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protocols::optimize_weights::IterativeOptEDriver Member List

This is the complete list of members for protocols::optimize_weights::IterativeOptEDriver, including all inherited members.

aa_exp_protocols::optimize_weights::IterativeOptEDriverprivate
aa_freq_exp_protocols::optimize_weights::IterativeOptEDriverprivate
aa_freq_obs_protocols::optimize_weights::IterativeOptEDriverprivate
aa_obs_protocols::optimize_weights::IterativeOptEDriverprivate
add_structure_based_on_rms(SingleStructureDataOP ssd, PNatStructureOptEDataOP structure_data, bool intended_native) const protocols::optimize_weights::IterativeOptEDriverprivate
after_minimization_reference_energies_protocols::optimize_weights::IterativeOptEDriverprivate
all_pssm_data_protocols::optimize_weights::IterativeOptEDriverprivate
barrier()protocols::optimize_weights::IterativeOptEDriverprivate
before_minimization_reference_energies_protocols::optimize_weights::IterativeOptEDriverprivate
collect_ddG_of_binding_data()protocols::optimize_weights::IterativeOptEDriverprivate
collect_ddG_of_mutation_data()protocols::optimize_weights::IterativeOptEDriverprivate
collect_decoy_discrimination_data()protocols::optimize_weights::IterativeOptEDriverprivate
collect_dG_of_binding_data()protocols::optimize_weights::IterativeOptEDriverprivate
collect_ligand_discrimination_data()protocols::optimize_weights::IterativeOptEDriverprivate
collect_rotamer_energies()protocols::optimize_weights::IterativeOptEDriverprivate
collect_rotamer_energies_from_slave_cpu(core::Size const which_cpu)protocols::optimize_weights::IterativeOptEDriverprivate
collect_rotamer_energies_from_slave_cpus()protocols::optimize_weights::IterativeOptEDriverprivate
collect_rotamer_recovery_data_from_slave_cpu(core::Size const which_cpu)protocols::optimize_weights::IterativeOptEDriverprivate
collect_rotamer_recovery_data_from_slave_cpus()protocols::optimize_weights::IterativeOptEDriverprivate
collect_sequence_recovery_data_from_slave_cpu(core::Size const which_cpu)protocols::optimize_weights::IterativeOptEDriverprivate
collect_sequence_recovery_data_from_slave_cpus()protocols::optimize_weights::IterativeOptEDriverprivate
component_weights_protocols::optimize_weights::IterativeOptEDriverprivate
compute_rotamer_energies_for_assigned_pdbs()protocols::optimize_weights::IterativeOptEDriverprivate
compute_rotamers_around_ligands()protocols::optimize_weights::IterativeOptEDriverprivate
configure_new_scorefunction() const protocols::optimize_weights::IterativeOptEDriverprivate
context_poses_protocols::optimize_weights::IterativeOptEDriverprivate
converged(core::scoring::EnergyMap &free_parameters_prev, core::scoring::EnergyMap &free_parameters_curr, utility::vector1< Real > const &reference_energies_prev, utility::vector1< Real > const &reference_energies_curr)protocols::optimize_weights::IterativeOptEDriverprivate
copy_native_packertask_logic(core::pose::Pose native_pose, core::pose::Pose context_pose, core::pack::task::TaskFactoryOP native_taskfactory)protocols::optimize_weights::IterativeOptEDriverprivate
count_recovered_protocols::optimize_weights::IterativeOptEDriverprivate
count_rotamers_recovered_protocols::optimize_weights::IterativeOptEDriverprivate
create_unweighted_scorefunction() const protocols::optimize_weights::IterativeOptEDriverprivate
create_weighted_scorefunction() const protocols::optimize_weights::IterativeOptEDriverprivate
ddG_bind_files_protocols::optimize_weights::IterativeOptEDriverprivate
ddG_bind_optE_data_protocols::optimize_weights::IterativeOptEDriverprivate
