erraser_wrapper::erraser_minimize(), PyCallBack_A2::f(), PyCallBack_A3::f(), PyCallBack_Base::f_v(), PyCallBack_Derived::f_v(), PyCallBack_Delete::f_v(), PyCallBack_Base::f_v_2(), PyCallBack_Derived::f_v_2(), PyCallBack_Delete::f_v_2(), PyCallBack_X::f_v_2(), fix_prolines(), PyCallBack_Base::foo(), PyCallBack_n1_A::foo(), PyCallBack_n1_n2_A::foo(), PyCallBack_Base::foo_int(), PyCallBack_Base::foo_protected(), PyCallBack_Derived::foo_protected(), PyCallBack_Delete::foo_protected(), PyCallBack_X::foo_protected(), PyCallBack_Base::foo_sring(), PyCallBack_Base::foo_sring_r(), PyCallBack_Base::foo_void(), PyCallBack_Base::foo_void_pure(), PyCallBack_Animal_1_t::isDog(), PyCallBack_Mammal_1_t::isDog(), PyCallBack_Dog_1_t::isDog(), main(), basic_memory_buffer< T, SIZE, Allocator >::move(), utility::deep_copy_vector1< T >::operator=(), PyCallBack_A4::operator=(), utility::thread::MutableCache< K, V >::operator=(), operator>>(), ui::viewers::parse_score_file(), detail::dynamic_arg_list::push(), detail::bigint::square(), stepwise_monte_carlo_legacy(), and StepWiseJobQueen::StepWiseJobQueen().

new_align_pdb

StringOptionKey const basic::options::OptionKeys::stepwise::new_align_pdb

extern

new_move_selector

BooleanOptionKey const basic::options::OptionKeys::stepwise::new_move_selector

extern

Referenced by main().

num_pose_minimize

IntegerOptionKey const basic::options::OptionKeys::stepwise::num_pose_minimize

extern

Referenced by main(), and rna_resample_test().

num_random_samples

IntegerOptionKey const basic::options::OptionKeys::stepwise::num_random_samples

extern

Referenced by erraser_monte_carlo(), and main().

output_cluster_size

BooleanOptionKey const basic::options::OptionKeys::stepwise::output_cluster_size

extern

output_minimized_pose_list

BooleanOptionKey const basic::options::OptionKeys::stepwise::output_minimized_pose_list

extern

pack_protein_side_chains

BooleanOptionKey const basic::options::OptionKeys::stepwise::pack_protein_side_chains

extern

preminimize

BooleanOptionKey const basic::options::OptionKeys::stepwise::preminimize

extern

Referenced by main().

rmsd_screen

RealOptionKey const basic::options::OptionKeys::stepwise::rmsd_screen

extern

Referenced by main(), and rna_fullatom_minimize_test().

s1

StringVectorOptionKey const basic::options::OptionKeys::stepwise::s1

extern

Referenced by assign_stack_faces(), attach_abego_pools(), attach_simple_abego_pools(), check_filter_base_stack(), convert_to_coarse_test(), ddg(), define_states_test(), dock(), DomainDescription::DomainDescription(), TCDock::get_contacts_by_component(), get_ddg(), hd(), numeric::nls::lm_enorm(), main(), utility::tools::make_map(), make_your_own_alignment(), ConstraintConfig::parse_residues(), run_diiron_glu(), run_m8(), run_tyr_his(), run_zn2his(), utility::same_ignoring_spaces(), ObjexxFCL::FArray< T >::size_of(), skip(), stepwise_template_test(), strip_comment_and_whitespace(), utility::trimmed_compare(), numeric::crick_equations::X_BUNDLE(), Xpos(), numeric::crick_equations::Y_BUNDLE(), Ypos(), and numeric::crick_equations::Z_BUNDLE().

s2

StringVectorOptionKey const basic::options::OptionKeys::stepwise::s2

extern

Referenced by assign_stack_faces(), attach_abego_pools(), attach_simple_abego_pools(), check_filter_base_stack(), convert_to_coarse_test(), define_states_test(), dock(), DomainDescription::DomainDescription(), TCDock::get_contacts_by_component(), hd(), numeric::nls::lm_enorm(), main(), utility::tools::make_map(), make_your_own_alignment(), ConstraintConfig::parse_residues(), rebuild_centroid_test(), run_diiron_glu(), run_m8(), run_tyr_his(), run_zn2his(), utility::same_ignoring_spaces(), ObjexxFCL::FArray< T >::size_of(), numeric::fourier::SHT::sph_standardize(), stepwise_template_test(), and utility::trimmed_compare().

sampler_silent_file

StringOptionKey const basic::options::OptionKeys::stepwise::sampler_silent_file

extern

silent1

StringVectorOptionKey const basic::options::OptionKeys::stepwise::silent1

extern

Referenced by main(), and stepwise_template_test().

silent2

StringVectorOptionKey const basic::options::OptionKeys::stepwise::silent2

extern

Referenced by main(), and stepwise_template_test().

skip_minimize

BooleanOptionKey const basic::options::OptionKeys::stepwise::skip_minimize

extern

skip_preminimize

BooleanOptionKey const basic::options::OptionKeys::stepwise::skip_preminimize

extern

slice_res1

IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::slice_res1

extern

Referenced by calculate_helical_parameters_helper(), main(), and stepwise_template_test().

slice_res2

IntegerVectorOptionKey const basic::options::OptionKeys::stepwise::slice_res2

extern

Referenced by calculate_helical_parameters_helper(), main(), and stepwise_template_test().

stepwise

BooleanOptionKey const basic::options::OptionKeys::stepwise::stepwise

extern

Referenced by StepWiseJobQueen::complete_larval_job_maturation(), create_base_pair_step_database_test(), erraser_monte_carlo(), pack_phosphates(), rna_fullatom_minimize_test(), and stepwise_monte_carlo_legacy().

superimpose_over_all

BooleanOptionKey const basic::options::OptionKeys::stepwise::superimpose_over_all

extern

Referenced by RNA_ScoreMover::apply(), BuildFullModel::fill_and_sample_full_model(), main(), rna_denovo(), rna_denovo_legacy(), rna_fullatom_minimize_test(), stepwise_monte_carlo_legacy(), and StepWiseJobQueen::StepWiseJobQueen().

tags1

StringVectorOptionKey const basic::options::OptionKeys::stepwise::tags1

extern

Referenced by main(), and stepwise_template_test().

tags2

StringVectorOptionKey const basic::options::OptionKeys::stepwise::tags2

extern

Referenced by main(), and stepwise_template_test().

test_all_moves

BooleanOptionKey const basic::options::OptionKeys::stepwise::test_all_moves

extern

test_encapsulation

BooleanOptionKey const basic::options::OptionKeys::stepwise::test_encapsulation

extern

Referenced by rebuild_test(), and swa_rna_sample().

use_green_packer

BooleanOptionKey const basic::options::OptionKeys::stepwise::use_green_packer

extern

Referenced by main().

VERBOSE

BooleanOptionKey const basic::options::OptionKeys::stepwise::VERBOSE

extern

Referenced by main(), rna_resample_test(), and swa_rna_cluster().

verbose_sampler

BooleanOptionKey const basic::options::OptionKeys::stepwise::verbose_sampler

extern

virtualize_free_moieties_in_native

BooleanOptionKey const basic::options::OptionKeys::stepwise::virtualize_free_moieties_in_native

extern

Referenced by BuildFullModel::BuildFullModel(), main(), and my_main().

virtualize_packable_moieties_in_screening_pose

BooleanOptionKey const basic::options::OptionKeys::stepwise::virtualize_packable_moieties_in_screening_pose

extern