protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters Class Reference

#include <StepWiseRNA_JobParameters.hh>

Public Member Functions
	StepWiseRNA_JobParameters ()
virtual	~StepWiseRNA_JobParameters ()
bool const &	output_extra_RMSDs () const
bool const &	is_simple_full_length_job_params () const
std::string const &	full_sequence () const
std::string const &	working_sequence () const
Size const &	moving_res () const
Size const &	working_moving_res () const
utility::vector1< core::Size > const &	working_moving_res_list () const
utility::vector1< core::Size >	working_res_list () const
Size	working_reference_res () const
Size	gap_size_to_anchor () const
Size const &	working_moving_suite () const
utility::vector1< core::Size > const &	working_moving_suite_list () const
Size	actually_moving_res () const
utility::vector1< core::Size > const &	is_working_res () const
std::map< core::Size, core::Size > &	full_to_sub ()
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::kinematics::FoldTree const &	fold_tree () const
std::map< core::Size, bool > const &	is_prepend_map () const
core::Size	full_to_sub (Size const i) const
utility::vector1< std::pair < core::Size, core::Size > > const &	chain_boundaries () const
Size const &	gap_size () const
Size const &	five_prime_chain_break_res () const
bool const &	is_prepend () const
bool const &	is_internal () const
bool const &	add_virt_res_as_root () const
bool const &	floating_base () const
Size const &	floating_base_anchor_res () const
Size	working_floating_base_anchor_res () const
bool const &	rebuild_bulge_mode () const
bool const &	sample_both_sugar_base_rotamer () const
ObjexxFCL::FArray1D< bool > const &	partition_definition () const
utility::vector1< core::Size > const &	working_fixed_res () const
utility::vector1< core::Size > const &	calc_rms_res () const
utility::vector1< core::Size > const &	terminal_res () const
utility::vector1< core::Size > const &	working_terminal_res () const
utility::vector1< core::Size > const &	working_moving_partition_pos () const
utility::vector1 < utility::vector1< core::Size > > const &	input_res_vectors () const
utility::vector1< core::Size > const &	cutpoint_closed_list () const
utility::vector1< core::Size > const &	cutpoint_open_list () const
utility::vector1< core::Size > const &	working_best_alignment () const
utility::vector1< core::Size > const &	native_alignment () const
utility::vector1< core::Size > const &	working_native_alignment () const
utility::vector1< core::Size > const &	global_sample_res_list () const
utility::vector1< core::Size > const &	working_global_sample_res_list () const
utility::vector1< core::Size > const &	force_syn_chi_res_list () const
utility::vector1< core::Size > const &	working_force_syn_chi_res_list () const
utility::vector1< core::Size > const &	force_north_sugar_list () const
utility::vector1< core::Size > const &	working_force_north_sugar_list () const
utility::vector1< core::Size > const &	force_south_sugar_list () const
utility::vector1< core::Size > const &	working_force_south_sugar_list () const
utility::vector1< core::Size > const &	protonated_H1_adenosine_list () const
utility::vector1< core::Size > const &	working_protonated_H1_adenosine_list () const
void	set_output_extra_RMSDs (bool const setting)
void	set_is_simple_full_length_job_params (bool const setting)
void	set_full_sequence (std::string const &setting)
void	set_moving_res (Size const &setting)
void	set_working_moving_res_list (utility::vector1< core::Size > const &setting)
void	set_is_working_res (utility::vector1< core::Size > const &setting)
void	set_full_to_sub (std::map< core::Size, core::Size > const &setting)
void	set_fold_tree (core::kinematics::FoldTree const &setting)
void	set_is_prepend_map (std::map< core::Size, bool > const &setting)
void	set_chain_boundaries (utility::vector1< std::pair< core::Size, core::Size > > const &setting)
void	set_gap_size (Size const &setting)
void	set_five_prime_chain_break_res (Size const &setting)
void	set_is_prepend (bool const &setting)
void	set_is_internal (bool const &setting)
void	set_partition_definition (ObjexxFCL::FArray1D< bool > const &setting)
void	set_partition_definition (utility::vector1< Size > const &partition_definition_vector)
void	set_working_native_pose (core::pose::PoseOP &pose)
void	set_working_native_pose (core::pose::PoseCOP pose)
void	set_working_fixed_res (utility::vector1< core::Size > const &working_fixed_res)
void	set_calc_rms_res (utility::vector1< core::Size > const &calc_rms_res)
void	set_terminal_res (utility::vector1< core::Size > const &terminal_res)
void	set_working_terminal_res (utility::vector1< core::Size > const &working_terminal_res)
void	set_working_moving_partition_pos (utility::vector1< core::Size > const &working_moving_partition_pos)
void	set_input_res_vectors (utility::vector1< utility::vector1< Size > > const &setting)
void	set_cutpoint_closed_list (utility::vector1< core::Size > const &setting)
void	set_cutpoint_open_list (utility::vector1< core::Size > const &setting)
void	set_working_best_alignment (utility::vector1< core::Size > const &setting)
void	set_native_alignment (utility::vector1< core::Size > const &setting)
void	set_working_native_alignment (utility::vector1< core::Size > const &setting)
void	set_global_sample_res_list (utility::vector1< core::Size > const &setting)
void	set_force_syn_chi_res_list (utility::vector1< core::Size > const &setting)
void	set_force_north_sugar_list (utility::vector1< core::Size > const &setting)
void	set_force_south_sugar_list (utility::vector1< core::Size > const &setting)
void	set_protonated_H1_adenosine_list (utility::vector1< core::Size > const &setting)
void	set_add_virt_res_as_root (bool const setting)
void	set_floating_base (bool const setting)
void	set_floating_base_anchor_res (Size const setting)
void	set_rebuild_bulge_mode (bool const setting)
void	set_sample_both_sugar_base_rotamer (bool const setting)
core::pose::PoseCOP	working_native_pose () const
void	update_working_moving_suite ()
void	update_working_sequence ()
std::map< core::Size, core::Size >	create_sub_to_full_map (std::map< core::Size, core::Size > const &full_to_sub) const