ddg_mut_wt_pairs_protocols::optimize_weights::IterativeOptEDriverprivate
ddG_mutation_data_protocols::optimize_weights::IterativeOptEDriverprivate
ddGs_protocols::optimize_weights::IterativeOptEDriverprivate
ddGs_binding_protocols::optimize_weights::IterativeOptEDriverprivate
decdisc_crystal_natives_protocols::optimize_weights::IterativeOptEDriverprivate
decdisc_decoy_poses_protocols::optimize_weights::IterativeOptEDriverprivate
decdisc_native_decoy_pairs_protocols::optimize_weights::IterativeOptEDriverprivate
decdisc_native_poses_protocols::optimize_weights::IterativeOptEDriverprivate
decdisc_xtal_natives_protocols::optimize_weights::IterativeOptEDriverprivate
decide_if_sequence_recovery_improved()protocols::optimize_weights::IterativeOptEDriverprivate
decoy_discrim_data_protocols::optimize_weights::IterativeOptEDriverprivate
dG_binding_protocols::optimize_weights::IterativeOptEDriverprivate
dG_binding_data_protocols::optimize_weights::IterativeOptEDriverprivate
dG_bound_unbound_pairs_protocols::optimize_weights::IterativeOptEDriverprivate
divide_up_pdbs()protocols::optimize_weights::IterativeOptEDriverprivate
EnergyMap typedefprotocols::optimize_weights::IterativeOptEDriver
exit_gracefully()protocols::optimize_weights::IterativeOptEDriverprivate
fixed_count_protocols::optimize_weights::IterativeOptEDriverprivate
fixed_parameters_protocols::optimize_weights::IterativeOptEDriverprivate
fixed_score_list_protocols::optimize_weights::IterativeOptEDriverprivate
free_count_protocols::optimize_weights::IterativeOptEDriverprivate
free_parameters_protocols::optimize_weights::IterativeOptEDriverprivate
free_score_list_protocols::optimize_weights::IterativeOptEDriverprivate
free_terms_energy_map_from_dofs(core::optimization::Multivec const &dofs) const protocols::optimize_weights::IterativeOptEDriverprivate
free_weights_after_minimization_protocols::optimize_weights::IterativeOptEDriverprivate
free_weights_and_refEs_from_vars(utility::vector1< Real > const &vars, core::scoring::EnergyMap &weights, utility::vector1< Real > &reference_energies) const protocols::optimize_weights::IterativeOptEDriverprivate
free_weights_before_minimization_protocols::optimize_weights::IterativeOptEDriverprivate
free_weights_inner_loop_protocols::optimize_weights::IterativeOptEDriverprivate
get_nat_aa_opte_data(std::string const &pdb_name, core::pose::Pose &pose, core::pose::Pose &native_pose, core::scoring::ScoreFunction const &scorefxn, ScoreTypes &score_list, ScoreTypes &fixed_score_vec, OptEData &opte_data)protocols::optimize_weights::IterativeOptEDriverprivate
get_nat_rot_opte_data(std::string const &pdb_name, core::pose::Pose &pose, core::pose::Pose &native_pose, utility::vector1< bool > include_rsd, core::scoring::ScoreFunction const &scorefxn, ScoreTypes &score_list, ScoreTypes &fixed_score_vec, OptEData &opte_data)protocols::optimize_weights::IterativeOptEDriverprivate
get_native_pdb_names()protocols::optimize_weights::IterativeOptEDriverprivate
get_scorefile_name()protocols::optimize_weights::IterativeOptEDriverprivate
go()protocols::optimize_weights::IterativeOptEDriver
include_count_protocols::optimize_weights::IterativeOptEDriverprivate
include_terms_protocols::optimize_weights::IterativeOptEDriverprivate
initialize_free_and_fixed(core::scoring::EnergyMap &free_parameters, core::scoring::EnergyMap &fixed_parameters)protocols::optimize_weights::IterativeOptEDriverprivate
inner_loop_counter_protocols::optimize_weights::IterativeOptEDriverprivate
inner_loop_rotamer_recovery_rate_protocols::optimize_weights::IterativeOptEDriverprivate
