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protocols::stepwise::modeler::options::StepWiseModelerOptions Member List

This is the complete list of members for protocols::stepwise::modeler::options::StepWiseModelerOptions, including all inherited members.

allow_base_pair_only_centroid_screen() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
allow_base_pair_only_centroid_screen_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
allow_bulge_at_chainbreak() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
allow_bulge_at_chainbreak_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
allow_rebuild_bulge_mode() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
allow_rebuild_bulge_mode_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
allow_syn_pyrimidine() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
allow_syn_pyrimidine_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
allow_virtual_o2prime_hydrogens() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
allow_virtual_o2prime_hydrogens_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
allow_virtual_side_chains() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
allow_virtual_side_chains_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
atr_rep_screen() constprotocols::stepwise::options::StepWiseBasicOptionsinline
atr_rep_screen_protocols::stepwise::options::StepWiseBasicOptionsprivate
atr_rep_screen_for_docking() constprotocols::stepwise::options::StepWiseBasicOptionsinline
atr_rep_screen_for_docking_protocols::stepwise::options::StepWiseBasicOptionsprivate
boltzmann_choice_post_enumerated_minimize() constprotocols::stepwise::options::StepWiseBasicOptionsinline
boltzmann_choice_post_enumerated_minimize_protocols::stepwise::options::StepWiseBasicOptionsprivate
bridge_res() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
bridge_res_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
cart_min() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
cart_min_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
ccd_close() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
ccd_close_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
centroid_output() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
centroid_output_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
centroid_score_diff_cut() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
centroid_score_diff_cut_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
centroid_screen() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
centroid_screen_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
centroid_weights() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
centroid_weights_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
choose_random() constprotocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
choose_random_protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsprotected
clone() constprotocols::stepwise::modeler::options::StepWiseModelerOptions
cluster_by_all_atom_rmsd() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
cluster_by_all_atom_rmsd_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
cluster_rmsd() constprotocols::stepwise::options::StepWiseBasicOptionsinline
cluster_rmsd_protocols::stepwise::options::StepWiseBasicOptionsprivate
combine_long_loop_mode() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
combine_long_loop_mode_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
coordinate_constraints_during_minimize() constprotocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
coordinate_constraints_during_minimize_protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsprotected
disable_sampling_of_loop_takeoff() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
disable_sampling_of_loop_takeoff_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
disallow_pack_polar_hydrogens() constprotocols::stepwise::options::StepWiseBasicOptionsinline
disallow_pack_polar_hydrogens_protocols::stepwise::options::StepWiseBasicOptionsprivate
disallow_realign() constprotocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
disallow_realign_protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsprotected
distinguish_pucker() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
distinguish_pucker_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
do_not_sample_multiple_virtual_sugar() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
do_not_sample_multiple_virtual_sugar_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
dump() constprotocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
dump_protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsprotected
expand_loop_takeoff() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
expand_loop_takeoff_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
extra_chi() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
extra_chi_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
filter_native_big_bins() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
filter_native_big_bins_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
finer_sampling_at_chain_closure() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
finer_sampling_at_chain_closure_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
force_centroid_interaction() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
force_centroid_interaction_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
force_phosphate_instantiation() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
force_phosphate_instantiation_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
frag_files() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
frag_files_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
get_sampler_options() constprotocols::stepwise::modeler::options::StepWiseModelerOptions
ghost_loops() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
ghost_loops_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
global_optimize() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
global_optimize_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
hydrate_magnesiums() constprotocols::stepwise::options::StepWiseBasicOptionsinline
hydrate_magnesiums_protocols::stepwise::options::StepWiseBasicOptionsprivate
initialize_from_command_line()protocols::stepwise::modeler::options::StepWiseModelerOptions
initialize_from_options_collection(utility::options::OptionCollection const &options)protocols::stepwise::options::StepWiseBasicOptionsprotected
initialize_variables()protocols::stepwise::modeler::options::StepWiseModelerOptionsprivate
integration_test_mode() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
integration_test_mode_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
kic_modeler_if_relevant() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
kic_modeler_if_relevant_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