Private Attributes
bool	output_extra_RMSDs_
bool	is_simple_full_length_job_params_
std::string	full_sequence_
std::string	working_sequence_
Size	moving_res_
utility::vector1< core::Size >	working_moving_res_list_
utility::vector1< core::Size >	working_moving_suite_list_
Size	working_moving_res_
Size	working_moving_suite_
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_
std::map< core::Size, bool >	is_prepend_map_
utility::vector1< std::pair < core::Size, core::Size > >	chain_boundaries_
Size	gap_size_
Size	five_prime_chain_break_res_
bool	is_prepend_
bool	is_internal_
bool	add_virt_res_as_root_
bool	floating_base_
Size	floating_base_anchor_res_
bool	rebuild_bulge_mode_
bool	sample_both_sugar_base_rotamer_
ObjexxFCL::FArray1D< bool >	partition_definition_
core::pose::PoseCOP	working_native_pose_
utility::vector1< core::Size >	working_fixed_res_
utility::vector1< core::Size >	calc_rms_res_
utility::vector1< core::Size >	terminal_res_
utility::vector1< core::Size >	working_terminal_res_
utility::vector1< core::Size >	working_moving_partition_pos_
core::kinematics::FoldTree	fold_tree_
utility::vector1 < utility::vector1< core::Size > >	input_res_vectors_
utility::vector1< core::Size >	cutpoint_closed_list_
utility::vector1< core::Size >	cutpoint_open_list_
utility::vector1< core::Size >	working_best_alignment_
utility::vector1< core::Size >	native_alignment_
utility::vector1< core::Size >	working_native_alignment_
utility::vector1< core::Size >	global_sample_res_list_
utility::vector1< core::Size >	working_global_sample_res_list_
utility::vector1< core::Size >	force_syn_chi_res_list_
utility::vector1< core::Size >	working_force_syn_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_

Constructor & Destructor Documentation

protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::StepWiseRNA_JobParameters

(

)

References calc_rms_res_, chain_boundaries_, core::kinematics::FoldTree::clear(), cutpoint_closed_list_, fold_tree_, force_north_sugar_list_, force_south_sugar_list_, force_syn_chi_res_list_, full_to_sub_, global_sample_res_list_, input_res_vectors_, is_prepend_map_, is_working_res_, native_alignment_, partition_definition_, protonated_H1_adenosine_list_, sub_to_full_, working_best_alignment_, working_fixed_res_, working_force_north_sugar_list_, working_force_south_sugar_list_, working_force_syn_chi_res_list_, working_global_sample_res_list_, working_moving_partition_pos_, working_moving_res_list_, working_moving_suite_list_, working_native_alignment_, working_protonated_H1_adenosine_list_, and working_terminal_res_.

protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::~StepWiseRNA_JobParameters ( )

virtual

Member Function Documentation

Size protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::actually_moving_res

(

)

const

References working_moving_res_.

bool const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::add_virt_res_as_root

(

)

const

References add_virt_res_as_root_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::calc_rms_res

(

)

const

References calc_rms_res_, and utility_exit_with_message.

