basic::options::OptionKeys::abinitio Namespace Reference

Namespaces
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Variables
BooleanOptionKey const	abinitio
BooleanOptionKey const	membrane
BooleanOptionKey const	use_loophash_filter
RealOptionKey const	loophash_filter_acceptance_rate
FileOptionKey const	kill_hairpins
RealOptionKey const	kill_hairpins_frequency
BooleanOptionKey const	smooth_cycles_only
BooleanOptionKey const	relax
BooleanOptionKey const	final_clean_relax
BooleanOptionKey const	fastrelax
BooleanOptionKey const	multifastrelax
BooleanOptionKey const	debug
BooleanOptionKey const	clear_pose_cache
BooleanOptionKey const	explicit_pdb_debug
BooleanOptionKey const	use_filters
BooleanOptionKey const	use_trRosetta_constraints
RealOptionKey const	increase_cycles
IntegerOptionKey const	number_3mer_frags
IntegerOptionKey const	number_9mer_frags
RealOptionKey const	temperature
RealOptionKey const	rg_reweight
RealOptionKey const	rsd_wt_helix
RealOptionKey const	rsd_wt_strand
RealOptionKey const	rsd_wt_loop
BooleanOptionKey const	skip_convergence_check
FileVectorOptionKey const	stage1_patch
FileVectorOptionKey const	stage2_patch
FileVectorOptionKey const	stage3a_patch
FileVectorOptionKey const	stage3b_patch
FileVectorOptionKey const	stage4_patch
FileVectorOptionKey const	stage5_patch
BooleanOptionKey const	steal_3mers
BooleanOptionKey const	steal_9mers
BooleanOptionKey const	no_write_failures
BooleanOptionKey const	relax_failures
BooleanOptionKey const	relax_with_jumps
BooleanOptionKey const	process_store
IntegerVectorOptionKey const	fix_residues_to_native
BooleanOptionKey const	return_full_atom
BooleanOptionKey const	detect_disulfide_before_relax
BooleanOptionKey const	close_loops
BooleanOptionKey const	bGDT
BooleanOptionKey const	dump_frags
BooleanOptionKey const	jdist_rerun
RealOptionKey const	perturb
BooleanOptionKey const	rerun
IntegerVectorOptionKey const	rmsd_residues
BooleanOptionKey const	start_native
BooleanOptionKey const	cyclic_peptide
BooleanOptionKey const	debug_structures
FileOptionKey const	log_frags
BooleanOptionKey const	only_stage1
RealOptionKey const	end_bias
BooleanOptionKey const	apply_end_bias
IntegerOptionKey const	symmetry_residue
RealOptionKey const	vdw_weight_stage1
BooleanOptionKey const	override_vdw_all_stages
IntegerVectorOptionKey const	recover_low_in_stages
IntegerVectorOptionKey const	skip_stages
BooleanOptionKey const	close_chbrk
BooleanOptionKey const	include_stage5
BooleanOptionKey const	close_loops_by_idealizing
BooleanOptionKey const	optimize_cutpoints_using_kic
IntegerOptionKey const	optimize_cutpoints_margin

Variable Documentation

abinitio

BooleanOptionKey const basic::options::OptionKeys::abinitio::abinitio

extern

Referenced by AbInitio_MPI::init_on_new_input(), main(), and DomainAssemblerNDocker::run().

apply_end_bias

BooleanOptionKey const basic::options::OptionKeys::abinitio::apply_end_bias

extern

bGDT

BooleanOptionKey const basic::options::OptionKeys::abinitio::bGDT

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::do_distributed_rerun(), protocols::abinitio::JumpSpecificAbrelax::do_rerun(), protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup().

clear_pose_cache

BooleanOptionKey const basic::options::OptionKeys::abinitio::clear_pose_cache

extern

close_chbrk

BooleanOptionKey const basic::options::OptionKeys::abinitio::close_chbrk

extern

close_loops

BooleanOptionKey const basic::options::OptionKeys::abinitio::close_loops

extern

close_loops_by_idealizing

BooleanOptionKey const basic::options::OptionKeys::abinitio::close_loops_by_idealizing

extern

cyclic_peptide

BooleanOptionKey const basic::options::OptionKeys::abinitio::cyclic_peptide

extern

Referenced by add_Cu_chains(), and build_polymer().

debug

BooleanOptionKey const basic::options::OptionKeys::abinitio::debug

extern

debug_structures

BooleanOptionKey const basic::options::OptionKeys::abinitio::debug_structures

extern

detect_disulfide_before_relax

BooleanOptionKey const basic::options::OptionKeys::abinitio::detect_disulfide_before_relax

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::relax().

dump_frags

BooleanOptionKey const basic::options::OptionKeys::abinitio::dump_frags

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup_fragments().