inner_loop_sequence_recovery_rate_protocols::optimize_weights::IterativeOptEDriverprivate
intialize_free_and_fixed_energy_terms()protocols::optimize_weights::IterativeOptEDriverprivate
IterativeOptEDriver()protocols::optimize_weights::IterativeOptEDriver
ligand_crystal_natives_protocols::optimize_weights::IterativeOptEDriverprivate
ligand_discrim_data_protocols::optimize_weights::IterativeOptEDriverprivate
ligand_native_decoy_pairs_protocols::optimize_weights::IterativeOptEDriverprivate
ligand_repack_native_poses_protocols::optimize_weights::IterativeOptEDriverprivate
ligand_repack_pdbs_protocols::optimize_weights::IterativeOptEDriverprivate
load_pose(core::pose::Pose &pose, std::string const &filename, bool ignore_centroid_input_flag)protocols::optimize_weights::IterativeOptEDriverprivate
load_pssm_data(std::string const &native_filename, core::Size const which_protein)protocols::optimize_weights::IterativeOptEDriverprivate
make_simple_ssd_from_pdb(std::string const &pdb_filename, core::scoring::ScoreFunctionOP sfxn, bool pretend_no_fa_rep=false) const protocols::optimize_weights::IterativeOptEDriverprivate
measure_rotamer_recovery(utility::vector1< std::string > const &native_pdb_names, utility::vector1< std::string > const &names_for_output_pdbs, core::scoring::ScoreFunctionOP sfxn, core::Size &npos, core::Size &nrecovered)protocols::optimize_weights::IterativeOptEDriverprivate
measure_sequence_recovery(utility::vector1< std::string > const &native_pdb_names, utility::vector1< std::string > const &names_for_output_pdbs, core::scoring::ScoreFunctionOP sfxn, core::Size &npos, core::Size &nrecovered)protocols::optimize_weights::IterativeOptEDriverprivate
minimizer_dofs_after_minimization_protocols::optimize_weights::IterativeOptEDriverprivate
minimizer_dofs_before_minimization_protocols::optimize_weights::IterativeOptEDriverprivate
minimizer_dofs_mixed_protocols::optimize_weights::IterativeOptEDriverprivate
mixing_factor_protocols::optimize_weights::IterativeOptEDriverprivate
MPI_nprocs_protocols::optimize_weights::IterativeOptEDriverprivate
MPI_rank_protocols::optimize_weights::IterativeOptEDriverprivate
native_pdbs_protocols::optimize_weights::IterativeOptEDriverprivate
native_poses_protocols::optimize_weights::IterativeOptEDriverprivate
next_iteration_pdbs_protocols::optimize_weights::IterativeOptEDriverprivate
node_name(int rank)protocols::optimize_weights::IterativeOptEDriverprivate
num_inner_iterations() const protocols::optimize_weights::IterativeOptEDriverprivate
num_outer_iterations() const protocols::optimize_weights::IterativeOptEDriverprivate
optE_data_protocols::optimize_weights::IterativeOptEDriverprivate
opte_weight_mixing_factor(core::Size outer_loop_counter, core::Size inner_loop_counter)protocols::optimize_weights::IterativeOptEDriverprivate
optimize_weights()protocols::optimize_weights::IterativeOptEDriverprivate
outer_loop_counter_protocols::optimize_weights::IterativeOptEDriverprivate
outer_loop_last_sequence_recovery_rate_protocols::optimize_weights::IterativeOptEDriverprivate
outer_loop_seq_profile_cross_entropy_protocols::optimize_weights::IterativeOptEDriverprivate
output_weighted_unfolded_energies()protocols::optimize_weights::IterativeOptEDriverprivate
pdbs_this_round_protocols::optimize_weights::IterativeOptEDriverprivate
print_energies(core::pose::Pose &, core::scoring::ScoreFunctionOP, std::ostream &os=std::cout)protocols::optimize_weights::IterativeOptEDriverprivate
pssm_data_protocols::optimize_weights::IterativeOptEDriverprivate
read_reference_energies_from_file(std::string const &fname) const protocols::optimize_weights::IterativeOptEDriverprivate
