basic::options::OptionKeys::remodel Namespace Reference

Namespaces
	design
	domainFusion
	RemodelLoopMover
	staged_sampling

Variables
BooleanOptionKey const	remodel
FileOptionKey const	blueprint
FileOptionKey const	cstfile
BooleanOptionKey const	cst_fa_only
IntegerOptionKey const	cstfilter
StringOptionKey const	cen_sfxn
BooleanOptionKey const	check_scored_centroid
IntegerOptionKey const	num_trajectory
IntegerOptionKey const	save_top
BooleanOptionKey const	swap_refine_confirm_protocols
BooleanOptionKey const	bypass_fragments
BooleanOptionKey const	use_same_length_fragments
BooleanOptionKey const	no_jumps
IntegerOptionKey const	reroot_tree
BooleanOptionKey const	use_blueprint_sequence
BooleanOptionKey const	quick_and_dirty
BooleanOptionKey const	checkpoint
BooleanOptionKey const	use_pose_relax
BooleanOptionKey const	use_cart_relax
BooleanOptionKey const	free_relax
StringOptionKey const	generic_aa
RealOptionKey const	cluster_radius
BooleanOptionKey const	use_clusters
BooleanOptionKey const	run_confirmation
BooleanOptionKey const	cluster_on_entire_pose
IntegerOptionKey const	dr_cycles
IntegerOptionKey const	two_chain_tree
IntegerOptionKey const	repeat_structure
IntegerOptionKey const	lh_ex_limit
StringVectorOptionKey const	lh_filter_string
IntegerOptionKey const	lh_cbreak_selection
BooleanOptionKey const	lh_closure_filter
BooleanOptionKey const	cen_minimize
IntegerOptionKey const	core_cutoff
IntegerOptionKey const	boundary_cutoff
StringOptionKey const	coreAA
StringOptionKey const	boundaryAA
StringOptionKey const	surfaceAA
BooleanOptionKey const	design_around_ligand
BooleanOptionKey const	move_ligand
BooleanOptionKey const	resclass_by_sasa
RealOptionKey const	helical_rise
RealOptionKey const	helical_radius
RealOptionKey const	helical_omega
RealVectorOptionKey const	filter_rise
RealVectorOptionKey const	filter_radius
RealVectorOptionKey const	filter_omega
RealOptionKey const	COM_sd
RealOptionKey const	COM_tolerance
RealOptionKey const	vdw
RealOptionKey const	rama
RealOptionKey const	cbeta
RealOptionKey const	cenpack
RealOptionKey const	rg_local
RealOptionKey const	hb_lrbb
RealOptionKey const	hb_srbb
RealOptionKey const	rg
RealOptionKey const	rsigma
RealOptionKey const	ss_pair
BooleanOptionKey const	build_disulf
RealOptionKey const	match_rt_limit
IntegerVectorOptionKey const	disulf_landing_range
BooleanOptionKey const	rank_by_bsasa

Variable Documentation

blueprint

FileOptionKey const basic::options::OptionKeys::remodel::blueprint

extern

Referenced by fill_optional_options().

boundary_cutoff

IntegerOptionKey const basic::options::OptionKeys::remodel::boundary_cutoff

extern

boundaryAA

StringOptionKey const basic::options::OptionKeys::remodel::boundaryAA

extern

build_disulf

BooleanOptionKey const basic::options::OptionKeys::remodel::build_disulf

extern

bypass_fragments

BooleanOptionKey const basic::options::OptionKeys::remodel::bypass_fragments

extern

cbeta

RealOptionKey const basic::options::OptionKeys::remodel::cbeta

extern

Referenced by doit(), FloppyTailMover::FloppyTailMover(), get_loop_scorefxn(), get_loop_scorefxn_old(), gpu_refold_test(), main(), RBSegmentRelax_test(), simple_centroid_test(), simple_loop_modeling_test(), and simple_opte_test().

cen_minimize

BooleanOptionKey const basic::options::OptionKeys::remodel::cen_minimize

extern

cen_sfxn

StringOptionKey const basic::options::OptionKeys::remodel::cen_sfxn

extern

Referenced by main().

