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protocols::swa::rna::StepWiseRNA_JobParameters Member List

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

actually_moving_res() const protocols::swa::rna::StepWiseRNA_JobParameters
add_virt_res_as_root() const protocols::swa::rna::StepWiseRNA_JobParameters
add_virt_res_as_root_protocols::swa::rna::StepWiseRNA_JobParametersprivate
chain_boundaries() const protocols::swa::rna::StepWiseRNA_JobParameters
chain_boundaries_protocols::swa::rna::StepWiseRNA_JobParametersprivate
const_full_to_sub() const protocols::swa::rna::StepWiseRNA_JobParameters
const_sub_to_full() const protocols::swa::rna::StepWiseRNA_JobParameters
create_sub_to_full_map(std::map< core::Size, core::Size > const &full_to_sub) const protocols::swa::rna::StepWiseRNA_JobParametersprivate
cutpoint_closed_list() const protocols::swa::rna::StepWiseRNA_JobParameters
cutpoint_closed_list_protocols::swa::rna::StepWiseRNA_JobParametersprivate
five_prime_chain_break_res() const protocols::swa::rna::StepWiseRNA_JobParameters
five_prime_chain_break_res_protocols::swa::rna::StepWiseRNA_JobParametersprivate
fold_tree() const protocols::swa::rna::StepWiseRNA_JobParameters
fold_tree_protocols::swa::rna::StepWiseRNA_JobParametersprivate
force_north_ribose_list() const protocols::swa::rna::StepWiseRNA_JobParameters
force_north_ribose_list_protocols::swa::rna::StepWiseRNA_JobParametersprivate
force_south_ribose_list() const protocols::swa::rna::StepWiseRNA_JobParameters
force_south_ribose_list_protocols::swa::rna::StepWiseRNA_JobParametersprivate
force_syn_chi_res_list() const protocols::swa::rna::StepWiseRNA_JobParameters
force_syn_chi_res_list_protocols::swa::rna::StepWiseRNA_JobParametersprivate
full_sequence() const protocols::swa::rna::StepWiseRNA_JobParameters
full_sequence_protocols::swa::rna::StepWiseRNA_JobParametersprivate
full_to_sub()protocols::swa::rna::StepWiseRNA_JobParameters
full_to_sub_protocols::swa::rna::StepWiseRNA_JobParametersprivate
gap_size() const protocols::swa::rna::StepWiseRNA_JobParameters
gap_size_protocols::swa::rna::StepWiseRNA_JobParametersprivate
global_sample_res_list() const protocols::swa::rna::StepWiseRNA_JobParameters
global_sample_res_list_protocols::swa::rna::StepWiseRNA_JobParametersprivate
input_res_vectors() const protocols::swa::rna::StepWiseRNA_JobParameters
input_res_vectors_protocols::swa::rna::StepWiseRNA_JobParametersprivate
Is_internal() const protocols::swa::rna::StepWiseRNA_JobParameters
Is_internal_protocols::swa::rna::StepWiseRNA_JobParametersprivate
Is_prepend() const protocols::swa::rna::StepWiseRNA_JobParameters
Is_prepend_protocols::swa::rna::StepWiseRNA_JobParametersprivate
Is_prepend_map() const protocols::swa::rna::StepWiseRNA_JobParameters
Is_prepend_map_protocols::swa::rna::StepWiseRNA_JobParametersprivate
Is_simple_full_length_job_params() const protocols::swa::rna::StepWiseRNA_JobParameters
Is_simple_full_length_job_params_protocols::swa::rna::StepWiseRNA_JobParametersprivate
is_working_res() const protocols::swa::rna::StepWiseRNA_JobParameters
is_working_res_protocols::swa::rna::StepWiseRNA_JobParametersprivate
moving_res() const protocols::swa::rna::StepWiseRNA_JobParameters
moving_res_protocols::swa::rna::StepWiseRNA_JobParametersprivate
native_alignment() const protocols::swa::rna::StepWiseRNA_JobParameters
native_alignment_protocols::swa::rna::StepWiseRNA_JobParametersprivate
output_extra_RMSDs() const protocols::swa::rna::StepWiseRNA_JobParameters
output_extra_RMSDs_protocols::swa::rna::StepWiseRNA_JobParametersprivate
partition_definition() const protocols::swa::rna::StepWiseRNA_JobParameters
partition_definition_protocols::swa::rna::StepWiseRNA_JobParametersprivate
protonated_H1_adenosine_list() const protocols::swa::rna::StepWiseRNA_JobParameters
protonated_H1_adenosine_list_protocols::swa::rna::StepWiseRNA_JobParametersprivate
rmsd_res_list() const protocols::swa::rna::StepWiseRNA_JobParameters
rmsd_res_list_protocols::swa::rna::StepWiseRNA_JobParametersprivate
set_add_virt_res_as_root(bool const setting)protocols::swa::rna::StepWiseRNA_JobParametersinline
set_chain_boundaries(utility::vector1< std::pair< core::Size, core::Size > > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_cutpoint_closed_list(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_five_prime_chain_break_res(Size const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_fold_tree(core::kinematics::FoldTree const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_force_north_ribose_list(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_force_south_ribose_list(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_force_syn_chi_res_list(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_full_sequence(std::string const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_full_to_sub(std::map< core::Size, core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_gap_size(Size