basic::options::OptionKeys::optE Namespace Reference

Namespaces
	rescore

Variables
BooleanOptionKey const	optE
StringOptionKey const	load_from_silent
StringOptionKey const	data_in
StringOptionKey const	data_out
StringOptionKey const	weights
StringVectorOptionKey const	fix
FileOptionKey const	free
FileOptionKey const	fixed
FileOptionKey const	parse_tagfile
FileOptionKey const	constant_logic_taskops_file
BooleanOptionKey const	optE_soft_rep
BooleanOptionKey const	no_hb_env_dependence
BooleanOptionKey const	no_hb_env_dependence_DNA
BooleanOptionKey const	optE_no_protein_fa_elec
BooleanOptionKey const	include_intra_res_protein
BooleanOptionKey const	centroid_rot
BooleanOptionKey const	centroid_rot_min
BooleanOptionKey const	design_first
IntegerOptionKey const	n_design_cycles
BooleanOptionKey const	recover_nat_rot
FileOptionKey const	component_weights
BooleanOptionKey const	optimize_nat_aa
BooleanOptionKey const	optimize_nat_rot
FileOptionKey const	optimize_ligand_rot
BooleanOptionKey const	optimize_pssm
FileOptionKey const	optimize_dGbinding
FileOptionKey const	optimize_ddG_bind_correlation
FileOptionKey const	optimize_ddGmutation
BooleanOptionKey const	optimize_ddGmutation_straight_mean
BooleanOptionKey const	optimize_ddGmutation_boltzman_average
RealOptionKey const	exclude_badrep_ddGs
BooleanOptionKey const	pretend_no_ddG_repulsion
FileOptionKey const	optimize_decoy_discrimination
StringOptionKey const	normalize_decoy_score_spread
BooleanOptionKey const	ramp_nativeness
IntegerOptionKey const	n_top_natives_to_optimize
RealOptionKey const	approximate_decoy_entropy
BooleanOptionKey const	repack_and_minimize_decoys
BooleanOptionKey const	repack_and_minimize_input_structures
IntegerOptionKey const	output_top_n_new_decoys
FileOptionKey const	optimize_ligand_discrimination
BooleanOptionKey const	no_design
BooleanOptionKey const	sqrt_pssm
RealOptionKey const	min_decoy_rms_to_native
RealOptionKey const	max_rms_from_native
BooleanOptionKey const	optimize_starting_free_weights
FileOptionKey const	wrap_dof_optimization
RealOptionKey const	randomly_perturb_starting_free_weights
RealOptionKey const	inv_kT_natrot
RealOptionKey const	inv_kT_nataa
RealOptionKey const	inv_kT_natstruct
BooleanOptionKey const	mpi_weight_minimization
BooleanOptionKey const	dont_use_reference_energies
IntegerOptionKey const	number_of_swarm_particles
IntegerOptionKey const	number_of_swarm_cycles
FileOptionKey const	constrain_weights
BooleanOptionKey const	fit_reference_energies_to_aa_profile_recovery
FileOptionKey const	starting_refEs
BooleanOptionKey const	repeat_swarm_optimization_until_fitness_improves
BooleanOptionKey const	design_with_minpack
BooleanOptionKey const	design_with_fast_design
BooleanOptionKey const	design_with_offrotpack
BooleanOptionKey const	limit_bad_scores
BooleanOptionKey const	no_design_pdb_output

Variable Documentation

approximate_decoy_entropy

RealOptionKey const basic::options::OptionKeys::optE::approximate_decoy_entropy

extern

centroid_rot

BooleanOptionKey const basic::options::OptionKeys::optE::centroid_rot

extern

centroid_rot_min

BooleanOptionKey const basic::options::OptionKeys::optE::centroid_rot_min

extern

component_weights

FileOptionKey const basic::options::OptionKeys::optE::component_weights

extern

Referenced by optimize_weights(), and simple_opte_test().