Referenced by set_calc_rms_res().

utility::vector1< std::pair< core::Size, core::Size > > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::chain_boundaries

(

)

const

References chain_boundaries_.

std::map< core::Size, core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::const_full_to_sub

(

)

const

References full_to_sub_, and utility_exit_with_message.

std::map< core::Size, core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::const_sub_to_full

(

)

const

References sub_to_full_, and utility_exit_with_message.

std::map< core::Size, core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::create_sub_to_full_map

(

std::map< core::Size, core::Size > const &

full_to_sub

)

const

References sub_to_full().

Referenced by set_full_to_sub().

utility::vector1< Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::cutpoint_closed_list

(

)

const

References cutpoint_closed_list_.

utility::vector1< Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::cutpoint_open_list

(

)

const

References cutpoint_open_list_.

Size const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::five_prime_chain_break_res

(

)

const

References five_prime_chain_break_res_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::floating_base ( ) const

inline

References floating_base_.

Size const& protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::floating_base_anchor_res ( ) const

inline

References floating_base_anchor_res_.

core::kinematics::FoldTree const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::fold_tree

(

)

const

References fold_tree_, core::kinematics::FoldTree::size(), and utility_exit_with_message.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::force_north_sugar_list

(

)

const

References force_north_sugar_list_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::force_south_sugar_list

(

)

const

References force_south_sugar_list_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::force_syn_chi_res_list

(

)

const

References force_syn_chi_res_list_.

std::string const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::full_sequence

(

)

const

References full_sequence_, and utility_exit_with_message.

std::map< core::Size, core::Size > & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::full_to_sub

(

)

References full_to_sub_, and utility_exit_with_message.

core::Size protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::full_to_sub ( Size const  i ) const

inline

References full_to_sub_.

Size const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::gap_size

(

)

const

References gap_size_.

Size protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::gap_size_to_anchor

(

)

const

References cutpoint_open_list_, GAP_SIZE_DUMMY, utility::vector1< T, class >::has_value(), moving_res_, runtime_assert, sub_to_full_, and working_reference_res().

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::global_sample_res_list

(

)

const

References global_sample_res_list_.

utility::vector1< utility::vector1< Size > > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::input_res_vectors

(

)

const

References input_res_vectors_, and utility_exit_with_message.

bool const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::is_internal

(

)

const

References is_internal_.

bool const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::is_prepend

(

)

const

References is_prepend_.

std::map< core::Size, bool > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::is_prepend_map

(

)

const

References is_prepend_map_, and utility_exit_with_message.

bool const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::is_simple_full_length_job_params

(

)

const

References is_simple_full_length_job_params_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::is_working_res

(

)

const

References is_working_res_, and utility_exit_with_message.

Size const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::moving_res

(

)

const

References moving_res_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::native_alignment

(

)

const

References native_alignment_.

bool const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::output_extra_RMSDs

(

)

const

References output_extra_RMSDs_.

ObjexxFCL::FArray1D< bool > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::partition_definition

(

)

const

References partition_definition_, and utility_exit_with_message.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::protonated_H1_adenosine_list

(

)

const

References protonated_H1_adenosine_list_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::rebuild_bulge_mode ( ) const

inline

References rebuild_bulge_mode_.

bool const& protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::sample_both_sugar_base_rotamer ( ) const

inline

References sample_both_sugar_base_rotamer_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_add_virt_res_as_root ( bool const  setting )

inline

References add_virt_res_as_root_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_calc_rms_res

(

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

calc_rms_res

)

References calc_rms_res(), calc_rms_res_, and protocols::stepwise::sampling::rna::sort_seq_num_list().

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_chain_boundaries

(

utility::vector1< std::pair< core::Size, core::Size > > const &

setting

)

References chain_boundaries_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_cutpoint_closed_list

(

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

setting

)

References cutpoint_closed_list_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_cutpoint_open_list

(

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

setting

)

References cutpoint_open_list_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_five_prime_chain_break_res

(

Size const &

setting

)

References five_prime_chain_break_res_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_floating_base ( bool const  setting )

inline

References floating_base_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_floating_base_anchor_res ( Size const  setting )

inline

References floating_base_anchor_res_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_fold_tree

(

core::kinematics::FoldTree const &

setting

)

References fold_tree_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_force_north_sugar_list

(

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

setting

)

