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protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters Class Reference

#include <StepWiseWorkingParameters.hh>

Inheritance diagram for protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters:
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Public Member Functions

 StepWiseWorkingParameters ()
 
 ~StepWiseWorkingParameters () override
 
bool const & output_extra_RMSDs () const
 
void set_output_extra_RMSDs (bool const setting)
 
bool const & is_simple_full_length_job_params () const
 
void set_is_simple_full_length_job_params (bool const setting)
 
core::Size gap_size_to_anchor () const
 
virtual core::Size actually_moving_res () const
 
core::Size working_reference_res () const
 
core::Size const & five_prime_chain_break_res () const
 
void set_five_prime_chain_break_res (core::Size const &setting)
 
bool const & add_virt_res_as_root () const
 
void set_add_virt_res_as_root (bool const setting)
 
bool const & floating_base () const
 
void set_floating_base (bool const setting)
 
core::Size const & floating_base_anchor_res () const
 
void set_floating_base_anchor_res (core::Size const setting)
 
core::Size working_floating_base_anchor_res () const
 
bool const & rebuild_bulge_mode () const
 
void set_rebuild_bulge_mode (bool const setting)
 
bool const & sample_both_sugar_base_rotamer () const
 
void set_sample_both_sugar_base_rotamer (bool const setting)
 
void set_is_prepend_map (std::map< core::Size, bool > const &setting)
 
std::map< core::Size, bool > const & is_prepend_map () const
 
utility::vector1< core::Size > const & native_alignment () const
 
void set_native_alignment (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Size > const & working_native_alignment () const
 
void set_working_native_alignment (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Size > const & working_best_alignment () const
 
void set_working_best_alignment (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Size > const & global_sample_res_list () const
 
void set_global_sample_res_list (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Size > const & working_global_sample_res_list () const
 
utility::vector1< core::Size > const & force_syn_chi_res_list () const
 
void set_force_syn_chi_res_list (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Size > const & working_force_syn_chi_res_list () const
 
utility::vector1< core::Size > const & force_anti_chi_res_list () const
 
void set_force_anti_chi_res_list (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Size > const & working_force_anti_chi_res_list () const
 
utility::vector1< core::Size > const & terminal_res () const
 
void set_terminal_res (utility::vector1< core::Size > const &terminal_res)
 
utility::vector1< core::Size > const & working_terminal_res () const
 
utility::vector1< core::Size > const & block_stack_above_res () const
 
void set_block_stack_above_res (utility::vector1< core::Size > const &block_stack_above_res)
 
utility::vector1< core::Size > const & working_block_stack_above_res () const
 
utility::vector1< core::Size > const & block_stack_below_res () const
 
void set_block_stack_below_res (utility::vector1< core::Size > const &block_stack_below_res)
 
utility::vector1< core::Size > const & working_block_stack_below_res () const
 
utility::vector1< core::Size > const & force_north_sugar_list () const
 
void set_force_north_sugar_list (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Size > const & working_force_north_sugar_list () const
 
utility::vector1< core::Size > const & force_south_sugar_list () const
 
void set_force_south_sugar_list (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Size > const & working_force_south_sugar_list () const
 
utility::vector1< core::Size > const & protonated_H1_adenosine_list () const
 
void set_protonated_H1_adenosine_list (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Size > const & working_protonated_H1_adenosine_list () const
 
core::kinematics::FoldTree const & fold_tree () const
 
void set_fold_tree (core::kinematics::FoldTree const &setting)
 
utility::vector1< utility::vector1< core::Size > > const & input_res_vectors () const
 
void set_input_res_vectors (utility::vector1< utility::vector1< core::Size > > const &setting)
 
utility::vector1< core::Size > const & working_bridge_res () const
 
void set_working_bridge_res (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Size > const & working_superimpose_res () const
 
void set_working_superimpose_res (utility::vector1< core::Size > const &working_superimpose_res)
 
ObjexxFCL::FArray1D< core::Size > const & is_moving_res () const
 
void set_is_moving_res (ObjexxFCL::FArray1D< core::Size > const &setting)
 
utility::vector1< bool > const is_pre_proline () const
 
- Public Member Functions inherited from protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
 StepWiseBasicWorkingParameters ()
 
