basic::options::OptionKeys::packing Namespace Reference

Namespaces
	ex1
	ex1aro
	ex1aro_exposed
	ex2
	ex2aro
	ex2aro_exposed
	ex3
	ex4
	exdna
	packer_palette

Variables
BooleanOptionKey const	packing
BooleanOptionKey const	repack_only
BooleanOptionKey const	prevent_repacking
RealOptionKey const	cenrot_cutoff
BooleanOptionKey const	ignore_ligand_chi
BooleanOptionKey const	quasisymmetry
IntegerOptionKey const	ndruns
BooleanOptionKey const	soft_rep_design
RealOptionKey const	mainchain_h_rebuild_threshold
BooleanOptionKey const	use_electrostatic_repulsion
BooleanOptionKey const	dump_rotamer_sets
RealOptionKey const	dunbrack_prob_buried
RealOptionKey const	dunbrack_prob_nonburied
RealOptionKey const	dunbrack_prob_buried_semi
RealOptionKey const	dunbrack_prob_nonburied_semi
BooleanOptionKey const	no_optH
BooleanOptionKey const	optH_MCA
BooleanOptionKey const	pack_missing_sidechains
BooleanOptionKey const	preserve_c_beta
BooleanOptionKey const	flip_HNQ
IntegerVectorOptionKey const	fix_his_tautomer
BooleanOptionKey const	print_pymol_selection
IntegerOptionKey const	extrachi_cutoff
FileVectorOptionKey const	resfile
BooleanOptionKey const	sc_branch_rotamers
RealOptionKey const	outeriterations_scaling
RealOptionKey const	inneriterations_scaling
StringVectorOptionKey const	adducts
BooleanOptionKey const	use_input_sc
FileVectorOptionKey const	unboundrot
RealOptionKey const	max_rotbump_energy
BooleanOptionKey const	lazy_ig
BooleanOptionKey const	double_lazy_ig
IntegerOptionKey const	linmem_ig
BooleanOptionKey const	precompute_ig
IntegerOptionKey const	multi_cool_annealer
BooleanOptionKey const	sequence_symmetric_annealer
BooleanOptionKey const	smart_annealer
StringOptionKey const	smart_annealer_model
RealOptionKey const	smart_annealer_cutoff
BooleanOptionKey const	smart_annealer_pick_again
BooleanOptionKey const	smart_annealer_disable_during_quench
RealVectorOptionKey const	minpack_temp_schedule
IntegerOptionKey const	minpack_inner_iteration_scale
BooleanOptionKey const	minpack_disable_bumpcheck

Variable Documentation

adducts

StringVectorOptionKey const basic::options::OptionKeys::packing::adducts

extern

cenrot_cutoff

RealOptionKey const basic::options::OptionKeys::packing::cenrot_cutoff

extern

double_lazy_ig

BooleanOptionKey const basic::options::OptionKeys::packing::double_lazy_ig

extern

dump_rotamer_sets

BooleanOptionKey const basic::options::OptionKeys::packing::dump_rotamer_sets

extern

dunbrack_prob_buried

RealOptionKey const basic::options::OptionKeys::packing::dunbrack_prob_buried

extern

Referenced by get_rsrpl().

dunbrack_prob_buried_semi

RealOptionKey const basic::options::OptionKeys::packing::dunbrack_prob_buried_semi

extern

dunbrack_prob_nonburied

RealOptionKey const basic::options::OptionKeys::packing::dunbrack_prob_nonburied

extern

Referenced by get_rsrpl().

dunbrack_prob_nonburied_semi

RealOptionKey const basic::options::OptionKeys::packing::dunbrack_prob_nonburied_semi

extern

extrachi_cutoff

IntegerOptionKey const basic::options::OptionKeys::packing::extrachi_cutoff

extern

Referenced by main().

fix_his_tautomer

IntegerVectorOptionKey const basic::options::OptionKeys::packing::fix_his_tautomer

extern

flip_HNQ

BooleanOptionKey const basic::options::OptionKeys::packing::flip_HNQ

extern

Referenced by main().

ignore_ligand_chi

BooleanOptionKey const basic::options::OptionKeys::packing::ignore_ligand_chi

extern

inneriterations_scaling

RealOptionKey const basic::options::OptionKeys::packing::inneriterations_scaling

extern

lazy_ig

BooleanOptionKey const basic::options::OptionKeys::packing::lazy_ig

extern

linmem_ig

IntegerOptionKey const basic::options::OptionKeys::packing::linmem_ig

extern

Referenced by rebuild_test().

