basic::options::OptionKeys::ddg Namespace Reference

Variables
BooleanOptionKey const	ddg
BooleanOptionKey const	opt_input_structure
BooleanOptionKey const	pack_until_converge
BooleanOptionKey const	no_constraints
BooleanOptionKey const	use_rotamer_constraints_to_native
BooleanOptionKey const	suppress_checkpointing
BooleanOptionKey const	wt_only
BooleanOptionKey const	mut_only
BooleanOptionKey const	optimize_wt
BooleanOptionKey const	output_silent
StringOptionKey const	minimization_scorefunction
StringOptionKey const	minimization_patch
BooleanOptionKey const	min_cst
IntegerOptionKey const	lowest_x_decoys
BooleanOptionKey const	local_opt_only
BooleanOptionKey const	print_per_res_diff
BooleanOptionKey const	mean
BooleanOptionKey const	min
BooleanOptionKey const	no_bb_movement
BooleanOptionKey const	initial_repack
IntegerOptionKey const	interface_ddg
RealOptionKey const	ens_variation
BooleanOptionKey const	sc_min_only
BooleanOptionKey const	rna_all_prot_sc_min_only
StringOptionKey const	min_cst_weights
RealOptionKey const	opt_radius
StringOptionKey const	output_dir
StringOptionKey const	last_accepted_pose_dir
BooleanOptionKey const	min_with_cst
RealOptionKey const	temperature
BooleanOptionKey const	ramp_repulsive
StringOptionKey const	mut_file
StringOptionKey const	out_pdb_prefix
RealOptionKey const	constraint_weight
RealOptionKey const	harmonic_ca_tether
IntegerOptionKey const	iterations
BooleanOptionKey const	force_iterations
StringOptionKey const	out
BooleanOptionKey const	debug_output
BooleanOptionKey const	dump_pdbs
StringOptionKey const	weight_file
RealOptionKey const	cst_dist_cutoff
BooleanOptionKey const	cartesian
IntegerOptionKey const	extract_element_nbrs
IntegerOptionKey const	frag_nbrs
IntegerOptionKey const	bbnbrs
IntegerOptionKey const	nfrags
IntegerOptionKey const	ntrials
BooleanOptionKey const	optimize_proline
BooleanOptionKey const	flex_bb
BooleanOptionKey const	fd_mode
BooleanOptionKey const	legacy
BooleanOptionKey const	json
IntegerOptionKey const	n_converged
RealOptionKey const	score_cutoff

Variable Documentation

bbnbrs

IntegerOptionKey const basic::options::OptionKeys::ddg::bbnbrs

extern

Referenced by compute_folding_energies(), and main().

cartesian

BooleanOptionKey const basic::options::OptionKeys::ddg::cartesian

extern

Referenced by Protocol_MolecularDynamics::apply(), MinTestMover::apply(), MinCenrotMover::apply(), CenRotRelaxMover::apply(), RepackMinCenrotMover::apply(), main(), myspace::ramp_repack_min(), and myspace::test_NMrelaxer().

constraint_weight

RealOptionKey const basic::options::OptionKeys::ddg::constraint_weight

extern

cst_dist_cutoff

RealOptionKey const basic::options::OptionKeys::ddg::cst_dist_cutoff

extern

Referenced by optimize_pose().

ddg

BooleanOptionKey const basic::options::OptionKeys::ddg::ddg

extern

Referenced by CrystRelax::apply(), calc_ddg(), CrystDesign::do_reversion(), CrystDesign::filter_and_report(), and main().

debug_output

BooleanOptionKey const basic::options::OptionKeys::ddg::debug_output

extern

Referenced by main().

dump_pdbs

BooleanOptionKey const basic::options::OptionKeys::ddg::dump_pdbs

extern

Referenced by calculate_distances(), TCDock::dump_top_hits(), main(), motif_scan(), register_options(), and single_position_motif_scan().

ens_variation

RealOptionKey const basic::options::OptionKeys::ddg::ens_variation

extern

Referenced by create_ensemble().

extract_element_nbrs

IntegerOptionKey const basic::options::OptionKeys::ddg::extract_element_nbrs

extern

fd_mode

BooleanOptionKey const basic::options::OptionKeys::ddg::fd_mode

extern

Referenced by main().

flex_bb

BooleanOptionKey const basic::options::OptionKeys::ddg::flex_bb

extern

force_iterations

BooleanOptionKey const basic::options::OptionKeys::ddg::force_iterations

extern

frag_nbrs

IntegerOptionKey const basic::options::OptionKeys::ddg::frag_nbrs

extern

harmonic_ca_tether

RealOptionKey const basic::options::OptionKeys::ddg::harmonic_ca_tether

extern

Referenced by main(), and optimize_pose().

initial_repack

BooleanOptionKey const basic::options::OptionKeys::ddg::initial_repack

extern

interface_ddg

IntegerOptionKey const basic::options::OptionKeys::ddg::interface_ddg

extern

Referenced by main().

iterations

IntegerOptionKey const basic::options::OptionKeys::ddg::iterations

extern

json

BooleanOptionKey const basic::options::OptionKeys::ddg::json

extern

Referenced by check_6D_potential(), ui::network::Argument::create(), ui::network::create_argument(), ui::network::BooleanArgument::encode(), ui::network::IntegerArgument::encode(), ui::network::FloatArgument::encode(), ui::network::StringArgument::encode(), ui::network::Bowman::on_bowman_thread_progress_data_received(), ui::network::Bowman::on_bowman_thread_result_received(), ui::network::Bowman::on_bowman_thread_specification_received(), numeric::read_tensor_from_file(), read_tensor_test(), and numeric::write_tensor_to_file().

