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

#include <StepWiseWorkingParameters.hh>

Inheritance diagram for protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters:

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::Size >	working_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::Size >	apply_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::Size >	create_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::Size >	native_alignment_
utility::vector1< core::Size >	working_native_alignment_
utility::vector1< core::Size >	working_best_alignment_
utility::vector1< core::Size >	global_sample_res_list_
utility::vector1< core::Size >	working_global_sample_res_list_
utility::vector1< core::Size >	terminal_res_
utility::vector1< core::Size >	working_terminal_res_
utility::vector1< core::Size >	block_stack_above_res_
utility::vector1< core::Size >	working_block_stack_above_res_
utility::vector1< core::Size >	block_stack_below_res_
utility::vector1< core::Size >	working_block_stack_below_res_
utility::vector1< core::Size >	force_syn_chi_res_list_
utility::vector1< core::Size >	working_force_syn_chi_res_list_
utility::vector1< core::Size >	force_anti_chi_res_list_
utility::vector1< core::Size >	working_force_anti_chi_res_list_
utility::vector1< core::Size >	force_north_sugar_list_
utility::vector1< core::Size >	working_force_north_sugar_list_
utility::vector1< core::Size >	force_south_sugar_list_
utility::vector1< core::Size >	working_force_south_sugar_list_
utility::vector1< core::Size >	protonated_H1_adenosine_list_
utility::vector1< core::Size >	working_protonated_H1_adenosine_list_
core::kinematics::FoldTree	fold_tree_
utility::vector1 < utility::vector1< core::Size > >	input_res_vectors_
ObjexxFCL::FArray1D< core::Size >	is_moving_res_
utility::vector1< core::Size >	working_bridge_res_
utility::vector1< core::Size >	working_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::Size >	working_moving_res_list_
utility::vector1< core::Size >	working_moving_suite_list_
utility::vector1< core::Size >	is_working_res_
std::map< core::Size, core::Size >	full_to_sub_
std::map< core::Size, core::Size >	sub_to_full_
utility::vector1< core::Size >	cutpoint_closed_list_
utility::vector1< core::Size >	cutpoint_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::Size >	fixed_res_
utility::vector1< core::Size >	working_fixed_res_
utility::vector1< core::Size >	calc_rms_res_
utility::vector1< core::Size >	working_calc_rms_res_
utility::vector1< core::Size >	working_moving_partition_res_

Constructor & Destructor Documentation

protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::StepWiseWorkingParameters

(

)

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

overridedefault

Member Function Documentation

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

virtual

References protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_res_.

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

inline

References add_virt_res_as_root_.

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

inline

References block_stack_above_res_.

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

inline

References block_stack_below_res_.

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

inline

References five_prime_chain_break_res_.

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

inline

References floating_base_.

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

inline

References floating_base_anchor_res_.

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

(

)

const

References fold_tree_.

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

inline

References force_anti_chi_res_list_.

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

inline

References force_north_sugar_list_.

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

inline

References force_south_sugar_list_.

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

inline

References force_syn_chi_res_list_.

Size protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::gap_size_to_anchor

(

)

const

References protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::cutpoint_open_list_, GAP_SIZE_DUMMY, protocols::mean_field::max(), protocols::mean_field::min(), protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::moving_res_, protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::sub_to_full_, and working_reference_res().

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

inline

References global_sample_res_list_.

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

inline

References input_res_vectors_.

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

inline

References is_moving_res_.

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

(

)

const

References protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::full_sequence(), core::pose::rna::remove_bracketed(), protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::sequence(), and protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_res_list().

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

inline

References is_prepend_map_.

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

inline

References is_simple_full_length_job_params_.

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

inline

References native_alignment_.

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

inline

References output_extra_RMSDs_.

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

inline

References protonated_H1_adenosine_list_.

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

inline

References rebuild_bulge_mode_.

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

inline

References sample_both_sugar_base_rotamer_.

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

inline

References add_virt_res_as_root_.

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_block_stack_above_res

(

utility::vector1< core::Size > const &

block_stack_above_res

)

References protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::apply_full_to_sub_mapping(), block_stack_above_res_, and working_block_stack_above_res_.

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_block_stack_below_res

(

utility::vector1< core::Size > const &

block_stack_below_res

)

References protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::apply_full_to_sub_mapping(), block_stack_below_res_, and working_block_stack_below_res_.

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

inline

References five_prime_chain_break_res_.

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

inline

References floating_base_.

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

inline

References floating_base_anchor_res_.

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_fold_tree

(

core::kinematics::FoldTree const &

setting

)

References fold_tree_.

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_force_anti_chi_res_list

(

utility::vector1< core::Size > const &

setting

)

References protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::apply_full_to_sub_mapping(), force_anti_chi_res_list_, and working_force_anti_chi_res_list_.

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_force_north_sugar_list

(

utility::vector1< core::Size > const &

setting

)

References protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::apply_full_to_sub_mapping(), force_north_sugar_list_, force_south_sugar_list_, and working_force_north_sugar_list_.

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_force_south_sugar_list

(

utility::vector1< core::Size > const &

setting

)

References protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::apply_full_to_sub_mapping(), force_north_sugar_list_, force_south_sugar_list_, and working_force_south_sugar_list_.

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_force_syn_chi_res_list

(

utility::vector1< core::Size > const &

setting

)

References protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::apply_full_to_sub_mapping(), force_syn_chi_res_list_, and working_force_syn_chi_res_list_.