end_bias

RealOptionKey const basic::options::OptionKeys::abinitio::end_bias

extern

explicit_pdb_debug

BooleanOptionKey const basic::options::OptionKeys::abinitio::explicit_pdb_debug

extern

fastrelax

BooleanOptionKey const basic::options::OptionKeys::abinitio::fastrelax

extern

Referenced by compute_folding_energies(), protocols::abinitio::JumpSpecificAbrelax::do_distributed_rerun(), protocols::abinitio::JumpSpecificAbrelax::fold(), rebuild_test(), protocols::abinitio::JumpSpecificAbrelax::relax(), protocols::abinitio::JumpSpecificAbrelax::setup_fold(), and sidechain_fastrelax().

final_clean_relax

BooleanOptionKey const basic::options::OptionKeys::abinitio::final_clean_relax

extern

fix_residues_to_native

IntegerVectorOptionKey const basic::options::OptionKeys::abinitio::fix_residues_to_native

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::setup_fold().

include_stage5

BooleanOptionKey const basic::options::OptionKeys::abinitio::include_stage5

extern

increase_cycles

RealOptionKey const basic::options::OptionKeys::abinitio::increase_cycles

extern

jdist_rerun

BooleanOptionKey const basic::options::OptionKeys::abinitio::jdist_rerun

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::run().

kill_hairpins

FileOptionKey const basic::options::OptionKeys::abinitio::kill_hairpins

extern

kill_hairpins_frequency

RealOptionKey const basic::options::OptionKeys::abinitio::kill_hairpins_frequency

extern

log_frags

FileOptionKey const basic::options::OptionKeys::abinitio::log_frags

extern

loophash_filter_acceptance_rate

RealOptionKey const basic::options::OptionKeys::abinitio::loophash_filter_acceptance_rate

extern

membrane

BooleanOptionKey const basic::options::OptionKeys::abinitio::membrane

extern

Referenced by MinTestMover::apply(), SampleTiltProtocol::apply(), ColorByLipidType::apply(), FindOptimalHydrophobicThk::apply(), MPframeworkTest1Mover::apply(), MembraneViewMover::apply(), MembraneMinMover::apply(), MembraneSfxnMover::apply(), MembraneDockingxMover::apply(), MembraneRelaxMover::apply(), MembraneSampleMover::apply(), MembraneTransformMover::apply(), MPInterfaceStatistics::apply(), TestQuickRelaxMover::apply(), MPFoldingMover::apply(), LoadMembraneMover::apply(), ViewMembraneProteinMover::apply(), MPDomainAssembly::apply(), MPScoreFunctionFingerprintMover::apply(), check_centroid(), check_fullatom(), create_MPpose(), helix_from_sequence(), main(), modify_foldtree(), my_main(), read_membrane(), test_membrane_conformation(), and test_membrane_fold_tree().

multifastrelax

BooleanOptionKey const basic::options::OptionKeys::abinitio::multifastrelax

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::fold(), and protocols::abinitio::JumpSpecificAbrelax::setup_fold().

no_write_failures

BooleanOptionKey const basic::options::OptionKeys::abinitio::no_write_failures

extern

number_3mer_frags

IntegerOptionKey const basic::options::OptionKeys::abinitio::number_3mer_frags

extern

Referenced by DomainAssemblerNDocker::DomainAssemblerNDocker(), get_fragments(), main(), setup_for_folding(), protocols::abinitio::JumpSpecificAbrelax::setup_fragments(), and TryScoreFilter::TryScoreFilter().

number_9mer_frags

IntegerOptionKey const basic::options::OptionKeys::abinitio::number_9mer_frags

extern

Referenced by DomainAssemblerNDocker::DomainAssemblerNDocker(), get_fragments(), main(), setup_for_folding(), protocols::abinitio::JumpSpecificAbrelax::setup_fragments(), and TryScoreFilter::TryScoreFilter().

only_stage1

BooleanOptionKey const basic::options::OptionKeys::abinitio::only_stage1

extern

optimize_cutpoints_margin

IntegerOptionKey const basic::options::OptionKeys::abinitio::optimize_cutpoints_margin

extern

optimize_cutpoints_using_kic

BooleanOptionKey const basic::options::OptionKeys::abinitio::optimize_cutpoints_using_kic

extern

override_vdw_all_stages

BooleanOptionKey const basic::options::OptionKeys::abinitio::override_vdw_all_stages

extern

perturb

RealOptionKey const basic::options::OptionKeys::abinitio::perturb

extern

process_store

BooleanOptionKey const basic::options::OptionKeys::abinitio::process_store

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::fold().