last_accepted_pose_dir

StringOptionKey const basic::options::OptionKeys::ddg::last_accepted_pose_dir

extern

Referenced by run_mc().

legacy

BooleanOptionKey const basic::options::OptionKeys::ddg::legacy

extern

Referenced by load_coordinates_from_database(), main(), and swa_rna_sample().

local_opt_only

BooleanOptionKey const basic::options::OptionKeys::ddg::local_opt_only

extern

Referenced by main().

lowest_x_decoys

IntegerOptionKey const basic::options::OptionKeys::ddg::lowest_x_decoys

extern

Referenced by calc_ddg().

mean

BooleanOptionKey const basic::options::OptionKeys::ddg::mean

extern

Referenced by add_agc(), add_apc(), add_dhc(), calc_ddg(), calc_mean(), calc_sdev(), get_mean_sdev(), main(), print_verbose_ddgs(), myspace::stdev(), and test_Vec().

min

BooleanOptionKey const basic::options::OptionKeys::ddg::min

extern

min_cst

BooleanOptionKey const basic::options::OptionKeys::ddg::min_cst

extern

Referenced by main(), and print_ddgs().

min_cst_weights

StringOptionKey const basic::options::OptionKeys::ddg::min_cst_weights

extern

Referenced by run_mc().

min_with_cst

BooleanOptionKey const basic::options::OptionKeys::ddg::min_with_cst

extern

Referenced by run_mc().

minimization_patch

StringOptionKey const basic::options::OptionKeys::ddg::minimization_patch

extern

Referenced by main().

minimization_scorefunction

StringOptionKey const basic::options::OptionKeys::ddg::minimization_scorefunction

extern

Referenced by main().

mut_file

StringOptionKey const basic::options::OptionKeys::ddg::mut_file

extern

Referenced by get_mutations_from_file(), and main().

mut_only

BooleanOptionKey const basic::options::OptionKeys::ddg::mut_only

extern

Referenced by main().

n_converged

IntegerOptionKey const basic::options::OptionKeys::ddg::n_converged

extern

nfrags

IntegerOptionKey const basic::options::OptionKeys::ddg::nfrags

extern

Referenced by DockFragmentsMover::cluster_frags(), gen_pep_bb_frag(), gen_pep_bb_frag_old(), gen_pep_bb_sequential(), main(), make_1mer_frags(), make_fragments(), RunPepSpec(), setup_loops_fragment_libraries_with_ss(), and simple_loop_modeling_test().

no_bb_movement

BooleanOptionKey const basic::options::OptionKeys::ddg::no_bb_movement

extern

Referenced by run_mc().

no_constraints

BooleanOptionKey const basic::options::OptionKeys::ddg::no_constraints

extern

Referenced by optimize_pose().

ntrials

IntegerOptionKey const basic::options::OptionKeys::ddg::ntrials

extern

opt_input_structure

BooleanOptionKey const basic::options::OptionKeys::ddg::opt_input_structure

extern

opt_radius

RealOptionKey const basic::options::OptionKeys::ddg::opt_radius

extern

optimize_proline

BooleanOptionKey const basic::options::OptionKeys::ddg::optimize_proline

extern

optimize_wt

BooleanOptionKey const basic::options::OptionKeys::ddg::optimize_wt

extern

out

StringOptionKey const basic::options::OptionKeys::ddg::out

extern

out_pdb_prefix

StringOptionKey const basic::options::OptionKeys::ddg::out_pdb_prefix

extern

Referenced by main(), and minimize_with_constraints().

output_dir

StringOptionKey const basic::options::OptionKeys::ddg::output_dir

extern

Referenced by minimize_with_constraints().

output_silent

BooleanOptionKey const basic::options::OptionKeys::ddg::output_silent

extern

Referenced by pyrosetta.io::poses_to_silent(), rna_build_helix_test(), rna_build_helix_test_OLD(), and rna_build_helix_test_precompute().

pack_until_converge

BooleanOptionKey const basic::options::OptionKeys::ddg::pack_until_converge

extern

print_per_res_diff

BooleanOptionKey const basic::options::OptionKeys::ddg::print_per_res_diff

extern

Referenced by main().

ramp_repulsive

BooleanOptionKey const basic::options::OptionKeys::ddg::ramp_repulsive

extern

Referenced by minimize_with_constraints().

rna_all_prot_sc_min_only

BooleanOptionKey const basic::options::OptionKeys::ddg::rna_all_prot_sc_min_only

extern

Referenced by minimize_with_constraints().

sc_min_only

BooleanOptionKey const basic::options::OptionKeys::ddg::sc_min_only

extern

Referenced by minimize_with_constraints(), and setup_ca_constraints().

score_cutoff

RealOptionKey const basic::options::OptionKeys::ddg::score_cutoff

extern

Referenced by attach_abego_pools(), initialize_rigid_body_sampler(), main(), search_translations(), and superimpose_smotifs().

suppress_checkpointing

BooleanOptionKey const basic::options::OptionKeys::ddg::suppress_checkpointing

extern

temperature

RealOptionKey const basic::options::OptionKeys::ddg::temperature

extern

use_rotamer_constraints_to_native

BooleanOptionKey const basic::options::OptionKeys::ddg::use_rotamer_constraints_to_native

extern

weight_file

StringOptionKey const basic::options::OptionKeys::ddg::weight_file

extern

Referenced by main(), and simple_opte_test().

wt_only

BooleanOptionKey const basic::options::OptionKeys::ddg::wt_only

extern

Referenced by main().