mainchain_h_rebuild_threshold

RealOptionKey const basic::options::OptionKeys::packing::mainchain_h_rebuild_threshold

extern

max_rotbump_energy

RealOptionKey const basic::options::OptionKeys::packing::max_rotbump_energy

extern

minpack_disable_bumpcheck

BooleanOptionKey const basic::options::OptionKeys::packing::minpack_disable_bumpcheck

extern

minpack_inner_iteration_scale

IntegerOptionKey const basic::options::OptionKeys::packing::minpack_inner_iteration_scale

extern

minpack_temp_schedule

RealVectorOptionKey const basic::options::OptionKeys::packing::minpack_temp_schedule

extern

multi_cool_annealer

IntegerOptionKey const basic::options::OptionKeys::packing::multi_cool_annealer

extern

ndruns

IntegerOptionKey const basic::options::OptionKeys::packing::ndruns

extern

Referenced by MSA_design().

no_optH

BooleanOptionKey const basic::options::OptionKeys::packing::no_optH

extern

Referenced by main().

optH_MCA

BooleanOptionKey const basic::options::OptionKeys::packing::optH_MCA

extern

outeriterations_scaling

RealOptionKey const basic::options::OptionKeys::packing::outeriterations_scaling

extern

pack_missing_sidechains

BooleanOptionKey const basic::options::OptionKeys::packing::pack_missing_sidechains

extern

Referenced by add_side_chains_partialthread(), and main().

packing

BooleanOptionKey const basic::options::OptionKeys::packing::packing

extern

Referenced by main().

precompute_ig

BooleanOptionKey const basic::options::OptionKeys::packing::precompute_ig

extern

preserve_c_beta

BooleanOptionKey const basic::options::OptionKeys::packing::preserve_c_beta

extern

prevent_repacking

BooleanOptionKey const basic::options::OptionKeys::packing::prevent_repacking

extern

Referenced by NativeEnsemble::apply(), mp_ddG::mutate_residue(), demo.D090_Ala_scan::mutate_residue(), pyrosetta.toolbox.mutants::restrict_non_nbrs_from_repacking(), sample_trp_test(), and SamplingManager::SamplingManager().

print_pymol_selection

BooleanOptionKey const basic::options::OptionKeys::packing::print_pymol_selection

extern

quasisymmetry

BooleanOptionKey const basic::options::OptionKeys::packing::quasisymmetry

extern

repack_only

BooleanOptionKey const basic::options::OptionKeys::packing::repack_only

extern

Referenced by main(), and register_options().

resfile

FileVectorOptionKey const basic::options::OptionKeys::packing::resfile

extern

Referenced by PeptoidRotamerRecoverer::apply(), Packing_energies::apply(), SSM_energies::apply(), MinPackMinMover::apply(), design_using_resfile(), dostuff(), fill_optional_options(), ga_main(), SetupHotspotMover::generate_csts(), graphics_main(), UBQ_E2Mover::init_on_new_input(), UBQ_GTPase_disulfide_Mover::init_on_new_input(), PhDocking::init_options(), JDtestmover::JDtestmover(), main(), make_motif_task(), MSA_design(), my_main(), register_options(), rna_design_test(), PhDocking::set_resfile(), zinc1_homodimer_design::setup_taskfactory(), zinc2_homodimer_design::setup_taskfactory_scorefunction_movers(), HDdesignMover::task_constraint_setup(), and ZincMinimize::zn_min_pack().

sc_branch_rotamers

BooleanOptionKey const basic::options::OptionKeys::packing::sc_branch_rotamers

extern

sequence_symmetric_annealer

BooleanOptionKey const basic::options::OptionKeys::packing::sequence_symmetric_annealer

extern

smart_annealer

BooleanOptionKey const basic::options::OptionKeys::packing::smart_annealer

extern

smart_annealer_cutoff

RealOptionKey const basic::options::OptionKeys::packing::smart_annealer_cutoff

extern

smart_annealer_disable_during_quench

BooleanOptionKey const basic::options::OptionKeys::packing::smart_annealer_disable_during_quench

extern

smart_annealer_model

StringOptionKey const basic::options::OptionKeys::packing::smart_annealer_model

extern

smart_annealer_pick_again

BooleanOptionKey const basic::options::OptionKeys::packing::smart_annealer_pick_again

extern

soft_rep_design

BooleanOptionKey const basic::options::OptionKeys::packing::soft_rep_design

extern

Referenced by main().

unboundrot

FileVectorOptionKey const basic::options::OptionKeys::packing::unboundrot

extern

Referenced by LigandRepackMinimizeProtocol::apply(), main(), and abbinding::setup_RepulsiveRampMover().

use_electrostatic_repulsion

BooleanOptionKey const basic::options::OptionKeys::packing::use_electrostatic_repulsion

extern

use_input_sc

BooleanOptionKey const basic::options::OptionKeys::packing::use_input_sc

extern

Referenced by main(), register_options(), HbondZinc::repack(), and HbondZincBackbone::repack().