cenpack

RealOptionKey const basic::options::OptionKeys::remodel::cenpack

extern

check_scored_centroid

BooleanOptionKey const basic::options::OptionKeys::remodel::check_scored_centroid

extern

checkpoint

BooleanOptionKey const basic::options::OptionKeys::remodel::checkpoint

extern

cluster_on_entire_pose

BooleanOptionKey const basic::options::OptionKeys::remodel::cluster_on_entire_pose

extern

cluster_radius

RealOptionKey const basic::options::OptionKeys::remodel::cluster_radius

extern

COM_sd

RealOptionKey const basic::options::OptionKeys::remodel::COM_sd

extern

COM_tolerance

RealOptionKey const basic::options::OptionKeys::remodel::COM_tolerance

extern

core_cutoff

IntegerOptionKey const basic::options::OptionKeys::remodel::core_cutoff

extern

Referenced by measure_sequence_recovery().

coreAA

StringOptionKey const basic::options::OptionKeys::remodel::coreAA

extern

cst_fa_only

BooleanOptionKey const basic::options::OptionKeys::remodel::cst_fa_only

extern

cstfile

FileOptionKey const basic::options::OptionKeys::remodel::cstfile

extern

cstfilter

IntegerOptionKey const basic::options::OptionKeys::remodel::cstfilter

extern

design_around_ligand

BooleanOptionKey const basic::options::OptionKeys::remodel::design_around_ligand

extern

disulf_landing_range

IntegerVectorOptionKey const basic::options::OptionKeys::remodel::disulf_landing_range

extern

dr_cycles

IntegerOptionKey const basic::options::OptionKeys::remodel::dr_cycles

extern

filter_omega

RealVectorOptionKey const basic::options::OptionKeys::remodel::filter_omega

extern

filter_radius

RealVectorOptionKey const basic::options::OptionKeys::remodel::filter_radius

extern

filter_rise

RealVectorOptionKey const basic::options::OptionKeys::remodel::filter_rise

extern

free_relax

BooleanOptionKey const basic::options::OptionKeys::remodel::free_relax

extern

generic_aa

StringOptionKey const basic::options::OptionKeys::remodel::generic_aa

extern

hb_lrbb

RealOptionKey const basic::options::OptionKeys::remodel::hb_lrbb

extern

hb_srbb

RealOptionKey const basic::options::OptionKeys::remodel::hb_srbb

extern

helical_omega

RealOptionKey const basic::options::OptionKeys::remodel::helical_omega

extern

helical_radius

RealOptionKey const basic::options::OptionKeys::remodel::helical_radius

extern

helical_rise

RealOptionKey const basic::options::OptionKeys::remodel::helical_rise

extern

lh_cbreak_selection

IntegerOptionKey const basic::options::OptionKeys::remodel::lh_cbreak_selection

extern

lh_closure_filter

BooleanOptionKey const basic::options::OptionKeys::remodel::lh_closure_filter

extern

lh_ex_limit

IntegerOptionKey const basic::options::OptionKeys::remodel::lh_ex_limit

extern

lh_filter_string

StringVectorOptionKey const basic::options::OptionKeys::remodel::lh_filter_string

extern

match_rt_limit

RealOptionKey const basic::options::OptionKeys::remodel::match_rt_limit

extern

move_ligand

BooleanOptionKey const basic::options::OptionKeys::remodel::move_ligand

extern

no_jumps

BooleanOptionKey const basic::options::OptionKeys::remodel::no_jumps

extern

num_trajectory

IntegerOptionKey const basic::options::OptionKeys::remodel::num_trajectory

extern

quick_and_dirty

BooleanOptionKey const basic::options::OptionKeys::remodel::quick_and_dirty

extern

rama

RealOptionKey const basic::options::OptionKeys::remodel::rama

extern

Referenced by CustomMover::apply(), PickBAB::apply(), RamaTestMover::apply(), calc_rama(), calc_rama2b(), calc_rama_scores(), myspace::DataClass::DataClass(), dna_coupled_rotamer_design_test(), doit(), fa_scorefxn_test(), FloppyTailMover::FloppyTailMover(), get_loop_scorefxn(), get_loop_scorefxn_old(), initialize_free_and_fixed(), main(), multivec2sf(), my_main(), print_energies(), BreadthMover::rama_apply(), rama_test(), Bola::random_close_phipsi_from_rama(), rb_test(), refine_fa_pep_bb(), relax_test(), RunPepSpec(), sample_rama_test(), SamplingManager::SamplingManager(), scan_Evalue(), FastRelaxPerformanceBenchmark::setup_for_sc12he(), InteractionGraphPerformanceBenchmark::setup_for_sc12he(), FastRelaxPerformanceBenchmark::setup_for_sc12sp2(), InteractionGraphPerformanceBenchmark::setup_for_sc12sp2(), FastRelaxPerformanceBenchmark::setup_for_score12(), InteractionGraphPerformanceBenchmark::setup_for_score12(), FastRelaxPerformanceBenchmark::setup_for_sp2hecart(), InteractionGraphPerformanceBenchmark::setup_for_sp2hecart(), sf2multivec(), simple_dna_test(), simple_opte_test(), small_min_test(), SSM_energies::SSM_energies(), and test_rama().

