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_offrotpack
BooleanOptionKey const	limit_bad_scores
BooleanOptionKey const	no_design_pdb_output

Variable Documentation

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11(), and numeric::random::mt19937_RG::period_certification().

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

Referenced by add_rosetta_options_11(), supercharge::design_supercharge(), supercharge::energy_comparison(), ObjexxFCL::format::F(), ObjexxFCL::fixed_Fstring_of(), ObjexxFCL::fixed_string_of(), ObjexxFCL::format::general(), basic::sampling::orientations::Quaternion::Print(), basic::sampling::orientations::QuatSet::Print(), ExposedStrandMover::print_sheets_extras(), basic::sampling::orientations::Quaternion::PrintEuler(), utility::Real2string(), and numeric::truncate_and_serialize_xyz_vector().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11().

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

Referenced by add_rosetta_options_11(), calc_rama_scores(), calculate_sasa(), find_close_motifs(), main(), read_input_weights(), and run().

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

Referenced by add_rosetta_options_11().