References protocols::stepwise::sampling::rna::apply_full_to_sub_mapping(), force_north_sugar_list_, force_south_sugar_list_, full_to_sub_, utility::vector1< T, class >::has_value(), is_working_res_, utility_exit_with_message, and working_force_north_sugar_list_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_force_south_sugar_list

(

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

setting

)

References protocols::stepwise::sampling::rna::apply_full_to_sub_mapping(), force_north_sugar_list_, force_south_sugar_list_, full_to_sub_, utility::vector1< T, class >::has_value(), is_working_res_, utility_exit_with_message, and working_force_south_sugar_list_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_force_syn_chi_res_list

(

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

setting

)

References protocols::stepwise::sampling::rna::apply_full_to_sub_mapping(), force_syn_chi_res_list_, full_to_sub_, is_working_res_, and working_force_syn_chi_res_list_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_full_sequence

(

std::string const &

setting

)

References full_sequence_, protocols::TR, update_working_sequence(), and working_sequence_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_full_to_sub

(

std::map< core::Size, core::Size > const &

setting

)

References create_sub_to_full_map(), full_to_sub_, and sub_to_full_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_gap_size

(

Size const &

setting

)

References gap_size_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_global_sample_res_list

(

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

setting

)

References protocols::stepwise::sampling::rna::apply_full_to_sub_mapping(), full_to_sub_, global_sample_res_list_, is_working_res_, and working_global_sample_res_list_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_input_res_vectors

(

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

setting

)

References input_res_vectors_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_is_internal

(

bool const &

setting

)

References is_internal_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_is_prepend

(

bool const &

setting

)

References is_prepend_, and update_working_moving_suite().

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_is_prepend_map

(

std::map< core::Size, bool > const &

setting

)

References is_prepend_map_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_is_simple_full_length_job_params

(

bool const

setting

)

References is_simple_full_length_job_params_.

Referenced by protocols::stepwise::sampling::rna::legacy::setup_simple_full_length_rna_job_parameters().

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_is_working_res

(

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

setting

)

References is_working_res_, and update_working_sequence().

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_moving_res

(

Size const &

setting

)

References moving_res_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_native_alignment

(

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

setting

)

References native_alignment_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_output_extra_RMSDs

(

bool const

setting

)

References output_extra_RMSDs_.

Referenced by protocols::stepwise::sampling::rna::setup_job_parameters_explicit().

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_partition_definition

(

ObjexxFCL::FArray1D< bool > const &

setting

)

References partition_definition_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_partition_definition

(

utility::vector1< Size > const &

partition_definition_vector

)

References partition_definition_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_protonated_H1_adenosine_list

(

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

setting

)

References protocols::stepwise::sampling::rna::apply_full_to_sub_mapping(), full_to_sub_, is_working_res_, protonated_H1_adenosine_list_, and working_protonated_H1_adenosine_list_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_rebuild_bulge_mode ( bool const  setting )

inline

References rebuild_bulge_mode_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_sample_both_sugar_base_rotamer ( bool const  setting )

inline

References sample_both_sugar_base_rotamer_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_terminal_res

(

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

terminal_res

)

References terminal_res(), and terminal_res_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_working_best_alignment

(

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

setting

)

References working_best_alignment_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_working_fixed_res

(

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

working_fixed_res

)

References working_fixed_res(), and working_fixed_res_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_working_moving_partition_pos

(

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

working_moving_partition_pos

)

References working_moving_partition_pos(), and working_moving_partition_pos_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_working_moving_res_list

(

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

setting

)

References update_working_moving_suite(), working_moving_res_, and working_moving_res_list_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_working_native_alignment

(

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

setting

)

References working_native_alignment_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_working_native_pose

(

core::pose::PoseOP &

pose

)

References working_native_pose_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_working_native_pose

(

core::pose::PoseCOP

pose

)

References working_native_pose_.

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_working_terminal_res

(

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

working_terminal_res

)

References working_terminal_res(), and working_terminal_res_.

std::map< core::Size, core::Size > & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::sub_to_full

(

)

References sub_to_full_, and utility_exit_with_message.

Referenced by create_sub_to_full_map().

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::terminal_res

(

)

const

References terminal_res_.

Referenced by set_terminal_res().

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::update_working_moving_suite

(

)

References is_prepend_, runtime_assert, utility_exit_with_message, working_moving_res_, working_moving_res_list_, working_moving_suite_, and working_moving_suite_list_.

Referenced by set_is_prepend(), and set_working_moving_res_list().

void protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::update_working_sequence

(

)

References full_sequence_, is_working_res_, and working_sequence_.