rank_by_bsasa

BooleanOptionKey const basic::options::OptionKeys::remodel::rank_by_bsasa

extern

remodel

BooleanOptionKey const basic::options::OptionKeys::remodel::remodel

extern

repeat_structure

IntegerOptionKey const basic::options::OptionKeys::remodel::repeat_structure

extern

Referenced by graphics_main(), and main().

reroot_tree

IntegerOptionKey const basic::options::OptionKeys::remodel::reroot_tree

extern

resclass_by_sasa

BooleanOptionKey const basic::options::OptionKeys::remodel::resclass_by_sasa

extern

rg

RealOptionKey const basic::options::OptionKeys::remodel::rg

extern

Referenced by SimulateCryoMover::add_flat_noise(), cen_fold(), get_loop_scorefxn(), get_loop_scorefxn_old(), gpu_refold_test(), main(), MPframeworkTest1Mover::move_together(), rb_entropy_test(), report(), rg2d(), run(), HubDenovo::run(), simple_opte_test(), and SimulateCryoMover::three_fine_projections_from_xyz().

rg_local

RealOptionKey const basic::options::OptionKeys::remodel::rg_local

extern

rsigma

RealOptionKey const basic::options::OptionKeys::remodel::rsigma

extern

Referenced by simple_opte_test(), and ss_test().

run_confirmation

BooleanOptionKey const basic::options::OptionKeys::remodel::run_confirmation

extern

save_top

IntegerOptionKey const basic::options::OptionKeys::remodel::save_top

extern

Referenced by graphics_main().

ss_pair

RealOptionKey const basic::options::OptionKeys::remodel::ss_pair

extern

Referenced by ddg(), simple_opte_test(), and ss_test().

surfaceAA

StringOptionKey const basic::options::OptionKeys::remodel::surfaceAA

extern

swap_refine_confirm_protocols

BooleanOptionKey const basic::options::OptionKeys::remodel::swap_refine_confirm_protocols

extern

two_chain_tree

IntegerOptionKey const basic::options::OptionKeys::remodel::two_chain_tree

extern

use_blueprint_sequence

BooleanOptionKey const basic::options::OptionKeys::remodel::use_blueprint_sequence

extern

use_cart_relax

BooleanOptionKey const basic::options::OptionKeys::remodel::use_cart_relax

extern

use_clusters

BooleanOptionKey const basic::options::OptionKeys::remodel::use_clusters

extern

use_pose_relax

BooleanOptionKey const basic::options::OptionKeys::remodel::use_pose_relax

extern

use_same_length_fragments

BooleanOptionKey const basic::options::OptionKeys::remodel::use_same_length_fragments

extern

vdw

RealOptionKey const basic::options::OptionKeys::remodel::vdw

extern

Referenced by CenRelaxMover::apply(), CustomMover::apply(), ChallengeMover::apply(), CenRotRelaxMover::apply(), CenRotRBRelaxMover::apply(), build_template(), CenRotDockingMover::CenRotDockingMover(), CenRotRBRelaxMover::CenRotRBRelaxMover(), CenRotRelaxMover::CenRotRelaxMover(), coarse_close_loop_test(), doit(), FloppyTailMover::FloppyTailMover(), gen_pep_bb_sequential(), generate_combined_model(), get_loop_scorefxn(), get_loop_scorefxn_old(), gpu_refold_test(), HubDenovo::HubDenovo(), initialize_free_and_fixed(), main(), modeler_map_test(), my_main(), process_the_pose(), RBSegmentRelax_test(), RunPepSpec(), setup_grids(), simple_centroid_test(), simple_loop_modeling_test(), simple_opte_test(), and CenRotDockingMover::slide_into_contact().