 ~StepWiseBasicWorkingParameters () override
 
std::string const & sequence () const
 
void set_sequence (std::string const &setting)
 
std::string const & full_sequence () const
 
void set_full_sequence (std::string const &setting)
 
std::string const & working_sequence () const
 
core::Size const & moving_res () const
 
void set_moving_res (core::Size const &setting)
 
core::Size const & working_moving_res () const
 
core::Size const & working_moving_suite () const
 
core::Size actually_moving_res () const
 
utility::vector1< core::Sizeworking_res_list () const
 
utility::vector1< core::Size > const & working_moving_res_list () const
 
void set_working_moving_res_list (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Size > const & working_moving_suite_list () const
 
utility::vector1< core::Size > const & is_working_res () const
 
void set_is_working_res (utility::vector1< core::Size > const &setting)
 
std::map< core::Size, core::Size > & full_to_sub ()
 
void set_full_to_sub (std::map< core::Size, core::Size > const &setting)
 
std::map< core::Size, core::Size > & sub_to_full ()
 
std::map< core::Size, core::Size > const & const_full_to_sub () const
 
std::map< core::Size, core::Size > const & const_sub_to_full () const
 
core::Size full_to_sub (core::Size const i) const
 
core::Size sub_to_full (core::Size const i) const
 
utility::vector1< core::Sizeapply_full_to_sub_mapping (utility::vector1< core::Size > const &res_vector)
 
core::Size apply_full_to_sub_mapping (core::Size const res) const
 
std::map< core::Size, core::Sizecreate_sub_to_full_map (std::map< core::Size, core::Size > const &full_to_sub) const
 
utility::vector1< core::Size > const & cutpoint_closed_list () const
 
void set_cutpoint_closed_list (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Size > const & cutpoint_open_list () const
 
void set_cutpoint_open_list (utility::vector1< core::Size > const &setting)
 
utility::vector1< std::pair< core::Size, core::Size > > const & chain_boundaries () const
 
void set_chain_boundaries (utility::vector1< std::pair< core::Size, core::Size > > const &setting)
 
ObjexxFCL::FArray1D< bool > const & partition_definition () const
 
void set_partition_definition (ObjexxFCL::FArray1D< bool > const &setting)
 
void set_partition_definition (utility::vector1< core::Size > const &partition_definition_vector)
 
bool const & is_prepend () const
 
void set_is_prepend (bool const &setting)
 
bool const & is_internal () const
 
void set_is_internal (bool const &setting)
 
core::Size const & gap_size () const
 
void set_gap_size (core::Size const &setting)
 
utility::vector1< core::Size > const & fixed_res () const
 
void set_fixed_res (utility::vector1< core::Size > const &fixed_res)
 
utility::vector1< core::Size > const & working_fixed_res () const
 
void set_working_fixed_res (utility::vector1< core::Size > const &working_fixed_res)
 
utility::vector1< core::Size > const & calc_rms_res () const
 
void set_calc_rms_res (utility::vector1< core::Size > const &calc_rms_res)
 
utility::vector1< core::Size > const & working_calc_rms_res () const
 
void set_working_calc_rms_res (utility::vector1< core::Size > const &working_calc_rms_res)
 
utility::vector1< core::Size > const & working_moving_partition_res () const
 
void set_working_moving_partition_res (utility::vector1< core::Size > const &working_moving_partition_res)
 
core::pose::PoseCOP working_native_pose () const
 
void set_working_native_pose (core::pose::PoseOP &pose)
 
void set_working_native_pose (core::pose::PoseCOP pose)
 