Referenced by set_full_sequence(), and set_is_working_res().

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_best_alignment

(

)

const

References utility_exit_with_message, and working_best_alignment_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_fixed_res

(

)

const

References working_fixed_res_.

Referenced by set_working_fixed_res().

Size protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_floating_base_anchor_res

(

)

const

References floating_base_anchor_res_, full_to_sub_, and is_working_res_.

Referenced by working_reference_res().

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_force_north_sugar_list

(

)

const

References working_force_north_sugar_list_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_force_south_sugar_list

(

)

const

References working_force_south_sugar_list_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_force_syn_chi_res_list

(

)

const

References working_force_syn_chi_res_list_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_global_sample_res_list

(

)

const

References working_global_sample_res_list_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_moving_partition_pos

(

)

const

References working_moving_partition_pos_.

Referenced by set_working_moving_partition_pos().

Size const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_moving_res

(

)

const

References working_moving_res_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_moving_res_list

(

)

const

References utility_exit_with_message, and working_moving_res_list_.

Size const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_moving_suite

(

)

const

References working_moving_suite_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_moving_suite_list

(

)

const

References utility_exit_with_message, and working_moving_suite_list_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_native_alignment

(

)

const

References working_native_alignment_.

core::pose::PoseCOP protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_native_pose

(

)

const

References working_native_pose_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_protonated_H1_adenosine_list

(

)

const

References working_protonated_H1_adenosine_list_.

Size protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_reference_res

(

)

const

References floating_base_anchor_res_, is_prepend_, runtime_assert, working_floating_base_anchor_res(), working_moving_res_, and working_moving_res_list_.

Referenced by gap_size_to_anchor().

utility::vector1< Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_res_list

(

)

const

References sub_to_full_, and utility_exit_with_message.

std::string const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_sequence

(

)

const

References utility_exit_with_message, and working_sequence_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_terminal_res

(

)

const

References working_terminal_res_.

Referenced by set_working_terminal_res().

Member Data Documentation

bool protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::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::sampling::rna::StepWiseRNA_JobParameters::calc_rms_res_

private

Referenced by calc_rms_res(), set_calc_rms_res(), and StepWiseRNA_JobParameters().

utility::vector1< std::pair < core::Size, core::Size > > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::chain_boundaries_

private

Referenced by chain_boundaries(), set_chain_boundaries(), and StepWiseRNA_JobParameters().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::cutpoint_closed_list_

private

Referenced by cutpoint_closed_list(), set_cutpoint_closed_list(), and StepWiseRNA_JobParameters().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::cutpoint_open_list_

private

Referenced by cutpoint_open_list(), gap_size_to_anchor(), and set_cutpoint_open_list().

Size protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::five_prime_chain_break_res_

private

Referenced by five_prime_chain_break_res(), and set_five_prime_chain_break_res().

bool protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::floating_base_

private

Referenced by floating_base(), and set_floating_base().

Size protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::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::sampling::rna::StepWiseRNA_JobParameters::fold_tree_

private

Referenced by fold_tree(), set_fold_tree(), and StepWiseRNA_JobParameters().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::force_north_sugar_list_

private

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

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::force_south_sugar_list_

private

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

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::force_syn_chi_res_list_

private

Referenced by force_syn_chi_res_list(), set_force_syn_chi_res_list(), and StepWiseRNA_JobParameters().

std::string protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::full_sequence_

private

Referenced by full_sequence(), set_full_sequence(), and update_working_sequence().

std::map< core::Size, core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::full_to_sub_

private

Referenced by const_full_to_sub(), full_to_sub(), set_force_north_sugar_list(), set_force_south_sugar_list(), set_force_syn_chi_res_list(), set_full_to_sub(), set_global_sample_res_list(), set_protonated_H1_adenosine_list(), StepWiseRNA_JobParameters(), and working_floating_base_anchor_res().

Size protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::gap_size_

private

Referenced by gap_size(), and set_gap_size().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::global_sample_res_list_

private

Referenced by global_sample_res_list(), set_global_sample_res_list(), and StepWiseRNA_JobParameters().

utility::vector1< utility::vector1< core::Size > > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::input_res_vectors_

private

Referenced by input_res_vectors(), set_input_res_vectors(), and StepWiseRNA_JobParameters().

bool protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::is_internal_

private

Referenced by is_internal(), and set_is_internal().

bool protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::is_prepend_

private

Referenced by is_prepend(), set_is_prepend(), update_working_moving_suite(), and working_reference_res().

std::map< core::Size, bool > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::is_prepend_map_

private

Referenced by is_prepend_map(), set_is_prepend_map(), and StepWiseRNA_JobParameters().

bool protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::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::sampling::rna::StepWiseRNA_JobParameters::is_working_res_

private

Referenced by is_working_res(), set_force_north_sugar_list(), set_force_south_sugar_list(), set_force_syn_chi_res_list(), set_global_sample_res_list(), set_is_working_res(), set_protonated_H1_adenosine_list(), StepWiseRNA_JobParameters(), update_working_sequence(), and working_floating_base_anchor_res().

