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protocols::swa::rna::StepWiseRNA_JobParameters_Setup Member List

This is the complete list of members for protocols::swa::rna::StepWiseRNA_JobParameters_Setup, including all inherited members.

added_cutpoint_closed_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
alignment_res_string_list_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
allow_chain_boundary_jump_partner_right_at_fixed_BP_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
allow_fixed_res_at_moving_res_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
apply()protocols::swa::rna::StepWiseRNA_JobParameters_Setupvirtual
check_moving_res_in_chain(Size const &start_chain, Size const &end_chain, Size const &num_chains, Size &which_chain_has_moving_res)protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
cutpoint_open_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
cuts_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
figure_out_best_working_alignment()protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
figure_out_chain_boundaries()protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
figure_out_cuts()protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
figure_out_gap_size_and_five_prime_chain_break_res()protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
figure_out_Is_prepend_map()protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
figure_out_Is_residue_prepend(core::Size const seq_num) const protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
figure_out_jump_partners()protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
figure_out_partition_definition()protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
figure_out_Prepend_Internal(core::Size const root_res, InternalWorkingResidueParameter const &internal_params)protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
figure_out_working_moving_suite()protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
figure_out_working_sequence_and_mapping()protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
filter_user_alignment_res_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
fixed_res_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
get_previously_closed_cutpoint_from_imported_silent_file() const protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
get_user_input_alignment_res_list(core::Size const root_res)protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
input_struct_definition(core::Size const working_seq_num)protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
input_tags_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
is_cutpoint_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
job_parameters()protocols::swa::rna::StepWiseRNA_JobParameters_Setup
job_parameters_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
jump_partners_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
jump_point_pair_list_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
moving_res_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
moving_res_list_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
reroot_fold_tree(core::Size const fake_working_moving_suite)protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
reroot_fold_tree_simple()protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
set_add_virt_res_as_root(bool const setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setup
set_alignment_res(utility::vector1< std::string > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setupinline
set_allow_chain_boundary_jump_partner_right_at_fixed_BP(bool const setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setupinline
set_allow_fixed_res_at_moving_res(bool const setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setupinline
set_filter_user_alignment_res(bool const setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setupinline
set_fixed_res(utility::vector1< core::Size > const &fixed_res)protocols::swa::rna::StepWiseRNA_JobParameters_Setup
set_force_north_ribose_list(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setup
set_force_south_ribose_list(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setup
set_force_syn_chi_res_list(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setup
set_global_sample_res_list(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setup
set_input_tags(utility::vector1< std::string > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setupinline
set_jump_point_pair_list(utility::vector1< std::string > const &jump_point_pairs_string)protocols::swa::rna::StepWiseRNA_JobParameters_Setup
set_native_alignment_res(utility::vector1< Size > const &native_alignment)protocols::swa::rna::StepWiseRNA_JobParameters_Setup
set_output_extra_RMSDs(bool const setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setup
set_protonated_H1_adenosine_list(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setup
set_rmsd_res_list(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setup
set_silent_files_in(utility::vector1< std::string > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setupinline
set_simple_append_map(bool const setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setupinline
set_skip_complicated_stuff(bool const setting)protocols::swa::rna::StepWiseRNA_JobParameters_Setupinline
set_terminal_res(utility::vector1< core::Size > const &terminal_res)protocols::swa::rna::StepWiseRNA_JobParameters_Setup
setup_additional_cutpoint_closed()protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
setup_fold_tree()protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
silent_files_in_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
simple_append_map_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
skip_complicated_stuff_protocols::swa::rna::StepWiseRNA_JobParameters_Setupprivate
StepWiseRNA_JobParameters_Setup(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, Size const &cutpoint_closed)protocols::swa::rna::StepWiseRNA_JobParameters_Setup
~StepWiseRNA_JobParameters_Setup()protocols::swa::rna::StepWiseRNA_JobParameters_Setupvirtual
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