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

approximate_decoy_entropy()

RealOptionKey const optE::approximate_decoy_entropy

(

"optE:approximate_decoy_entropy"

)

centroid_rot()

BooleanOptionKey const optE::centroid_rot

(

"optE:centroid_rot"

)

centroid_rot_min()

BooleanOptionKey const optE::centroid_rot_min

(

"optE:centroid_rot_min"

)

component_weights()

FileOptionKey const optE::component_weights

(

"optE:component_weights"

)

constant_logic_taskops_file()

FileOptionKey const optE::constant_logic_taskops_file

(

"optE:constant_logic_taskops_file"

)

constrain_weights()

FileOptionKey const optE::constrain_weights

(

"optE:constrain_weights"

)

data_in()

StringOptionKey const optE::data_in

(

"optE:data_in"

)

Referenced by simple_opte_test().

data_out()

StringOptionKey const optE::data_out

(

"optE:data_out"

)

Referenced by simple_opte_test().

design_first()

BooleanOptionKey const optE::design_first

(

"optE:design_first"

)

design_with_fast_design()

BooleanOptionKey const optE::design_with_fast_design

(

"optE:design_with_fast_design"

)

design_with_minpack()

BooleanOptionKey const optE::design_with_minpack

(

"optE:design_with_minpack"

)

design_with_offrotpack()

BooleanOptionKey const optE::design_with_offrotpack

(

"optE:design_with_offrotpack"

)

dont_use_reference_energies()

BooleanOptionKey const optE::dont_use_reference_energies

(

"optE:dont_use_reference_energies"

)

exclude_badrep_ddGs()

RealOptionKey const optE::exclude_badrep_ddGs

(

"optE:exclude_badrep_ddGs"

)

fit_reference_energies_to_aa_profile_recovery()

BooleanOptionKey const optE::fit_reference_energies_to_aa_profile_recovery

(

"optE:fit_reference_energies_to_aa_profile_recovery"

)

fix()

StringVectorOptionKey const optE::fix

(

"optE:fix"

)

Referenced by simple_opte_test().

fixed()

FileOptionKey const optE::fixed

(

"optE:fixed"

)

free()

FileOptionKey const optE::free

(

"optE:free"

)

include_intra_res_protein()

BooleanOptionKey const optE::include_intra_res_protein

(

"optE:include_intra_res_protein"

)

inv_kT_nataa()

RealOptionKey const optE::inv_kT_nataa

(

"optE:inv_kT_nataa"

)

inv_kT_natrot()

RealOptionKey const optE::inv_kT_natrot

(

"optE:inv_kT_natrot"

)

inv_kT_natstruct()

RealOptionKey const optE::inv_kT_natstruct

(

"optE:inv_kT_natstruct"

)

limit_bad_scores()

BooleanOptionKey const optE::limit_bad_scores

(

"optE:limit_bad_scores"

)

load_from_silent()

StringOptionKey const optE::load_from_silent

(

"optE:load_from_silent"

)

max_rms_from_native()

RealOptionKey const optE::max_rms_from_native

(

"optE:max_rms_from_native"

)

min_decoy_rms_to_native()

RealOptionKey const optE::min_decoy_rms_to_native

(

"optE:min_decoy_rms_to_native"

)

mpi_weight_minimization()

BooleanOptionKey const optE::mpi_weight_minimization

(

"optE:mpi_weight_minimization"

)

n_design_cycles()

IntegerOptionKey const optE::n_design_cycles

(

"optE:n_design_cycles"

)

n_top_natives_to_optimize()

IntegerOptionKey const optE::n_top_natives_to_optimize

(

"optE:n_top_natives_to_optimize"

)

no_design()

BooleanOptionKey const optE::no_design

(

"optE:no_design"

)

no_design_pdb_output()

BooleanOptionKey const optE::no_design_pdb_output

(

"optE:no_design_pdb_output"

)

no_hb_env_dependence()

BooleanOptionKey const optE::no_hb_env_dependence

(

"optE:no_hb_env_dependence"

)

no_hb_env_dependence_DNA()

BooleanOptionKey const optE::no_hb_env_dependence_DNA

(

"optE:no_hb_env_dependence_DNA"

)

normalize_decoy_score_spread()

StringOptionKey const optE::normalize_decoy_score_spread

(

"optE:normalize_decoy_score_spread"

)

number_of_swarm_cycles()