list_options_read(utility::options::OptionKeyList &opt)protocols::stepwise::options::StepWiseBasicOptionsstatic
lores() constprotocols::stepwise::options::StepWiseBasicOptionsinline
lores_protocols::stepwise::options::StepWiseBasicOptionsprivate
mapfile_activated() constprotocols::stepwise::options::StepWiseBasicOptionsinline
mapfile_activated_protocols::stepwise::options::StepWiseBasicOptionsprivate
max_tries_multiplier_for_ccd() constprotocols::stepwise::options::StepWiseBasicOptionsinline
max_tries_multiplier_for_ccd_protocols::stepwise::options::StepWiseBasicOptionsprivate
min_tolerance() constprotocols::stepwise::options::StepWiseBasicOptionsinline
min_tolerance_protocols::stepwise::options::StepWiseBasicOptionsprivate
min_type() constprotocols::stepwise::options::StepWiseBasicOptionsinline
min_type_protocols::stepwise::options::StepWiseBasicOptionsprivate
minimize_and_score_native_pose() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
minimize_and_score_native_pose_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
minimize_and_score_sugar() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
minimize_and_score_sugar_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
minimize_waters() constprotocols::stepwise::options::StepWiseBasicOptionsinline
minimize_waters_protocols::stepwise::options::StepWiseBasicOptionsprivate
minimizer_mode() constprotocols::stepwise::options::StepWiseBasicOptionsinline
minimizer_mode_protocols::stepwise::options::StepWiseBasicOptionsprivate
minimizer_rename_tag() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
minimizer_rename_tag_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
move_jumps_between_chains() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
move_jumps_between_chains_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
n_cycles() constprotocols::stepwise::options::StepWiseBasicOptionsinline
n_cycles_protocols::stepwise::options::StepWiseBasicOptionsprivate
n_sample() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
n_sample_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
native_edensity_score_cutoff() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
native_edensity_score_cutoff_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
nstruct_centroid() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
nstruct_centroid_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
num_pose_minimize() constprotocols::stepwise::options::StepWiseBasicOptionsinline
num_pose_minimize_protocols::stepwise::options::StepWiseBasicOptionsprivate
num_random_samples() constprotocols::stepwise::options::StepWiseBasicOptionsinline
num_random_samples_protocols::stepwise::options::StepWiseBasicOptionsprivate
o2prime_legacy_mode() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
o2prime_legacy_mode_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
output_cluster_size() constprotocols::stepwise::options::StepWiseBasicOptionsinline
output_cluster_size_protocols::stepwise::options::StepWiseBasicOptionsprivate
output_minimized_pose_list() constprotocols::stepwise::options::StepWiseBasicOptionsinline
output_minimized_pose_list_protocols::stepwise::options::StepWiseBasicOptionsprivate
pack_protein_side_chains() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
pack_protein_side_chains_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
pack_weights() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
pack_weights_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
parin_favorite_output() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
parin_favorite_output_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
parse_my_tag(utility::tag::TagCOP) overrideprotocols::stepwise::modeler::options::StepWiseModelerOptionsinlinevirtual
PBP_clustering_at_chain_closure() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
PBP_clustering_at_chain_closure_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
prepack() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
prepack_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
reinitialize_CCD_torsions() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
reinitialize_CCD_torsions_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
rm_virt_phosphate() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
rm_virt_phosphate_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
rmsd_screen() constprotocols::stepwise::options::StepWiseBasicOptionsinline
rmsd_screen_protocols::stepwise::options::StepWiseBasicOptionsprivate
rna_legacy_output_mode() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
rna_legacy_output_mode_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
sample_all_chi() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
sample_all_chi_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
sample_beta() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
sample_beta_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
sample_ONLY_multiple_virtual_sugar() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
sample_ONLY_multiple_virtual_sugar_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
sample_pH() constprotocols::stepwise::options::StepWiseBasicOptionsinline
sample_pH_protocols::stepwise::options::StepWiseBasicOptionsprivate
sampler_assert_no_virt_sugar_sampling() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
sampler_assert_no_virt_sugar_sampling_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
sampler_extra_beta_rotamer() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
sampler_extra_beta_rotamer_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
sampler_extra_epsilon_rotamer() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
sampler_extra_epsilon_rotamer_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
sampler_include_torsion_value_in_tag() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
sampler_include_torsion_value_in_tag_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
sampler_max_centroid_distance() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
sampler_max_centroid_distance_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
sampler_num_pose_kept() constprotocols::stepwise::options::StepWiseBasicOptionsinline
sampler_num_pose_kept_protocols::stepwise::options::StepWiseBasicOptionsprivate
sampler_perform_phosphate_pack() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
sampler_perform_phosphate_pack_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
sampler_silent_file() constprotocols::stepwise::options::StepWiseBasicOptionsinline
sampler_silent_file_protocols::stepwise::options::StepWiseBasicOptionsprivate
sampler_try_sugar_instantiation() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
sampler_try_sugar_instantiation_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