recover_low_in_stages

IntegerVectorOptionKey const basic::options::OptionKeys::abinitio::recover_low_in_stages

extern

relax

BooleanOptionKey const basic::options::OptionKeys::abinitio::relax

extern

Referenced by LoopHashRelax_Sampler::apply(), HBondReporter::apply(), MembraneDockingxMover::apply(), MembraneRelaxMover::apply(), CrystRelax::CrystRelax(), HBondReporter::decoyify(), protocols::abinitio::JumpSpecificAbrelax::do_distributed_rerun(), helix_from_sequence(), AbInitio_MPI::init_on_new_input(), LoopBuild_main(), main(), my_main(), predict_AE(), protocols::abinitio::JumpSpecificAbrelax::relax(), relax_with_restraints_on_constres(), MPI_Refinement_Launcher::run(), MPI_LoopHash_Launcher::run(), protocols::abinitio::JumpSpecificAbrelax::setup_fold(), FastRelaxPerformanceBenchmark::setup_for_mmstd(), FastRelaxPerformanceBenchmark::setup_for_sc12he(), FastRelaxPerformanceBenchmark::setup_for_sc12sp2(), FastRelaxPerformanceBenchmark::setup_for_score12(), FastRelaxPerformanceBenchmark::setup_for_sp2hecart(), simple_relax(), and myspace::test_relax().

relax_failures

BooleanOptionKey const basic::options::OptionKeys::abinitio::relax_failures

extern

relax_with_jumps

BooleanOptionKey const basic::options::OptionKeys::abinitio::relax_with_jumps

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::do_distributed_rerun(), and protocols::abinitio::JumpSpecificAbrelax::fold().

rerun

BooleanOptionKey const basic::options::OptionKeys::abinitio::rerun

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::register_options(), protocols::abinitio::JumpSpecificAbrelax::run(), and protocols::abinitio::JumpSpecificAbrelax::setup().

return_full_atom

BooleanOptionKey const basic::options::OptionKeys::abinitio::return_full_atom

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::setup_fold().

rg_reweight

RealOptionKey const basic::options::OptionKeys::abinitio::rg_reweight

extern

rmsd_residues

IntegerVectorOptionKey const basic::options::OptionKeys::abinitio::rmsd_residues

extern

Referenced by RNA_ScoreMover::apply(), drrafter_error_estimation(), get_rmsd(), main(), protocols::abinitio::JumpSpecificAbrelax::register_options(), protocols::abinitio::JumpSpecificAbrelax::setup(), setup_per_residue_rmsd_atom_map(), and setup_rmsd_atom_map().

rsd_wt_helix

RealOptionKey const basic::options::OptionKeys::abinitio::rsd_wt_helix

extern

rsd_wt_loop

RealOptionKey const basic::options::OptionKeys::abinitio::rsd_wt_loop

extern

rsd_wt_strand

RealOptionKey const basic::options::OptionKeys::abinitio::rsd_wt_strand

extern

skip_convergence_check

BooleanOptionKey const basic::options::OptionKeys::abinitio::skip_convergence_check

extern

skip_stages

IntegerVectorOptionKey const basic::options::OptionKeys::abinitio::skip_stages

extern

smooth_cycles_only

BooleanOptionKey const basic::options::OptionKeys::abinitio::smooth_cycles_only

extern

stage1_patch

FileVectorOptionKey const basic::options::OptionKeys::abinitio::stage1_patch

extern

stage2_patch

FileVectorOptionKey const basic::options::OptionKeys::abinitio::stage2_patch

extern

stage3a_patch

FileVectorOptionKey const basic::options::OptionKeys::abinitio::stage3a_patch

extern

stage3b_patch

FileVectorOptionKey const basic::options::OptionKeys::abinitio::stage3b_patch

extern

stage4_patch

FileVectorOptionKey const basic::options::OptionKeys::abinitio::stage4_patch

extern

stage5_patch

FileVectorOptionKey const basic::options::OptionKeys::abinitio::stage5_patch

extern

start_native

BooleanOptionKey const basic::options::OptionKeys::abinitio::start_native

extern

Referenced by protocols::abinitio::ApplicationContext::ApplicationContext(), protocols::abinitio::ApplicationContext::register_options(), protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup_fold().

steal_3mers

BooleanOptionKey const basic::options::OptionKeys::abinitio::steal_3mers

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup_fragments().

steal_9mers

BooleanOptionKey const basic::options::OptionKeys::abinitio::steal_9mers

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup_fragments().

symmetry_residue

IntegerOptionKey const basic::options::OptionKeys::abinitio::symmetry_residue

extern

temperature

RealOptionKey const basic::options::OptionKeys::abinitio::temperature

extern

use_filters

BooleanOptionKey const basic::options::OptionKeys::abinitio::use_filters

extern

Referenced by protocols::abinitio::JumpSpecificAbrelax::check_filters().

use_loophash_filter

BooleanOptionKey const basic::options::OptionKeys::abinitio::use_loophash_filter

extern

use_trRosetta_constraints

BooleanOptionKey const basic::options::OptionKeys::abinitio::use_trRosetta_constraints

extern

vdw_weight_stage1

RealOptionKey const basic::options::OptionKeys::abinitio::vdw_weight_stage1

extern