Private Attributes

bool output_extra_RMSDs_
 
bool is_simple_full_length_job_params_
 
core::Size five_prime_chain_break_res_
 
std::map< core::Size, bool > is_prepend_map_
 
bool add_virt_res_as_root_
 
bool floating_base_
 
core::Size floating_base_anchor_res_
 
bool rebuild_bulge_mode_
 
bool sample_both_sugar_base_rotamer_
 
utility::vector1< core::Sizenative_alignment_
 
utility::vector1< core::Sizeworking_native_alignment_
 
utility::vector1< core::Sizeworking_best_alignment_
 
utility::vector1< core::Sizeglobal_sample_res_list_
 
utility::vector1< core::Sizeworking_global_sample_res_list_
 
utility::vector1< core::Sizeterminal_res_
 
utility::vector1< core::Sizeworking_terminal_res_
 
utility::vector1< core::Sizeblock_stack_above_res_
 
utility::vector1< core::Sizeworking_block_stack_above_res_
 
utility::vector1< core::Sizeblock_stack_below_res_
 
utility::vector1< core::Sizeworking_block_stack_below_res_
 
utility::vector1< core::Sizeforce_syn_chi_res_list_
 
utility::vector1< core::Sizeworking_force_syn_chi_res_list_
 
utility::vector1< core::Sizeforce_anti_chi_res_list_
 
utility::vector1< core::Sizeworking_force_anti_chi_res_list_
 
utility::vector1< core::Sizeforce_north_sugar_list_
 
utility::vector1< core::Sizeworking_force_north_sugar_list_
 
utility::vector1< core::Sizeforce_south_sugar_list_
 
utility::vector1< core::Sizeworking_force_south_sugar_list_
 
utility::vector1< core::Sizeprotonated_H1_adenosine_list_
 
utility::vector1< core::Sizeworking_protonated_H1_adenosine_list_
 
core::kinematics::FoldTree fold_tree_
 
utility::vector1< utility::vector1< core::Size > > input_res_vectors_
 
ObjexxFCL::FArray1D< core::Sizeis_moving_res_
 
utility::vector1< core::Sizeworking_bridge_res_
 
utility::vector1< core::Sizeworking_superimpose_res_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
std::string full_sequence_
 
std::string working_sequence_
 
core::Size moving_res_
 
core::Size working_moving_res_
 
core::Size working_moving_suite_
 
utility::vector1< core::Sizeworking_moving_res_list_
 
utility::vector1< core::Sizeworking_moving_suite_list_
 
utility::vector1< core::Sizeis_working_res_
 
std::map< core::Size, core::Sizefull_to_sub_
 
std::map< core::Size, core::Sizesub_to_full_
 
utility::vector1< core::Sizecutpoint_closed_list_
 
utility::vector1< core::Sizecutpoint_open_list_
 
utility::vector1< std::pair< core::Size, core::Size > > chain_boundaries_
 
ObjexxFCL::FArray1D< bool > partition_definition_
 
bool is_prepend_
 
bool is_internal_
 
core::Size gap_size_
 
core::pose::PoseCOP working_native_pose_
 
utility::vector1< core::Sizefixed_res_
 
utility::vector1< core::Sizeworking_fixed_res_
 
utility::vector1< core::Sizecalc_rms_res_
 
utility::vector1< core::Sizeworking_calc_rms_res_
 
utility::vector1< core::Sizeworking_moving_partition_res_
 

Constructor & Destructor Documentation

◆ StepWiseWorkingParameters()

protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::StepWiseWorkingParameters ( )

◆ ~StepWiseWorkingParameters()

protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::~StepWiseWorkingParameters ( )
overridedefault

Member Function Documentation

◆ actually_moving_res()

Size protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::actually_moving_res ( ) const
virtual

◆ add_virt_res_as_root()

bool const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::add_virt_res_as_root ( ) const
inline

References add_virt_res_as_root_.

◆ block_stack_above_res()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::block_stack_above_res ( ) const
inline

◆ block_stack_below_res()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::block_stack_below_res ( ) const
inline

◆ five_prime_chain_break_res()

core::Size const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::five_prime_chain_break_res ( ) const
inline

◆ floating_base()

bool const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::floating_base ( ) const
inline

References floating_base_.

◆ floating_base_anchor_res()

core::Size const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::floating_base_anchor_res ( ) const
inline

◆ fold_tree()

core::kinematics::FoldTree const & protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::fold_tree ( ) const

References fold_tree_.

◆ force_anti_chi_res_list()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::force_anti_chi_res_list ( ) const
inline

◆ force_north_sugar_list()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::force_north_sugar_list ( ) const
inline

◆ force_south_sugar_list()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::force_south_sugar_list ( ) const
inline

◆ force_syn_chi_res_list()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::force_syn_chi_res_list ( ) const
inline

◆ gap_size_to_anchor()

Size protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::gap_size_to_anchor ( ) const

◆ global_sample_res_list()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::global_sample_res_list ( ) const
inline

◆ input_res_vectors()

utility::vector1< utility::vector1< core::Size > > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::input_res_vectors ( ) const
inline

References input_res_vectors_.

◆ is_moving_res()

ObjexxFCL::FArray1D< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::is_moving_res ( ) const
inline

References is_moving_res_.