set_allow_base_pair_only_centroid_screen(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_allow_bulge_at_chainbreak(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_allow_rebuild_bulge_mode(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_allow_syn_pyrimidine(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_allow_virtual_o2prime_hydrogens(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_allow_virtual_side_chains(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_atr_rep_screen(bool const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_atr_rep_screen_for_docking(bool const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_boltzmann_choice_post_enumerated_minimize(bool const setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_bridge_res(utility::vector1< core::Size > const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_cart_min(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_ccd_close(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_centroid_output(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_centroid_score_diff_cut(core::Real const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_centroid_screen(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_centroid_weights(std::string const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_choose_random(bool const &setting)protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
set_cluster_by_all_atom_rmsd(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_cluster_rmsd(core::Real const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_combine_long_loop_mode(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_coordinate_constraints_during_minimize(bool const setting)protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
set_disable_sampling_of_loop_takeoff(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_disallow_pack_polar_hydrogens(bool const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_disallow_realign(bool const setting)protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
set_distinguish_pucker(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_do_not_sample_multiple_virtual_sugar(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_dump(bool const &setting)protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
set_expand_loop_takeoff(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_extra_chi(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_filter_native_big_bins(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_finer_sampling_at_chain_closure(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_force_centroid_interaction(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_force_phosphate_instantiation(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_frag_files(utility::vector1< std::string > const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_ghost_loops(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_global_optimize(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_hydrate_magnesiums(bool const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_integration_test_mode(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_kic_modeler_if_relevant(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_lores(bool const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_mapfile_activated(bool const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_max_tries_multiplier_for_ccd(core::Size const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_min_tolerance(core::Real const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_min_type(std::string const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_minimize_and_score_native_pose(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_minimize_and_score_sugar(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_minimize_waters(bool const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_minimizer_mode(modeler::MinimizerMode const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_minimizer_rename_tag(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_move_jumps_between_chains(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_n_cycles(core::Size const setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_n_sample(core::Size const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_native_edensity_score_cutoff(core::Real const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_nstruct_centroid(core::Size const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_num_pose_minimize(core::Size const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_num_random_samples(core::Size const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_o2prime_legacy_mode(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_output_cluster_size(bool const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_output_minimized_pose_list(bool const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_pack_protein_side_chains(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_pack_weights(std::string const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_parin_favorite_output(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_PBP_clustering_at_chain_closure(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_prepack(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_reinitialize_CCD_torsions(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_rm_virt_phosphate(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_rmsd_screen(core::Real const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_rna_legacy_output_mode(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_sample_all_chi(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_sample_beta(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_sample_ONLY_multiple_virtual_sugar(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_sample_pH(bool const setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_sampler_assert_no_virt_sugar_sampling(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_sampler_extra_beta_rotamer(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_sampler_extra_epsilon_rotamer(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_sampler_include_torsion_value_in_tag(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_sampler_max_centroid_distance(core::Real const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_sampler_num_pose_kept(core::Size const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_sampler_perform_phosphate_pack(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_sampler_silent_file(std::string const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_sampler_try_sugar_instantiation(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_silent_file(std::string const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_skip_coord_constraints(bool const &setting)protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
set_skip_minimize(bool const &setting)protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