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_global_sample_res_list

(

utility::vector1< core::Size > const &

setting

)

References protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::apply_full_to_sub_mapping(), global_sample_res_list_, and working_global_sample_res_list_.

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

inline

References input_res_vectors_.

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

inline

References is_moving_res_.

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

inline

References is_prepend_map_.

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

inline

References is_simple_full_length_job_params_.

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

inline

References native_alignment_.

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

inline

References output_extra_RMSDs_.

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_protonated_H1_adenosine_list

(

utility::vector1< core::Size > const &

setting

)

References protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::apply_full_to_sub_mapping(), protonated_H1_adenosine_list_, and working_protonated_H1_adenosine_list_.

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

inline

References rebuild_bulge_mode_.

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

inline

References sample_both_sugar_base_rotamer_.

void protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_terminal_res

(

utility::vector1< core::Size > const &

terminal_res

)

References protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::apply_full_to_sub_mapping(), terminal_res_, and working_terminal_res_.

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

inline

References working_best_alignment_.

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

inline

References working_bridge_res_.

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

inline

References working_native_alignment_.

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

inline

References working_superimpose_res(), and working_superimpose_res_.

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

inline

References terminal_res_.

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

inline

References working_best_alignment_.

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

inline

References working_block_stack_above_res_.

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

inline

References working_block_stack_below_res_.

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

inline

References working_bridge_res_.

Size protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_floating_base_anchor_res

(

)

const

References floating_base_anchor_res_, protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::full_to_sub_, and protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::is_working_res_.

Referenced by working_reference_res().

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

inline

References working_force_anti_chi_res_list_.

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

inline

References working_force_north_sugar_list_.

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

inline

References working_force_south_sugar_list_.

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

inline

References working_force_syn_chi_res_list_.

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

inline

References working_global_sample_res_list_.

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

inline

References working_native_alignment_.

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

inline

References working_protonated_H1_adenosine_list_.

Size protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_reference_res

(

)

const

References floating_base_anchor_res_, protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::is_prepend_, working_floating_base_anchor_res(), protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_res_, and protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_res_list_.

Referenced by gap_size_to_anchor().

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

inline

References working_superimpose_res_.

Referenced by set_working_superimpose_res().

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

inline

References working_terminal_res_.

Member Data Documentation

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

private

Referenced by add_virt_res_as_root(), and set_add_virt_res_as_root().

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

private

Referenced by block_stack_above_res(), and set_block_stack_above_res().

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

private

Referenced by block_stack_below_res(), and set_block_stack_below_res().

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

private

Referenced by five_prime_chain_break_res(), and set_five_prime_chain_break_res().

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

private

Referenced by floating_base(), and set_floating_base().

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

private

Referenced by floating_base_anchor_res(), set_floating_base_anchor_res(), working_floating_base_anchor_res(), and working_reference_res().

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

private

Referenced by fold_tree(), and set_fold_tree().

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

private

Referenced by force_anti_chi_res_list(), and set_force_anti_chi_res_list().

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

private

Referenced by force_north_sugar_list(), set_force_north_sugar_list(), and set_force_south_sugar_list().

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

private

Referenced by force_south_sugar_list(), set_force_north_sugar_list(), and set_force_south_sugar_list().

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

private

Referenced by force_syn_chi_res_list(), and set_force_syn_chi_res_list().

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

private

Referenced by global_sample_res_list(), and set_global_sample_res_list().

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

private

Referenced by input_res_vectors(), and set_input_res_vectors().

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

private

Referenced by is_moving_res(), and set_is_moving_res().

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

private

Referenced by is_prepend_map(), and set_is_prepend_map().

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

private

Referenced by is_simple_full_length_job_params(), and set_is_simple_full_length_job_params().

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

private

Referenced by native_alignment(), and set_native_alignment().

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

private

Referenced by output_extra_RMSDs(), and set_output_extra_RMSDs().

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

private

Referenced by protonated_H1_adenosine_list(), and set_protonated_H1_adenosine_list().

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

private

Referenced by rebuild_bulge_mode(), and set_rebuild_bulge_mode().

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

private

Referenced by sample_both_sugar_base_rotamer(), and set_sample_both_sugar_base_rotamer().

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

private

Referenced by set_terminal_res(), and terminal_res().

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

private

Referenced by set_working_best_alignment(), and working_best_alignment().

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

private

Referenced by set_block_stack_above_res(), and working_block_stack_above_res().

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

private

Referenced by set_block_stack_below_res(), and working_block_stack_below_res().

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

private

Referenced by set_working_bridge_res(), and working_bridge_res().

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

private

Referenced by set_force_anti_chi_res_list(), and working_force_anti_chi_res_list().

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

private

Referenced by set_force_north_sugar_list(), and working_force_north_sugar_list().

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

private

Referenced by set_force_south_sugar_list(), and working_force_south_sugar_list().

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

private

Referenced by set_force_syn_chi_res_list(), and working_force_syn_chi_res_list().

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

private

Referenced by set_global_sample_res_list(), and working_global_sample_res_list().

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

private

Referenced by set_working_native_alignment(), and working_native_alignment().

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

private

Referenced by set_protonated_H1_adenosine_list(), and working_protonated_H1_adenosine_list().

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

private

Referenced by set_working_superimpose_res(), and working_superimpose_res().

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

private

Referenced by set_terminal_res(), and working_terminal_res().

---

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

• src/protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.hh
• src/protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.cc