constant_logic_taskops_file

FileOptionKey const basic::options::OptionKeys::optE::constant_logic_taskops_file

extern

constrain_weights

FileOptionKey const basic::options::OptionKeys::optE::constrain_weights

extern

data_in

StringOptionKey const basic::options::OptionKeys::optE::data_in

extern

Referenced by numeric::get_cluster_data(), and main().

data_out

StringOptionKey const basic::options::OptionKeys::optE::data_out

extern

Referenced by numeric::get_cluster_data(), and main().

design_first

BooleanOptionKey const basic::options::OptionKeys::optE::design_first

extern

design_with_fast_design

BooleanOptionKey const basic::options::OptionKeys::optE::design_with_fast_design

extern

design_with_minpack

BooleanOptionKey const basic::options::OptionKeys::optE::design_with_minpack

extern

design_with_offrotpack

BooleanOptionKey const basic::options::OptionKeys::optE::design_with_offrotpack

extern

dont_use_reference_energies

BooleanOptionKey const basic::options::OptionKeys::optE::dont_use_reference_energies

extern

exclude_badrep_ddGs

RealOptionKey const basic::options::OptionKeys::optE::exclude_badrep_ddGs

extern

fit_reference_energies_to_aa_profile_recovery

BooleanOptionKey const basic::options::OptionKeys::optE::fit_reference_energies_to_aa_profile_recovery

extern

fix

StringVectorOptionKey const basic::options::OptionKeys::optE::fix

extern

Referenced by numeric::random::mt19937_RG::period_certification().

fixed

FileOptionKey const basic::options::OptionKeys::optE::fixed

extern

Referenced by PeptoidRotamerRecoverer::apply(), B3AADihedralGrabber::apply(), calculate_theoretical_RNA_length_with_bond_angle_dependence(), devel_main(), dostuff(), double_helix_test(), ObjexxFCL::format::F(), ObjexxFCL::fixed_Fstring_of(), ObjexxFCL::fixed_string_of(), ObjexxFCL::format::general(), helix_ST(), hessian_estimate(), main(), MC_run(), my_main(), one_chain_MC_sampling(), print_tree(), protocols_main(), utility::Real2string(), xtal_water_bunsat::report_sasa_if_contacting_water(), score_loop(), setup_pdb_line(), numeric::truncate_and_serialize_xyz_vector(), and detail::write_float().

free

FileOptionKey const basic::options::OptionKeys::optE::free

extern

include_intra_res_protein

BooleanOptionKey const basic::options::OptionKeys::optE::include_intra_res_protein

extern

inv_kT_nataa

RealOptionKey const basic::options::OptionKeys::optE::inv_kT_nataa

extern

inv_kT_natrot

RealOptionKey const basic::options::OptionKeys::optE::inv_kT_natrot

extern

inv_kT_natstruct

RealOptionKey const basic::options::OptionKeys::optE::inv_kT_natstruct

extern

limit_bad_scores

BooleanOptionKey const basic::options::OptionKeys::optE::limit_bad_scores

extern

load_from_silent

StringOptionKey const basic::options::OptionKeys::optE::load_from_silent

extern

max_rms_from_native

RealOptionKey const basic::options::OptionKeys::optE::max_rms_from_native

extern

min_decoy_rms_to_native

RealOptionKey const basic::options::OptionKeys::optE::min_decoy_rms_to_native

extern

mpi_weight_minimization

BooleanOptionKey const basic::options::OptionKeys::optE::mpi_weight_minimization

extern

n_design_cycles

IntegerOptionKey const basic::options::OptionKeys::optE::n_design_cycles

extern

n_top_natives_to_optimize

IntegerOptionKey const basic::options::OptionKeys::optE::n_top_natives_to_optimize

extern

no_design

BooleanOptionKey const basic::options::OptionKeys::optE::no_design

extern

no_design_pdb_output

BooleanOptionKey const basic::options::OptionKeys::optE::no_design_pdb_output

extern

no_hb_env_dependence

BooleanOptionKey const basic::options::OptionKeys::optE::no_hb_env_dependence

extern

no_hb_env_dependence_DNA

BooleanOptionKey const basic::options::OptionKeys::optE::no_hb_env_dependence_DNA

