aa_exp_ | protocols::optimize_weights::IterativeOptEDriver | private |
aa_freq_exp_ | protocols::optimize_weights::IterativeOptEDriver | private |
aa_freq_obs_ | protocols::optimize_weights::IterativeOptEDriver | private |
aa_obs_ | protocols::optimize_weights::IterativeOptEDriver | private |
add_structure_based_on_rms(SingleStructureDataOP ssd, PNatStructureOptEDataOP structure_data, bool intended_native) const | protocols::optimize_weights::IterativeOptEDriver | private |
after_minimization_reference_energies_ | protocols::optimize_weights::IterativeOptEDriver | private |
all_pssm_data_ | protocols::optimize_weights::IterativeOptEDriver | private |
barrier() | protocols::optimize_weights::IterativeOptEDriver | private |
before_minimization_reference_energies_ | protocols::optimize_weights::IterativeOptEDriver | private |
collect_ddG_of_binding_data() | protocols::optimize_weights::IterativeOptEDriver | private |
collect_ddG_of_mutation_data() | protocols::optimize_weights::IterativeOptEDriver | private |
collect_decoy_discrimination_data() | protocols::optimize_weights::IterativeOptEDriver | private |
collect_dG_of_binding_data() | protocols::optimize_weights::IterativeOptEDriver | private |
collect_ligand_discrimination_data() | protocols::optimize_weights::IterativeOptEDriver | private |
collect_rotamer_energies() | protocols::optimize_weights::IterativeOptEDriver | private |
collect_rotamer_energies_from_slave_cpu(Size const which_cpu) | protocols::optimize_weights::IterativeOptEDriver | private |
collect_rotamer_energies_from_slave_cpus() | protocols::optimize_weights::IterativeOptEDriver | private |
collect_rotamer_recovery_data_from_slave_cpu(Size const which_cpu) | protocols::optimize_weights::IterativeOptEDriver | private |
collect_rotamer_recovery_data_from_slave_cpus() | protocols::optimize_weights::IterativeOptEDriver | private |
collect_sequence_recovery_data_from_slave_cpu(Size const which_cpu) | protocols::optimize_weights::IterativeOptEDriver | private |
collect_sequence_recovery_data_from_slave_cpus() | protocols::optimize_weights::IterativeOptEDriver | private |
component_weights_ | protocols::optimize_weights::IterativeOptEDriver | private |
compute_rotamer_energies_for_assigned_pdbs() | protocols::optimize_weights::IterativeOptEDriver | private |
compute_rotamers_around_ligands() | protocols::optimize_weights::IterativeOptEDriver | private |
configure_new_scorefunction() const | protocols::optimize_weights::IterativeOptEDriver | private |
context_poses_ | protocols::optimize_weights::IterativeOptEDriver | private |
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::IterativeOptEDriver | private |
copy_native_packertask_logic(core::pose::Pose native_pose, core::pose::Pose context_pose, core::pack::task::TaskFactoryOP native_taskfactory) | protocols::optimize_weights::IterativeOptEDriver | private |
count_recovered_ | protocols::optimize_weights::IterativeOptEDriver | private |
count_rotamers_recovered_ | protocols::optimize_weights::IterativeOptEDriver | private |
create_unweighted_scorefunction() const | protocols::optimize_weights::IterativeOptEDriver | private |
create_weighted_scorefunction() const | protocols::optimize_weights::IterativeOptEDriver | private |
ddG_bind_files_ | protocols::optimize_weights::IterativeOptEDriver | private |
ddG_bind_optE_data_ | protocols::optimize_weights::IterativeOptEDriver | private |
ddg_mut_wt_pairs_ | protocols::optimize_weights::IterativeOptEDriver | private |
ddG_mutation_data_ | protocols::optimize_weights::IterativeOptEDriver | private |
ddGs_ | protocols::optimize_weights::IterativeOptEDriver | private |
ddGs_binding_ | protocols::optimize_weights::IterativeOptEDriver | private |
decdisc_crystal_natives_ | protocols::optimize_weights::IterativeOptEDriver | private |
decdisc_decoy_poses_ | protocols::optimize_weights::IterativeOptEDriver | private |
decdisc_native_decoy_pairs_ | protocols::optimize_weights::IterativeOptEDriver | private |
decdisc_native_poses_ | protocols::optimize_weights::IterativeOptEDriver | private |
decdisc_xtal_natives_ | protocols::optimize_weights::IterativeOptEDriver | private |
decide_if_sequence_recovery_improved() | protocols::optimize_weights::IterativeOptEDriver | private |
decoy_discrim_data_ | protocols::optimize_weights::IterativeOptEDriver | private |
dG_binding_ | protocols::optimize_weights::IterativeOptEDriver | private |
dG_binding_data_ | protocols::optimize_weights::IterativeOptEDriver | private |
dG_bound_unbound_pairs_ | protocols::optimize_weights::IterativeOptEDriver | private |
divide_up_pdbs() | protocols::optimize_weights::IterativeOptEDriver | private |
EnergyMap typedef | protocols::optimize_weights::IterativeOptEDriver | |