Size protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::moving_res_

private

Referenced by gap_size_to_anchor(), moving_res(), and set_moving_res().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::native_alignment_

private

Referenced by native_alignment(), set_native_alignment(), and StepWiseRNA_JobParameters().

bool protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::output_extra_RMSDs_

private

Referenced by output_extra_RMSDs(), and set_output_extra_RMSDs().

ObjexxFCL::FArray1D< bool > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::partition_definition_

private

Referenced by partition_definition(), set_partition_definition(), and StepWiseRNA_JobParameters().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::protonated_H1_adenosine_list_

private

Referenced by protonated_H1_adenosine_list(), set_protonated_H1_adenosine_list(), and StepWiseRNA_JobParameters().

bool protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::rebuild_bulge_mode_

private

Referenced by rebuild_bulge_mode(), and set_rebuild_bulge_mode().

bool protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::sample_both_sugar_base_rotamer_

private

Referenced by sample_both_sugar_base_rotamer(), and set_sample_both_sugar_base_rotamer().

std::map< core::Size, core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::sub_to_full_

private

Referenced by const_sub_to_full(), gap_size_to_anchor(), set_full_to_sub(), StepWiseRNA_JobParameters(), sub_to_full(), and working_res_list().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::terminal_res_

private

Referenced by set_terminal_res(), and terminal_res().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_best_alignment_

private

Referenced by set_working_best_alignment(), StepWiseRNA_JobParameters(), and working_best_alignment().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_fixed_res_

private

Referenced by set_working_fixed_res(), StepWiseRNA_JobParameters(), and working_fixed_res().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_force_north_sugar_list_

private

Referenced by set_force_north_sugar_list(), StepWiseRNA_JobParameters(), and working_force_north_sugar_list().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_force_south_sugar_list_

private

Referenced by set_force_south_sugar_list(), StepWiseRNA_JobParameters(), and working_force_south_sugar_list().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_force_syn_chi_res_list_

private

Referenced by set_force_syn_chi_res_list(), StepWiseRNA_JobParameters(), and working_force_syn_chi_res_list().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_global_sample_res_list_

private

Referenced by set_global_sample_res_list(), StepWiseRNA_JobParameters(), and working_global_sample_res_list().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_moving_partition_pos_

private

Referenced by set_working_moving_partition_pos(), StepWiseRNA_JobParameters(), and working_moving_partition_pos().

Size protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_moving_res_

private

Referenced by actually_moving_res(), set_working_moving_res_list(), update_working_moving_suite(), working_moving_res(), and working_reference_res().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_moving_res_list_

private

Referenced by set_working_moving_res_list(), StepWiseRNA_JobParameters(), update_working_moving_suite(), working_moving_res_list(), and working_reference_res().

Size protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_moving_suite_

private

Referenced by update_working_moving_suite(), and working_moving_suite().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_moving_suite_list_

private

Referenced by StepWiseRNA_JobParameters(), update_working_moving_suite(), and working_moving_suite_list().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_native_alignment_

private

Referenced by set_working_native_alignment(), StepWiseRNA_JobParameters(), and working_native_alignment().

core::pose::PoseCOP protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_native_pose_

private

Referenced by set_working_native_pose(), and working_native_pose().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_protonated_H1_adenosine_list_

private

Referenced by set_protonated_H1_adenosine_list(), StepWiseRNA_JobParameters(), and working_protonated_H1_adenosine_list().

std::string protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_sequence_

private

Referenced by set_full_sequence(), update_working_sequence(), and working_sequence().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::working_terminal_res_

private

Referenced by set_working_terminal_res(), StepWiseRNA_JobParameters(), and working_terminal_res().

---

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

• symlinks/rosetta/src/protocols/stepwise/sampling/rna/StepWiseRNA_JobParameters.hh
• symlinks/rosetta/src/protocols/stepwise/sampling/rna/StepWiseRNA_JobParameters.cc