read_tagfile_to_taskfactory(std::string tagfile_name, core::pack::task::TaskFactoryOP task_factory)protocols::optimize_weights::IterativeOptEDriverprivate
Real typedefprotocols::optimize_weights::IterativeOptEDriver
reference_energies_inner_loop_protocols::optimize_weights::IterativeOptEDriverprivate
repack_and_minimize_pose(core::pose::Pose &pose, core::scoring::ScoreFunctionOP sfxn) const protocols::optimize_weights::IterativeOptEDriverprivate
repack_assigned_pdbs()protocols::optimize_weights::IterativeOptEDriverprivate
residue_has_bad_bfactor(core::pose::Pose const &pose, core::Size const resid) const protocols::optimize_weights::IterativeOptEDriverprivate
residue_has_unacceptably_bad_dunbrack_energy(core::pose::Pose const &pose, core::Size const resid) const protocols::optimize_weights::IterativeOptEDriverprivate
rotamer_recovery_context_poses_protocols::optimize_weights::IterativeOptEDriverprivate
run_design_on_assigned_pdbs()protocols::optimize_weights::IterativeOptEDriverprivate
score_ligand_interface(core::scoring::ScoreFunction const &scorefxn, core::pose::Pose &pose)protocols::optimize_weights::IterativeOptEDriverprivate
score_position_data()protocols::optimize_weights::IterativeOptEDriverprivate
ScoreTypes typedefprotocols::optimize_weights::IterativeOptEDriver
send_rotamer_energies_to_master_cpu()protocols::optimize_weights::IterativeOptEDriverprivate
send_rotamer_recovery_data_to_master_cpu()protocols::optimize_weights::IterativeOptEDriverprivate
send_sequence_recovery_data_to_master_cpu()protocols::optimize_weights::IterativeOptEDriverprivate
set_aa_periodicity(PNatRotOptEPositionDataOP pos_data, core::chemical::AA aa) const protocols::optimize_weights::IterativeOptEDriverprivate
setup_derived_free_and_fixed_data()protocols::optimize_weights::IterativeOptEDriverprivate
setup_pdbnames_next_round(core::Size const outer_loop_counter, utility::vector1< std::string > &pdbs_next_round, utility::vector1< std::string > const &native_pdb_names)protocols::optimize_weights::IterativeOptEDriverprivate
single_structure_data_for_pose(core::scoring::ScoreFunctionOP scorefxn, core::pose::Pose &pose, core::pose::Pose const &crystal_native, utility::vector1< Real > &free_data, utility::vector1< Real > &fixed_data, std::string const &structure_tag="") const protocols::optimize_weights::IterativeOptEDriverprivate
Size typedefprotocols::optimize_weights::IterativeOptEDriver
task_factory(core::pack::task::TaskFactoryCOP)protocols::optimize_weights::IterativeOptEDriver
task_factory_protocols::optimize_weights::IterativeOptEDriverprivate
test_sequence_recovery()protocols::optimize_weights::IterativeOptEDriverprivate
test_weight_sensitivity(OptEMultifunc const &func, core::optimization::Multivec const &dofs) const protocols::optimize_weights::IterativeOptEDriverprivate
total_positions_protocols::optimize_weights::IterativeOptEDriverprivate
total_rotamer_positions_protocols::optimize_weights::IterativeOptEDriverprivate
using_unfolded_energy_term_protocols::optimize_weights::IterativeOptEDriverprivate
wrapped_opt_min_protocols::optimize_weights::IterativeOptEDriverprivate
write_new_scorefile()protocols::optimize_weights::IterativeOptEDriverprivate
write_parameters_to_std_out(core::scoring::EnergyMap &free_parameters, utility::vector1< Real > const &reference_energies)protocols::optimize_weights::IterativeOptEDriverprivate
zero_aa_counts()protocols::optimize_weights::IterativeOptEDriverprivate
~IterativeOptEDriver()protocols::optimize_weights::IterativeOptEDriver
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