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protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup Member List

This is the complete list of members for protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup, including all inherited members.

added_cutpoint_closed_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
alignment_res_string_list_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
allow_chain_boundary_jump_partner_right_at_fixed_BP_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
allow_fixed_res_at_moving_res_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
apply()protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupvirtual
assert_jump_point_in_fixed_res_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
check_moving_res_in_chain(core::Size const &start_chain, core::Size const &end_chain, core::Size const &num_chains, core::Size &which_chain_has_moving_res)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
cutpoint_open_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
cuts_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
figure_out_best_working_alignment()protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
figure_out_chain_boundaries()protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
figure_out_cuts()protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
figure_out_gap_size_and_five_prime_chain_break_res()protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
figure_out_is_prepend_map()protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
figure_out_is_residue_prepend(core::Size const seq_num) const protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
figure_out_jump_partners()protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
figure_out_partition_definition()protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
figure_out_prepend_internal(core::Size const root_res, stepwise::modeler::rna::InternalWorkingResidueParameter const &internal_params)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
figure_out_working_alignment(core::Size const &root_res)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
figure_out_working_moving_suite()protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
figure_out_working_sequence_and_mapping()protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
filter_user_alignment_res_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
fixed_res_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
force_fold_tree(core::kinematics::FoldTree const &fold_tree)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
force_fold_tree_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
force_internal_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
force_user_defined_jumps_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
get_previously_closed_cutpoint_from_imported_silent_file() const protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
get_user_input_alignment_res_list(core::Size const root_res)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
input_struct_definition(core::Size const working_seq_num)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
input_tags_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
is_cutpoint_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
jump_partners_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
jump_point_pair_list_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
moving_res_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
moving_res_list_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
reroot_fold_tree(core::Size const fake_working_moving_suite)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
reroot_fold_tree_simple()protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
set_add_virt_res_as_root(bool const setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_alignment_res(utility::vector1< std::string > const &setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupinline
set_allow_chain_boundary_jump_partner_right_at_fixed_BP(bool const setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupinline
set_allow_fixed_res_at_moving_res(bool const setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupinline
set_assert_jump_point_in_fixed_res(bool const setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupinline
set_calc_rms_res(utility::vector1< core::Size > const &setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_cutpoint_closed_list(utility::vector1< core::Size > const &setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_filter_user_alignment_res(bool const setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupinline
set_fixed_res(utility::vector1< core::Size > const &fixed_res)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_floating_base(bool const setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_floating_base_anchor_res(core::Size const setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_force_anti_chi_res_list(utility::vector1< core::Size > const &setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_force_internal(bool const setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupinline
set_force_north_sugar_list(utility::vector1< core::Size > const &setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_force_south_sugar_list(utility::vector1< core::Size > const &setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_force_syn_chi_res_list(utility::vector1< core::Size > const &setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_force_user_defined_jumps(bool const setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupinline
set_global_sample_res_list(utility::vector1< core::Size > const &setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_input_tags(utility::vector1< std::string > const &setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupinline
set_jump_point_pair_list(utility::vector1< std::string > const &jump_point_pairs_string)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_native_alignment_res(utility::vector1< core::Size > const &native_alignment)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_output_extra_RMSDs(bool const setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_protonated_H1_adenosine_list(utility::vector1< core::Size > const &setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_rebuild_bulge_mode(bool const setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_sample_both_sugar_base_rotamer(bool const setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
set_silent_files_in(utility::vector1< std::string > const &setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupinline
set_simple_append_map(bool const setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupinline
set_skip_complicated_stuff(bool const setting)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupinline
set_terminal_res(utility::vector1< core::Size > const &terminal_res)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
setup_additional_cutpoint_closed()protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
setup_floating_base_jump_to_anchor()protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
setup_fold_tree()protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
silent_files_in_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
simple_append_map_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
skip_complicated_stuff_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
StepWiseWorkingParametersSetup(utility::vector1< core::Size > const &moving_res_list, std::string const &full_sequence, utility::vector1< core::Size > const &input_res, utility::vector1< core::Size > const &input_res2, utility::vector1< core::Size > const &cutpoint_open, core::Size const cutpoint_closed)protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
working_parameters()protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
working_parameters_protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetupprivate
~StepWiseWorkingParametersSetup() overrideprotocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
Generated on Fri Apr 23 2021 03:46:54 for Rosetta by   doxygen 1.8.7