set_test_all_mg_hydration_frames(bool const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_tether_jump(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_thermal_sampler_output_min_pose(bool const setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_turn_off_rna_chem_map_during_optimize(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_use_green_packer(bool const &setting)protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
set_use_packer_instead_of_rotamer_trials(bool const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_use_phenix_geo(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_vary_polar_hydrogen_geometry(bool const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_vary_rna_bond_geometry(bool const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_VDW_rep_alignment_RMSD_CUTOFF(core::Real const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_VDW_rep_delete_matching_res(utility::vector1< std::string > const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_VDW_rep_screen_info(utility::vector1< std::string > const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_VDW_rep_screen_physical_pose_clash_dist_cutoff(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_verbose(bool const &setting)protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
set_verbose_sampler(bool const &setting)protocols::stepwise::options::StepWiseBasicOptionsinline
set_virtual_sugar_do_minimize(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_virtual_sugar_do_screens(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_virtual_sugar_keep_base_fixed(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_virtual_sugar_legacy_mode(bool const &setting)protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
set_virtualize_packable_moieties_in_screening_pose(bool const setting)protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
setup_options_for_VDW_bin_checker(rna::checker::RNA_VDW_BinCheckerOP user_input_VDW_bin_checker) constprotocols::stepwise::modeler::options::StepWiseModelerOptions
show(std::ostream &) const overrideprotocols::stepwise::modeler::options::StepWiseModelerOptionsinlinevirtual
silent_file() constprotocols::stepwise::options::StepWiseBasicOptionsinline
silent_file_protocols::stepwise::options::StepWiseBasicOptionsprivate
skip_coord_constraints() constprotocols::stepwise::modeler::options::StepWiseProteinModelerOptionsinline
skip_coord_constraints_protocols::stepwise::modeler::options::StepWiseProteinModelerOptionsprivate
skip_minimize() constprotocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
skip_minimize_protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsprotected
StepWiseBasicModelerOptions()protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
StepWiseBasicOptions()protocols::stepwise::options::StepWiseBasicOptions
StepWiseModelerOptions()protocols::stepwise::modeler::options::StepWiseModelerOptions
StepWiseProteinModelerOptions()protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
StepWiseRNA_ModelerOptions()protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
test_all_mg_hydration_frames() constprotocols::stepwise::options::StepWiseBasicOptionsinline
test_all_mg_hydration_frames_protocols::stepwise::options::StepWiseBasicOptionsprivate
tether_jump() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
tether_jump_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
thermal_sampler_output_min_pose() constprotocols::stepwise::options::StepWiseBasicOptionsinline
thermal_sampler_output_min_pose_protocols::stepwise::options::StepWiseBasicOptionsprivate
thermal_sampler_temperature() constprotocols::stepwise::options::StepWiseBasicOptionsinline
thermal_sampler_temperature_protocols::stepwise::options::StepWiseBasicOptionsprivate
turn_off_rna_chem_map_during_optimize() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
turn_off_rna_chem_map_during_optimize_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
type() const overrideprotocols::stepwise::modeler::options::StepWiseModelerOptionsinlinevirtual
use_green_packer() constprotocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
use_green_packer_protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsprotected
use_packer_instead_of_rotamer_trials() constprotocols::stepwise::options::StepWiseBasicOptionsinline
use_packer_instead_of_rotamer_trials_protocols::stepwise::options::StepWiseBasicOptionsprivate
use_phenix_geo() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
use_phenix_geo_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
vary_polar_hydrogen_geometry() constprotocols::stepwise::options::StepWiseBasicOptionsinline
vary_polar_hydrogen_geometry_protocols::stepwise::options::StepWiseBasicOptionsprivate
vary_rna_bond_geometry() constprotocols::stepwise::options::StepWiseBasicOptionsinline
vary_rna_bond_geometry_protocols::stepwise::options::StepWiseBasicOptionsprivate
VDW_rep_alignment_RMSD_CUTOFF() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
VDW_rep_alignment_RMSD_CUTOFF_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
VDW_rep_delete_matching_res() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
VDW_rep_delete_matching_res_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
VDW_rep_screen_info() constprotocols::stepwise::options::StepWiseBasicOptionsinline
VDW_rep_screen_info_protocols::stepwise::options::StepWiseBasicOptionsprivate
VDW_rep_screen_physical_pose_clash_dist_cutoff() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
VDW_rep_screen_physical_pose_clash_dist_cutoff_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
verbose() constprotocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
verbose_protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsprotected
verbose_sampler() constprotocols::stepwise::options::StepWiseBasicOptionsinline
verbose_sampler_protocols::stepwise::options::StepWiseBasicOptionsprivate
virtual_sugar_do_minimize() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
virtual_sugar_do_minimize_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
virtual_sugar_do_screens() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
virtual_sugar_do_screens_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
virtual_sugar_keep_base_fixed() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
virtual_sugar_keep_base_fixed_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
virtual_sugar_legacy_mode() constprotocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsinline
virtual_sugar_legacy_mode_protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptionsprivate
virtualize_packable_moieties_in_screening_pose() constprotocols::stepwise::modeler::options::StepWiseBasicModelerOptionsinline
virtualize_packable_moieties_in_screening_pose_protocols::stepwise::modeler::options::StepWiseBasicModelerOptionsprotected
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