Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Namespaces | Functions
optE Namespace Reference

Namespaces

 rescore
 

Functions

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

Function Documentation

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