extern

normalize_decoy_score_spread

StringOptionKey const basic::options::OptionKeys::optE::normalize_decoy_score_spread

extern

number_of_swarm_cycles

IntegerOptionKey const basic::options::OptionKeys::optE::number_of_swarm_cycles

extern

number_of_swarm_particles

IntegerOptionKey const basic::options::OptionKeys::optE::number_of_swarm_particles

extern

optE

BooleanOptionKey const basic::options::OptionKeys::optE::optE

extern

optE_no_protein_fa_elec

BooleanOptionKey const basic::options::OptionKeys::optE::optE_no_protein_fa_elec

extern

optE_soft_rep

BooleanOptionKey const basic::options::OptionKeys::optE::optE_soft_rep

extern

optimize_ddG_bind_correlation

FileOptionKey const basic::options::OptionKeys::optE::optimize_ddG_bind_correlation

extern

optimize_ddGmutation

FileOptionKey const basic::options::OptionKeys::optE::optimize_ddGmutation

extern

optimize_ddGmutation_boltzman_average

BooleanOptionKey const basic::options::OptionKeys::optE::optimize_ddGmutation_boltzman_average

extern

optimize_ddGmutation_straight_mean

BooleanOptionKey const basic::options::OptionKeys::optE::optimize_ddGmutation_straight_mean

extern

optimize_decoy_discrimination

FileOptionKey const basic::options::OptionKeys::optE::optimize_decoy_discrimination

extern

optimize_dGbinding

FileOptionKey const basic::options::OptionKeys::optE::optimize_dGbinding

extern

optimize_ligand_discrimination

FileOptionKey const basic::options::OptionKeys::optE::optimize_ligand_discrimination

extern

optimize_ligand_rot

FileOptionKey const basic::options::OptionKeys::optE::optimize_ligand_rot

extern

optimize_nat_aa

BooleanOptionKey const basic::options::OptionKeys::optE::optimize_nat_aa

extern

optimize_nat_rot

BooleanOptionKey const basic::options::OptionKeys::optE::optimize_nat_rot

extern

optimize_pssm

BooleanOptionKey const basic::options::OptionKeys::optE::optimize_pssm

extern

optimize_starting_free_weights

BooleanOptionKey const basic::options::OptionKeys::optE::optimize_starting_free_weights

extern

output_top_n_new_decoys

IntegerOptionKey const basic::options::OptionKeys::optE::output_top_n_new_decoys

extern

parse_tagfile

FileOptionKey const basic::options::OptionKeys::optE::parse_tagfile

extern

pretend_no_ddG_repulsion

BooleanOptionKey const basic::options::OptionKeys::optE::pretend_no_ddG_repulsion

extern

ramp_nativeness

BooleanOptionKey const basic::options::OptionKeys::optE::ramp_nativeness

extern

randomly_perturb_starting_free_weights

RealOptionKey const basic::options::OptionKeys::optE::randomly_perturb_starting_free_weights

extern

recover_nat_rot

BooleanOptionKey const basic::options::OptionKeys::optE::recover_nat_rot

extern

repack_and_minimize_decoys

BooleanOptionKey const basic::options::OptionKeys::optE::repack_and_minimize_decoys

extern

repack_and_minimize_input_structures

BooleanOptionKey const basic::options::OptionKeys::optE::repack_and_minimize_input_structures

extern

repeat_swarm_optimization_until_fitness_improves

BooleanOptionKey const basic::options::OptionKeys::optE::repeat_swarm_optimization_until_fitness_improves

extern

sqrt_pssm

BooleanOptionKey const basic::options::OptionKeys::optE::sqrt_pssm

extern

starting_refEs

FileOptionKey const basic::options::OptionKeys::optE::starting_refEs

extern

weights

StringOptionKey const basic::options::OptionKeys::optE::weights

extern

wrap_dof_optimization

FileOptionKey const basic::options::OptionKeys::optE::wrap_dof_optimization

extern