exit_gracefully() | protocols::optimize_weights::IterativeOptEDriver | private |
fixed_count_ | protocols::optimize_weights::IterativeOptEDriver | private |
fixed_parameters_ | protocols::optimize_weights::IterativeOptEDriver | private |
fixed_score_list_ | protocols::optimize_weights::IterativeOptEDriver | private |
free_count_ | protocols::optimize_weights::IterativeOptEDriver | private |
free_parameters_ | protocols::optimize_weights::IterativeOptEDriver | private |
free_score_list_ | protocols::optimize_weights::IterativeOptEDriver | private |
free_terms_energy_map_from_dofs(core::optimization::Multivec const &dofs) const | protocols::optimize_weights::IterativeOptEDriver | private |
free_weights_after_minimization_ | protocols::optimize_weights::IterativeOptEDriver | private |
free_weights_and_refEs_from_vars(utility::vector1< Real > const &vars, core::scoring::EnergyMap &weights, utility::vector1< Real > &reference_energies) const | protocols::optimize_weights::IterativeOptEDriver | private |
free_weights_before_minimization_ | protocols::optimize_weights::IterativeOptEDriver | private |
free_weights_inner_loop_ | protocols::optimize_weights::IterativeOptEDriver | private |
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::IterativeOptEDriver | private |
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::IterativeOptEDriver | private |
get_native_pdb_names() | protocols::optimize_weights::IterativeOptEDriver | private |
get_scorefile_name() | protocols::optimize_weights::IterativeOptEDriver | private |
go() | protocols::optimize_weights::IterativeOptEDriver | |
include_count_ | protocols::optimize_weights::IterativeOptEDriver | private |
include_terms_ | protocols::optimize_weights::IterativeOptEDriver | private |
initialize_free_and_fixed(core::scoring::EnergyMap &free_parameters, core::scoring::EnergyMap &fixed_parameters) | protocols::optimize_weights::IterativeOptEDriver | private |
inner_loop_counter_ | protocols::optimize_weights::IterativeOptEDriver | private |
inner_loop_rotamer_recovery_rate_ | protocols::optimize_weights::IterativeOptEDriver | private |
inner_loop_sequence_recovery_rate_ | protocols::optimize_weights::IterativeOptEDriver | private |
intialize_free_and_fixed_energy_terms() | protocols::optimize_weights::IterativeOptEDriver | private |
IterativeOptEDriver() | protocols::optimize_weights::IterativeOptEDriver | |
ligand_crystal_natives_ | protocols::optimize_weights::IterativeOptEDriver | private |
ligand_discrim_data_ | protocols::optimize_weights::IterativeOptEDriver | private |
ligand_native_decoy_pairs_ | protocols::optimize_weights::IterativeOptEDriver | private |
ligand_repack_native_poses_ | protocols::optimize_weights::IterativeOptEDriver | private |
ligand_repack_pdbs_ | protocols::optimize_weights::IterativeOptEDriver | private |
load_pose(core::pose::Pose &pose, std::string const &filename, bool ignore_centroid_input_flag) | protocols::optimize_weights::IterativeOptEDriver | private |
load_pssm_data(std::string const &native_filename, Size const which_protein) | protocols::optimize_weights::IterativeOptEDriver | private |
make_simple_ssd_from_pdb(std::string const &pdb_filename, core::scoring::ScoreFunctionOP sfxn, bool pretend_no_fa_rep=false) const | protocols::optimize_weights::IterativeOptEDriver | private |
measure_rotamer_recovery(utility::vector1< std::string > const &native_pdb_names, utility::vector1< std::string > const &names_for_output_pdbs, core::scoring::ScoreFunctionOP sfxn, Size &npos, Size &nrecovered) | protocols::optimize_weights::IterativeOptEDriver | private |
measure_sequence_recovery(utility::vector1< std::string > const &native_pdb_names, utility::vector1< std::string > const &names_for_output_pdbs, core::scoring::ScoreFunctionOP sfxn, Size &npos, Size &nrecovered) | protocols::optimize_weights::IterativeOptEDriver | private |
minimizer_dofs_after_minimization_ | protocols::optimize_weights::IterativeOptEDriver | private |
minimizer_dofs_before_minimization_ | protocols::optimize_weights::IterativeOptEDriver | private |
minimizer_dofs_mixed_ | protocols::optimize_weights::IterativeOptEDriver | private |
mixing_factor_ | protocols::optimize_weights::IterativeOptEDriver | private |
MPI_nprocs_ | protocols::optimize_weights::IterativeOptEDriver | private |
MPI_rank_ | protocols::optimize_weights::IterativeOptEDriver | private |
native_pdbs_ | protocols::optimize_weights::IterativeOptEDriver | private |
native_poses_ | protocols::optimize_weights::IterativeOptEDriver | private |
next_iteration_pdbs_ | protocols::optimize_weights::IterativeOptEDriver | private |
node_name(int rank) | protocols::optimize_weights::IterativeOptEDriver | private |
num_inner_iterations() const | protocols::optimize_weights::IterativeOptEDriver | private |