◆ is_pre_proline()

utility::vector1< bool > const protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::is_pre_proline ( ) const

◆ is_prepend_map()

std::map< core::Size, bool > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::is_prepend_map ( ) const
inline

References is_prepend_map_.

◆ is_simple_full_length_job_params()

bool const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::is_simple_full_length_job_params ( ) const
inline

◆ native_alignment()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::native_alignment ( ) const
inline

References native_alignment_.

◆ output_extra_RMSDs()

bool const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::output_extra_RMSDs ( ) const
inline

References output_extra_RMSDs_.

◆ protonated_H1_adenosine_list()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::protonated_H1_adenosine_list ( ) const
inline

◆ rebuild_bulge_mode()

bool const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::rebuild_bulge_mode ( ) const
inline

References rebuild_bulge_mode_.

◆ sample_both_sugar_base_rotamer()

bool const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::sample_both_sugar_base_rotamer ( ) const
inline

◆ set_add_virt_res_as_root()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_add_virt_res_as_root ( bool const  setting)
inline

References add_virt_res_as_root_.

◆ set_block_stack_above_res()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_block_stack_above_res ( utility::vector1< core::Size > const &  block_stack_above_res)

◆ set_block_stack_below_res()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_block_stack_below_res ( utility::vector1< core::Size > const &  block_stack_below_res)

◆ set_five_prime_chain_break_res()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_five_prime_chain_break_res ( core::Size const &  setting)
inline

◆ set_floating_base()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_floating_base ( bool const  setting)
inline

References floating_base_.

◆ set_floating_base_anchor_res()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_floating_base_anchor_res ( core::Size const  setting)
inline

◆ set_fold_tree()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_fold_tree ( core::kinematics::FoldTree const &  setting)

References fold_tree_.

◆ set_force_anti_chi_res_list()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_force_anti_chi_res_list ( utility::vector1< core::Size > const &  setting)

◆ set_force_north_sugar_list()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_force_north_sugar_list ( utility::vector1< core::Size > const &  setting)

◆ set_force_south_sugar_list()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_force_south_sugar_list ( utility::vector1< core::Size > const &  setting)

◆ set_force_syn_chi_res_list()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_force_syn_chi_res_list ( utility::vector1< core::Size > const &  setting)

◆ set_global_sample_res_list()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_global_sample_res_list ( utility::vector1< core::Size > const &  setting)

◆ set_input_res_vectors()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_input_res_vectors ( utility::vector1< utility::vector1< core::Size > > const &  setting)
inline

References input_res_vectors_.

◆ set_is_moving_res()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_is_moving_res ( ObjexxFCL::FArray1D< core::Size > const &  setting)
inline

References is_moving_res_.

◆ set_is_prepend_map()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_is_prepend_map ( std::map< core::Size, bool > const &  setting)
inline

References is_prepend_map_.

◆ set_is_simple_full_length_job_params()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_is_simple_full_length_job_params ( bool const  setting)
inline

◆ set_native_alignment()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_native_alignment ( utility::vector1< core::Size > const &  setting)
inline

References native_alignment_.

◆ set_output_extra_RMSDs()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_output_extra_RMSDs ( bool const  setting)
inline

References output_extra_RMSDs_.

◆ set_protonated_H1_adenosine_list()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_protonated_H1_adenosine_list ( utility::vector1< core::Size > const &  setting)

◆ set_rebuild_bulge_mode()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_rebuild_bulge_mode ( bool const  setting)
inline

References rebuild_bulge_mode_.

◆ set_sample_both_sugar_base_rotamer()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_sample_both_sugar_base_rotamer ( bool const  setting)
inline

◆ set_terminal_res()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_terminal_res ( utility::vector1< core::Size > const &  terminal_res)

◆ set_working_best_alignment()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_working_best_alignment ( utility::vector1< core::Size > const &  setting)
inline

◆ set_working_bridge_res()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_working_bridge_res ( utility::vector1< core::Size > const &  setting)
inline

References working_bridge_res_.

◆ set_working_native_alignment()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_working_native_alignment ( utility::vector1< core::Size > const &  setting)
inline

◆ set_working_superimpose_res()

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_working_superimpose_res ( utility::vector1< core::Size > const &  working_superimpose_res)
inline

◆ terminal_res()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::terminal_res ( ) const
inline

References terminal_res_.