IntegerOptionKey const optE::number_of_swarm_cycles

(

"optE:number_of_swarm_cycles"

)

number_of_swarm_particles()

IntegerOptionKey const optE::number_of_swarm_particles

(

"optE:number_of_swarm_particles"

)

optE()

BooleanOptionKey const optE::optE

(

"optE"

)

optE_no_protein_fa_elec()

BooleanOptionKey const optE::optE_no_protein_fa_elec

(

"optE:optE_no_protein_fa_elec"

)

optE_soft_rep()

BooleanOptionKey const optE::optE_soft_rep

(

"optE:optE_soft_rep"

)

optimize_ddG_bind_correlation()

FileOptionKey const optE::optimize_ddG_bind_correlation

(

"optE:optimize_ddG_bind_correlation"

)

optimize_ddGmutation()

FileOptionKey const optE::optimize_ddGmutation

(

"optE:optimize_ddGmutation"

)

optimize_ddGmutation_boltzman_average()

BooleanOptionKey const optE::optimize_ddGmutation_boltzman_average

(

"optE:optimize_ddGmutation_boltzman_average"

)

optimize_ddGmutation_straight_mean()

BooleanOptionKey const optE::optimize_ddGmutation_straight_mean

(

"optE:optimize_ddGmutation_straight_mean"

)

optimize_decoy_discrimination()

FileOptionKey const optE::optimize_decoy_discrimination

(

"optE:optimize_decoy_discrimination"

)

optimize_dGbinding()

FileOptionKey const optE::optimize_dGbinding

(

"optE:optimize_dGbinding"

)

optimize_ligand_discrimination()

FileOptionKey const optE::optimize_ligand_discrimination

(

"optE:optimize_ligand_discrimination"

)

optimize_ligand_rot()

FileOptionKey const optE::optimize_ligand_rot

(

"optE:optimize_ligand_rot"

)

optimize_nat_aa()

BooleanOptionKey const optE::optimize_nat_aa

(

"optE:optimize_nat_aa"

)

optimize_nat_rot()

BooleanOptionKey const optE::optimize_nat_rot

(

"optE:optimize_nat_rot"

)

optimize_pssm()

BooleanOptionKey const optE::optimize_pssm

(

"optE:optimize_pssm"

)

optimize_starting_free_weights()

BooleanOptionKey const optE::optimize_starting_free_weights

(

"optE:optimize_starting_free_weights"

)

output_top_n_new_decoys()

IntegerOptionKey const optE::output_top_n_new_decoys

(

"optE:output_top_n_new_decoys"

)

parse_tagfile()

FileOptionKey const optE::parse_tagfile

(

"optE:parse_tagfile"

)

Referenced by fill_designable_set(), XMLprinterMover::setup_tf(), and setup_tf().

pretend_no_ddG_repulsion()

BooleanOptionKey const optE::pretend_no_ddG_repulsion

(

"optE:pretend_no_ddG_repulsion"

)

ramp_nativeness()

BooleanOptionKey const optE::ramp_nativeness

(

"optE:ramp_nativeness"

)

randomly_perturb_starting_free_weights()

RealOptionKey const optE::randomly_perturb_starting_free_weights

(

"optE:randomly_perturb_starting_free_weights"

)

recover_nat_rot()

BooleanOptionKey const optE::recover_nat_rot

(

"optE:recover_nat_rot"

)

repack_and_minimize_decoys()

BooleanOptionKey const optE::repack_and_minimize_decoys

(

"optE:repack_and_minimize_decoys"

)

repack_and_minimize_input_structures()

BooleanOptionKey const optE::repack_and_minimize_input_structures

(

"optE:repack_and_minimize_input_structures"

)

repeat_swarm_optimization_until_fitness_improves()

BooleanOptionKey const optE::repeat_swarm_optimization_until_fitness_improves

(

"optE:repeat_swarm_optimization_until_fitness_improves"

)

sqrt_pssm()

BooleanOptionKey const optE::sqrt_pssm

(

"optE:sqrt_pssm"

)

starting_refEs()

FileOptionKey const optE::starting_refEs

(

"optE:starting_refEs"

)

weights()

StringOptionKey const optE::weights

(

"optE:weights"

)

Referenced by simple_opte_test().

wrap_dof_optimization()

FileOptionKey const optE::wrap_dof_optimization

(

"optE:wrap_dof_optimization"

)