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

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

Referenced by add_rosetta_options_13(), main(), and rebuild_test().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13(), main(), and rebuild_test().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13(), main(), and rna_sample_virtual_sugar().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13(), initialize_native_pose(), post_rebuild_bulge_assembly(), and swa_rna_cluster().

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

Referenced by pyrosetta.distributed.cluster.base::_get_packed_pose_kwargs_pairs_list(), add_rosetta_options_13(), pyrosetta.distributed.viewer.modules.setDisulfides::apply(), auto-DRRAFTER_setup::auto_setup_helices(), pyrosetta.bindings.pose::display_secstruct(), pyrosetta.distributed.cluster.core.PyRosettaCluster::distribute(), 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(), get_lowest_scoring_relaxed_models::main(), sidechain_cst_3::main(), options::main(), main(), erraser_util::phenix_rna_validate(), 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.protocols.indexed_structure_store.test_search.TestStructureSearch::test_rep_search(), options_class::wrapCStrig(), and arls_impl::write_setup_script().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13(), get_stepwise_score_function(), and StepWiseJobQueen::StepWiseJobQueen().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13(), binder::bind_member_functions_for_call_back(), StepWiseJobQueen::complete_larval_job_maturation(), erraser_wrapper::erraser_minimize(), main(), utility::thread::MutableCache< K, V >::operator=(), stepwise_monte_carlo_legacy(), and StepWiseJobQueen::StepWiseJobQueen().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13(), and main().

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

Referenced by add_rosetta_options_13(), and main().

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

Referenced by add_rosetta_options_13(), and main().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13(), and main().

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

Referenced by add_rosetta_options_13(), main(), and rna_fullatom_minimize_test().

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

Referenced by add_rosetta_options_13(), numeric::nls::lm_enorm(), utility::tools::make_map(), ObjexxFCL::FArray< T >::size_of(), numeric::crick_equations::X_BUNDLE(), numeric::crick_equations::Y_BUNDLE(), and numeric::crick_equations::Z_BUNDLE().

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

Referenced by add_rosetta_options_13(), numeric::nls::lm_enorm(), utility::tools::make_map(), ObjexxFCL::FArray< T >::size_of(), and numeric::fourier::SHT::sph_standardize().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13(), StepWiseJobQueen::complete_larval_job_maturation(), create_base_pair_step_database_test(), rna_fullatom_minimize_test(), and stepwise_monte_carlo_legacy().

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

Referenced by add_rosetta_options_13(), 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().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13(), rebuild_test(), and swa_rna_sample().

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

Referenced by add_rosetta_options_13(), and main().

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

Referenced by add_rosetta_options_13(), main(), and swa_rna_cluster().

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

Referenced by add_rosetta_options_13().

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

Referenced by add_rosetta_options_13(), BuildFullModel::BuildFullModel(), main(), and my_main().

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

Referenced by add_rosetta_options_13().