num_outer_iterations() const | protocols::optimize_weights::IterativeOptEDriver | private |
optE_data_ | protocols::optimize_weights::IterativeOptEDriver | private |
opte_weight_mixing_factor(Size outer_loop_counter, Size inner_loop_counter) | protocols::optimize_weights::IterativeOptEDriver | private |
optimize_weights() | protocols::optimize_weights::IterativeOptEDriver | private |
outer_loop_counter_ | protocols::optimize_weights::IterativeOptEDriver | private |
outer_loop_last_sequence_recovery_rate_ | protocols::optimize_weights::IterativeOptEDriver | private |
outer_loop_seq_profile_cross_entropy_ | protocols::optimize_weights::IterativeOptEDriver | private |
output_weighted_unfolded_energies() | protocols::optimize_weights::IterativeOptEDriver | private |
pdbs_this_round_ | protocols::optimize_weights::IterativeOptEDriver | private |
print_energies(core::pose::Pose &, core::scoring::ScoreFunctionOP, std::ostream &os=std::cout) | protocols::optimize_weights::IterativeOptEDriver | private |
pssm_data_ | protocols::optimize_weights::IterativeOptEDriver | private |
read_reference_energies_from_file(std::string const &fname) const | protocols::optimize_weights::IterativeOptEDriver | private |
read_tagfile_to_taskfactory(std::string tagfile_name, core::pack::task::TaskFactoryOP task_factory) | protocols::optimize_weights::IterativeOptEDriver | private |
Real typedef | protocols::optimize_weights::IterativeOptEDriver | |
reference_energies_inner_loop_ | protocols::optimize_weights::IterativeOptEDriver | private |
repack_and_minimize_pose(core::pose::Pose &pose, core::scoring::ScoreFunctionOP sfxn) const | protocols::optimize_weights::IterativeOptEDriver | private |
repack_assigned_pdbs() | protocols::optimize_weights::IterativeOptEDriver | private |
residue_has_bad_bfactor(core::pose::Pose const &pose, Size const resid) const | protocols::optimize_weights::IterativeOptEDriver | private |
residue_has_unacceptably_bad_dunbrack_energy(core::pose::Pose const &pose, Size const resid) const | protocols::optimize_weights::IterativeOptEDriver | private |
rotamer_recovery_context_poses_ | protocols::optimize_weights::IterativeOptEDriver | private |
run_design_on_assigned_pdbs() | protocols::optimize_weights::IterativeOptEDriver | private |
score_ligand_interface(core::scoring::ScoreFunction const &scorefxn, core::pose::Pose &pose) | protocols::optimize_weights::IterativeOptEDriver | private |
score_position_data() | protocols::optimize_weights::IterativeOptEDriver | private |
ScoreTypes typedef | protocols::optimize_weights::IterativeOptEDriver | |
send_rotamer_energies_to_master_cpu() | protocols::optimize_weights::IterativeOptEDriver | private |
send_rotamer_recovery_data_to_master_cpu() | protocols::optimize_weights::IterativeOptEDriver | private |
send_sequence_recovery_data_to_master_cpu() | protocols::optimize_weights::IterativeOptEDriver | private |
set_aa_periodicity(PNatRotOptEPositionDataOP pos_data, core::chemical::AA aa) const | protocols::optimize_weights::IterativeOptEDriver | private |
setup_derived_free_and_fixed_data() | protocols::optimize_weights::IterativeOptEDriver | private |
setup_pdbnames_next_round(Size const outer_loop_counter, utility::vector1< std::string > &pdbs_next_round, utility::vector1< std::string > const &native_pdb_names) | protocols::optimize_weights::IterativeOptEDriver | private |
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::IterativeOptEDriver | private |
Size typedef | protocols::optimize_weights::IterativeOptEDriver | |
task_factory(core::pack::task::TaskFactoryCOP) | protocols::optimize_weights::IterativeOptEDriver | |
task_factory_ | protocols::optimize_weights::IterativeOptEDriver | private |
test_sequence_recovery() | protocols::optimize_weights::IterativeOptEDriver | private |
test_weight_sensitivity(OptEMultifunc const &func, core::optimization::Multivec const &dofs) const | protocols::optimize_weights::IterativeOptEDriver | private |
total_positions_ | protocols::optimize_weights::IterativeOptEDriver | private |
total_rotamer_positions_ | protocols::optimize_weights::IterativeOptEDriver | private |
using_unfolded_energy_term_ | protocols::optimize_weights::IterativeOptEDriver | private |
wrapped_opt_min_ | protocols::optimize_weights::IterativeOptEDriver | private |
write_new_scorefile() | protocols::optimize_weights::IterativeOptEDriver | private |
write_parameters_to_std_out(core::scoring::EnergyMap &free_parameters, utility::vector1< Real > const &reference_energies) | protocols::optimize_weights::IterativeOptEDriver | private |
zero_aa_counts() | protocols::optimize_weights::IterativeOptEDriver | private |
~IterativeOptEDriver() | protocols::optimize_weights::IterativeOptEDriver | |