const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_global_sample_res_list(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_input_res_vectors(utility::vector1< utility::vector1< Size > > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_Is_internal(bool const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_Is_prepend(bool const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_Is_prepend_map(std::map< core::Size, bool > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_Is_simple_full_length_job_params(bool const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_is_working_res(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_moving_res(Size const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_native_alignment(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_output_extra_RMSDs(bool const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_partition_definition(ObjexxFCL::FArray1D< bool > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_protonated_H1_adenosine_list(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_rmsd_res_list(utility::vector1< core::Size > const &rmsd_res_list)protocols::swa::rna::StepWiseRNA_JobParameters
set_working_best_alignment(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_working_fixed_res(utility::vector1< core::Size > const &working_fixed_res)protocols::swa::rna::StepWiseRNA_JobParameters
set_working_moving_partition_pos(utility::vector1< core::Size > const &working_moving_partition_pos)protocols::swa::rna::StepWiseRNA_JobParameters
set_working_moving_res_list(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_working_native_alignment(utility::vector1< core::Size > const &setting)protocols::swa::rna::StepWiseRNA_JobParameters
set_working_native_pose(core::pose::PoseOP &pose)protocols::swa::rna::StepWiseRNA_JobParameters
set_working_terminal_res(utility::vector1< core::Size > const &working_terminal_res)protocols::swa::rna::StepWiseRNA_JobParameters
StepWiseRNA_JobParameters()protocols::swa::rna::StepWiseRNA_JobParameters
sub_to_full()protocols::swa::rna::StepWiseRNA_JobParameters
sub_to_full_protocols::swa::rna::StepWiseRNA_JobParametersprivate
update_working_moving_suite()protocols::swa::rna::StepWiseRNA_JobParametersprivate
update_working_sequence()protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_best_alignment() const protocols::swa::rna::StepWiseRNA_JobParameters
working_best_alignment_protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_fixed_res() const protocols::swa::rna::StepWiseRNA_JobParameters
working_fixed_res_protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_force_north_ribose_list() const protocols::swa::rna::StepWiseRNA_JobParameters
working_force_north_ribose_list_protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_force_south_ribose_list() const protocols::swa::rna::StepWiseRNA_JobParameters
working_force_south_ribose_list_protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_force_syn_chi_res_list() const protocols::swa::rna::StepWiseRNA_JobParameters
working_force_syn_chi_res_list_protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_global_sample_res_list() const protocols::swa::rna::StepWiseRNA_JobParameters
working_global_sample_res_list_protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_moving_partition_pos() const protocols::swa::rna::StepWiseRNA_JobParameters
working_moving_partition_pos_protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_moving_res() const protocols::swa::rna::StepWiseRNA_JobParameters
working_moving_res_protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_moving_res_list() const protocols::swa::rna::StepWiseRNA_JobParameters
working_moving_res_list_protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_moving_suite() const protocols::swa::rna::StepWiseRNA_JobParameters
working_moving_suite_protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_moving_suite_list() const protocols::swa::rna::StepWiseRNA_JobParameters
working_moving_suite_list_protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_native_alignment() const protocols::swa::rna::StepWiseRNA_JobParameters
working_native_alignment_protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_native_pose() const protocols::swa::rna::StepWiseRNA_JobParameters
working_native_pose_protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_protonated_H1_adenosine_list() const protocols::swa::rna::StepWiseRNA_JobParameters
working_protonated_H1_adenosine_list_protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_reference_res() const protocols::swa::rna::StepWiseRNA_JobParameters
working_sequence() const protocols::swa::rna::StepWiseRNA_JobParameters
working_sequence_protocols::swa::rna::StepWiseRNA_JobParametersprivate
working_terminal_res() const protocols::swa::rna::StepWiseRNA_JobParameters
working_terminal_res_protocols::swa::rna::StepWiseRNA_JobParametersprivate
~StepWiseRNA_JobParameters()protocols::swa::rna::StepWiseRNA_JobParametersvirtual