protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters Member List

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

actually_moving_res() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
add_virt_res_as_root() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
add_virt_res_as_root_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
calc_rms_res() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
calc_rms_res_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
chain_boundaries() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
chain_boundaries_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
const_full_to_sub() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
const_sub_to_full() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
create_sub_to_full_map(std::map< core::Size, core::Size > const &full_to_sub) const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
cutpoint_closed_list() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
cutpoint_closed_list_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
cutpoint_open_list() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
cutpoint_open_list_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
five_prime_chain_break_res() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
five_prime_chain_break_res_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
floating_base() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	inline
floating_base_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
floating_base_anchor_res() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	inline
floating_base_anchor_res_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
fold_tree() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
fold_tree_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
force_north_sugar_list() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
force_north_sugar_list_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
force_south_sugar_list() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
force_south_sugar_list_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
force_syn_chi_res_list() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
force_syn_chi_res_list_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
full_sequence() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
full_sequence_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
full_to_sub()	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
full_to_sub(Size const i) const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	inline
full_to_sub_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
gap_size() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
gap_size_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
gap_size_to_anchor() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
global_sample_res_list() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
global_sample_res_list_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
input_res_vectors() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
input_res_vectors_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
is_internal() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
is_internal_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
is_prepend() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
is_prepend_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
is_prepend_map() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
is_prepend_map_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
is_simple_full_length_job_params() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
is_simple_full_length_job_params_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
is_working_res() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
is_working_res_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
moving_res() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
moving_res_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
native_alignment() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
native_alignment_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
output_extra_RMSDs() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
output_extra_RMSDs_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
partition_definition() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
partition_definition_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
protonated_H1_adenosine_list() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
protonated_H1_adenosine_list_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
rebuild_bulge_mode() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	inline
rebuild_bulge_mode_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
sample_both_sugar_base_rotamer() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	inline
sample_both_sugar_base_rotamer_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
set_add_virt_res_as_root(bool const setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	inline
set_calc_rms_res(utility::vector1< core::Size > const &calc_rms_res)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_chain_boundaries(utility::vector1< std::pair< core::Size, core::Size > > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_cutpoint_closed_list(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_cutpoint_open_list(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_five_prime_chain_break_res(Size const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_floating_base(bool const setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	inline
set_floating_base_anchor_res(Size const setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	inline
set_fold_tree(core::kinematics::FoldTree const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_force_north_sugar_list(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_force_south_sugar_list(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_force_syn_chi_res_list(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_full_sequence(std::string const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_full_to_sub(std::map< core::Size, core::Size > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_gap_size(Size const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_global_sample_res_list(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_input_res_vectors(utility::vector1< utility::vector1< Size > > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_is_internal(bool const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_is_prepend(bool const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_is_prepend_map(std::map< core::Size, bool > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_is_simple_full_length_job_params(bool const setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_is_working_res(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_moving_res(Size const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_native_alignment(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_output_extra_RMSDs(bool const setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_partition_definition(ObjexxFCL::FArray1D< bool > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_partition_definition(utility::vector1< Size > const &partition_definition_vector)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_protonated_H1_adenosine_list(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_rebuild_bulge_mode(bool const setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	inline
set_sample_both_sugar_base_rotamer(bool const setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	inline
set_terminal_res(utility::vector1< core::Size > const &terminal_res)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_working_best_alignment(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_working_fixed_res(utility::vector1< core::Size > const &working_fixed_res)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_working_moving_partition_pos(utility::vector1< core::Size > const &working_moving_partition_pos)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_working_moving_res_list(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_working_native_alignment(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_working_native_pose(core::pose::PoseOP &pose)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_working_native_pose(core::pose::PoseCOP pose)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
set_working_terminal_res(utility::vector1< core::Size > const &working_terminal_res)	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
StepWiseRNA_JobParameters()	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
sub_to_full()	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
sub_to_full_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
terminal_res() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
terminal_res_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
update_working_moving_suite()	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
update_working_sequence()	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_best_alignment() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_best_alignment_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
working_fixed_res() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_fixed_res_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
working_floating_base_anchor_res() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_force_north_sugar_list() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_force_north_sugar_list_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
working_force_south_sugar_list() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_force_south_sugar_list_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
working_force_syn_chi_res_list() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_force_syn_chi_res_list_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
working_global_sample_res_list() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_global_sample_res_list_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
working_moving_partition_pos() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_moving_partition_pos_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
working_moving_res() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_moving_res_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
working_moving_res_list() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_moving_res_list_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
working_moving_suite() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_moving_suite_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
working_moving_suite_list() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_moving_suite_list_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
working_native_alignment() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_native_alignment_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
working_native_pose() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_native_pose_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
working_protonated_H1_adenosine_list() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_protonated_H1_adenosine_list_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
working_reference_res() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_res_list() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_sequence() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_sequence_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
working_terminal_res() const	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters
working_terminal_res_	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	private
~StepWiseRNA_JobParameters()	protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters	virtual