◆ working_best_alignment()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_best_alignment ( ) const
inline

◆ working_block_stack_above_res()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_block_stack_above_res ( ) const
inline

◆ working_block_stack_below_res()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_block_stack_below_res ( ) const
inline

◆ working_bridge_res()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_bridge_res ( ) const
inline

References working_bridge_res_.

◆ working_floating_base_anchor_res()

Size protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_floating_base_anchor_res ( ) const

◆ working_force_anti_chi_res_list()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_force_anti_chi_res_list ( ) const
inline

◆ working_force_north_sugar_list()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_force_north_sugar_list ( ) const
inline

◆ working_force_south_sugar_list()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_force_south_sugar_list ( ) const
inline

◆ working_force_syn_chi_res_list()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_force_syn_chi_res_list ( ) const
inline

◆ working_global_sample_res_list()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_global_sample_res_list ( ) const
inline

◆ working_native_alignment()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_native_alignment ( ) const
inline

◆ working_protonated_H1_adenosine_list()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_protonated_H1_adenosine_list ( ) const
inline

◆ working_reference_res()

Size protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_reference_res ( ) const

◆ working_superimpose_res()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_superimpose_res ( ) const
inline

◆ working_terminal_res()

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_terminal_res ( ) const
inline

References working_terminal_res_.

Member Data Documentation

◆ add_virt_res_as_root_

bool protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::add_virt_res_as_root_
private

◆ block_stack_above_res_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::block_stack_above_res_
private

◆ block_stack_below_res_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::block_stack_below_res_
private

◆ five_prime_chain_break_res_

core::Size protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::five_prime_chain_break_res_
private

◆ floating_base_

bool protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::floating_base_
private

Referenced by floating_base(), and set_floating_base().

◆ floating_base_anchor_res_

core::Size protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::floating_base_anchor_res_
private

◆ fold_tree_

core::kinematics::FoldTree protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::fold_tree_
private

Referenced by fold_tree(), and set_fold_tree().

◆ force_anti_chi_res_list_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::force_anti_chi_res_list_
private

◆ force_north_sugar_list_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::force_north_sugar_list_
private

◆ force_south_sugar_list_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::force_south_sugar_list_
private

◆ force_syn_chi_res_list_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::force_syn_chi_res_list_
private

◆ global_sample_res_list_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::global_sample_res_list_
private

◆ input_res_vectors_

utility::vector1< utility::vector1< core::Size > > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::input_res_vectors_
private

◆ is_moving_res_

ObjexxFCL::FArray1D< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::is_moving_res_
private

Referenced by is_moving_res(), and set_is_moving_res().

◆ is_prepend_map_

std::map< core::Size, bool > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::is_prepend_map_
private

◆ is_simple_full_length_job_params_

bool protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::is_simple_full_length_job_params_
private

◆ native_alignment_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::native_alignment_
private

◆ output_extra_RMSDs_

bool protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::output_extra_RMSDs_
private

◆ protonated_H1_adenosine_list_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::protonated_H1_adenosine_list_
private

◆ rebuild_bulge_mode_

bool protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::rebuild_bulge_mode_
private

◆ sample_both_sugar_base_rotamer_

bool protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::sample_both_sugar_base_rotamer_
private

◆ terminal_res_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::terminal_res_
private

Referenced by set_terminal_res(), and terminal_res().

◆ working_best_alignment_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_best_alignment_
private

◆ working_block_stack_above_res_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_block_stack_above_res_
private

◆ working_block_stack_below_res_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_block_stack_below_res_
private

◆ working_bridge_res_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_bridge_res_
private

◆ working_force_anti_chi_res_list_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_force_anti_chi_res_list_
private

◆ working_force_north_sugar_list_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_force_north_sugar_list_
private

◆ working_force_south_sugar_list_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_force_south_sugar_list_
private

◆ working_force_syn_chi_res_list_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_force_syn_chi_res_list_
private

◆ working_global_sample_res_list_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_global_sample_res_list_
private

◆ working_native_alignment_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_native_alignment_
private

◆ working_protonated_H1_adenosine_list_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_protonated_H1_adenosine_list_
private

◆ working_superimpose_res_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_superimpose_res_
private

◆ working_terminal_res_

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_terminal_res_
private

The documentation for this class was generated from the following files: