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protocols::swa::rna::StepWiseRNA_JobParameters Class Reference

#include <StepWiseRNA_JobParameters.hh>

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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
 
Size working_reference_res () 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
 
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
 
ObjexxFCL::FArray1D< bool > const & partition_definition () const
 
utility::vector1< core::Size >
const & 		working_fixed_res () const
 
utility::vector1< core::Size >
const & 		rmsd_res_list () 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 & 		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_ribose_list () const
 
utility::vector1< core::Size >
const & 		working_force_north_ribose_list () const
 
utility::vector1< core::Size >
const & 		force_south_ribose_list () const
 
utility::vector1< core::Size >
const & 		working_force_south_ribose_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_working_native_pose (core::pose::PoseOP &pose)
 
void set_working_fixed_res (utility::vector1< core::Size > const &working_fixed_res)
 
void set_rmsd_res_list (utility::vector1< core::Size > const &rmsd_res_list)
 
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_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_ribose_list (utility::vector1< core::Size > const &setting)
 
void set_force_south_ribose_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)
 
core::pose::PoseCOP working_native_pose () const
 

Private Member Functions

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_
 
ObjexxFCL::FArray1D< bool > partition_definition_
 
core::pose::PoseOP working_native_pose_
 
utility::vector1< core::Size > working_fixed_res_
 
utility::vector1< core::Size > rmsd_res_list_
 
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 > 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_ribose_list_
 
utility::vector1< core::Size > working_force_north_ribose_list_
 
utility::vector1< core::Size > force_south_ribose_list_
 
utility::vector1< core::Size > working_force_south_ribose_list_
 
utility::vector1< core::Size > protonated_H1_adenosine_list_
 
utility::vector1< core::Size > working_protonated_H1_adenosine_list_
 

Detailed Description

Definition at line 40 of file StepWiseRNA_JobParameters.hh.

Constructor & Destructor Documentation

protocols::swa::rna::StepWiseRNA_JobParameters::StepWiseRNA_JobParameters ( )

Definition at line 36 of file StepWiseRNA_JobParameters.cc.

References chain_boundaries_, core::kinematics::FoldTree::clear(), cutpoint_closed_list_, fold_tree_, force_north_ribose_list_, force_south_ribose_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_, rmsd_res_list_, sub_to_full_, working_best_alignment_, working_fixed_res_, working_force_north_ribose_list_, working_force_south_ribose_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::swa::rna::StepWiseRNA_JobParameters::~StepWiseRNA_JobParameters ( )
virtual

Definition at line 83 of file StepWiseRNA_JobParameters.cc.

Member Function Documentation

Size protocols::swa::rna::StepWiseRNA_JobParameters::actually_moving_res ( ) const

Definition at line 399 of file StepWiseRNA_JobParameters.cc.

References working_moving_res_.

bool const & protocols::swa::rna::StepWiseRNA_JobParameters::add_virt_res_as_root ( ) const

Definition at line 201 of file StepWiseRNA_JobParameters.cc.

References add_virt_res_as_root_.

utility::vector1< std::pair< core::Size, core::Size > > const & protocols::swa::rna::StepWiseRNA_JobParameters::chain_boundaries ( ) const

Definition at line 177 of file StepWiseRNA_JobParameters.cc.

References chain_boundaries_.

std::map< core::Size, core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::const_full_to_sub ( ) const

Definition at line 157 of file StepWiseRNA_JobParameters.cc.

References full_to_sub_.

std::map< core::Size, core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::const_sub_to_full ( ) const

Definition at line 162 of file StepWiseRNA_JobParameters.cc.

References sub_to_full_.

std::map< core::Size, core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::create_sub_to_full_map ( std::map< core::Size, core::Size > const &  full_to_sub) const
private

Definition at line 533 of file StepWiseRNA_JobParameters.cc.

References sub_to_full().

Referenced by set_full_to_sub().

utility::vector1< Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::cutpoint_closed_list ( ) const

Definition at line 232 of file StepWiseRNA_JobParameters.cc.

References cutpoint_closed_list_.

Size const & protocols::swa::rna::StepWiseRNA_JobParameters::five_prime_chain_break_res ( ) const

Definition at line 189 of file StepWiseRNA_JobParameters.cc.

References five_prime_chain_break_res_.

core::kinematics::FoldTree const & protocols::swa::rna::StepWiseRNA_JobParameters::fold_tree ( ) const

Definition at line 167 of file StepWiseRNA_JobParameters.cc.

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

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::force_north_ribose_list ( ) const

Definition at line 268 of file StepWiseRNA_JobParameters.cc.

References force_north_ribose_list_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::force_south_ribose_list ( ) const

Definition at line 276 of file StepWiseRNA_JobParameters.cc.

References force_south_ribose_list_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::force_syn_chi_res_list ( ) const

Definition at line 260 of file StepWiseRNA_JobParameters.cc.

References force_syn_chi_res_list_.

std::string const & protocols::swa::rna::StepWiseRNA_JobParameters::full_sequence ( ) const

Definition at line 94 of file StepWiseRNA_JobParameters.cc.

References full_sequence_.

std::map< core::Size, core::Size > & protocols::swa::rna::StepWiseRNA_JobParameters::full_to_sub ( )

Definition at line 147 of file StepWiseRNA_JobParameters.cc.

References full_to_sub_.

Size const & protocols::swa::rna::StepWiseRNA_JobParameters::gap_size ( ) const

Definition at line 185 of file StepWiseRNA_JobParameters.cc.

References gap_size_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::global_sample_res_list ( ) const

Definition at line 252 of file StepWiseRNA_JobParameters.cc.

References global_sample_res_list_.

utility::vector1< utility::vector1< Size > > const & protocols::swa::rna::StepWiseRNA_JobParameters::input_res_vectors ( ) const

Definition at line 227 of file StepWiseRNA_JobParameters.cc.

References input_res_vectors_.

bool const & protocols::swa::rna::StepWiseRNA_JobParameters::Is_internal ( ) const

Definition at line 197 of file StepWiseRNA_JobParameters.cc.

References Is_internal_.

bool const & protocols::swa::rna::StepWiseRNA_JobParameters::Is_prepend ( ) const

Definition at line 193 of file StepWiseRNA_JobParameters.cc.

References Is_prepend_.

std::map< core::Size, bool > const & protocols::swa::rna::StepWiseRNA_JobParameters::Is_prepend_map ( ) const

Definition at line 172 of file StepWiseRNA_JobParameters.cc.

References Is_prepend_map_.

bool const & protocols::swa::rna::StepWiseRNA_JobParameters::Is_simple_full_length_job_params ( ) const

Definition at line 90 of file StepWiseRNA_JobParameters.cc.

References Is_simple_full_length_job_params_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::is_working_res ( ) const

Definition at line 142 of file StepWiseRNA_JobParameters.cc.

References is_working_res_.

Size const & protocols::swa::rna::StepWiseRNA_JobParameters::moving_res ( ) const

Definition at line 106 of file StepWiseRNA_JobParameters.cc.

References moving_res_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::native_alignment ( ) const

Definition at line 243 of file StepWiseRNA_JobParameters.cc.

References native_alignment_.

bool const & protocols::swa::rna::StepWiseRNA_JobParameters::output_extra_RMSDs ( ) const

Definition at line 86 of file StepWiseRNA_JobParameters.cc.

References output_extra_RMSDs_.

ObjexxFCL::FArray1D< bool > const & protocols::swa::rna::StepWiseRNA_JobParameters::partition_definition ( ) const

Definition at line 205 of file StepWiseRNA_JobParameters.cc.

References partition_definition_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::protonated_H1_adenosine_list ( ) const

Definition at line 284 of file StepWiseRNA_JobParameters.cc.

References protonated_H1_adenosine_list_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::rmsd_res_list ( ) const

Definition at line 214 of file StepWiseRNA_JobParameters.cc.

References rmsd_res_list_.

Referenced by set_rmsd_res_list().

void protocols::swa::rna::StepWiseRNA_JobParameters::set_add_virt_res_as_root ( bool const  setting)
inline

Definition at line 159 of file StepWiseRNA_JobParameters.hh.

References add_virt_res_as_root_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_chain_boundaries ( utility::vector1< std::pair< core::Size, core::Size > > const &  setting)

Definition at line 357 of file StepWiseRNA_JobParameters.cc.

References chain_boundaries_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_cutpoint_closed_list ( utility::vector1< core::Size > const &  setting)

Definition at line 431 of file StepWiseRNA_JobParameters.cc.

References cutpoint_closed_list_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_five_prime_chain_break_res ( Size const &  setting)

Definition at line 369 of file StepWiseRNA_JobParameters.cc.

References five_prime_chain_break_res_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_fold_tree ( core::kinematics::FoldTree const &  setting)

Definition at line 349 of file StepWiseRNA_JobParameters.cc.

References fold_tree_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_force_north_ribose_list ( utility::vector1< core::Size > const &  setting)

Definition at line 465 of file StepWiseRNA_JobParameters.cc.

References protocols::swa::rna::apply_full_to_sub_mapping(), protocols::swa::rna::Contain_seq_num(), force_north_ribose_list_, force_south_ribose_list_, full_to_sub_, is_working_res_, and working_force_north_ribose_list_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_force_south_ribose_list ( utility::vector1< core::Size > const &  setting)

Definition at line 477 of file StepWiseRNA_JobParameters.cc.

References protocols::swa::rna::apply_full_to_sub_mapping(), protocols::swa::rna::Contain_seq_num(), force_north_ribose_list_, force_south_ribose_list_, full_to_sub_, is_working_res_, and working_force_south_ribose_list_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_force_syn_chi_res_list ( utility::vector1< core::Size > const &  setting)

Definition at line 459 of file StepWiseRNA_JobParameters.cc.

References protocols::swa::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::swa::rna::StepWiseRNA_JobParameters::set_full_sequence ( std::string const &  setting)

Definition at line 300 of file StepWiseRNA_JobParameters.cc.

References full_sequence_, update_working_sequence(), and working_sequence_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_full_to_sub ( std::map< core::Size, core::Size > const &  setting)

Definition at line 343 of file StepWiseRNA_JobParameters.cc.

References create_sub_to_full_map(), full_to_sub_, and sub_to_full_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_gap_size ( Size const &  setting)

Definition at line 365 of file StepWiseRNA_JobParameters.cc.

References gap_size_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_global_sample_res_list ( utility::vector1< core::Size > const &  setting)

Definition at line 452 of file StepWiseRNA_JobParameters.cc.

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

void protocols::swa::rna::StepWiseRNA_JobParameters::set_input_res_vectors ( utility::vector1< utility::vector1< Size > > const &  setting)

Definition at line 426 of file StepWiseRNA_JobParameters.cc.

References input_res_vectors_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_Is_internal ( bool const &  setting)

Definition at line 378 of file StepWiseRNA_JobParameters.cc.

References Is_internal_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_Is_prepend ( bool const &  setting)

Definition at line 373 of file StepWiseRNA_JobParameters.cc.

References Is_prepend_, and update_working_moving_suite().

void protocols::swa::rna::StepWiseRNA_JobParameters::set_Is_prepend_map ( std::map< core::Size, bool > const &  setting)

Definition at line 353 of file StepWiseRNA_JobParameters.cc.

References Is_prepend_map_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_Is_simple_full_length_job_params ( bool const &  setting)

Definition at line 296 of file StepWiseRNA_JobParameters.cc.

References Is_simple_full_length_job_params_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_is_working_res ( utility::vector1< core::Size > const &  setting)

Definition at line 337 of file StepWiseRNA_JobParameters.cc.

References is_working_res_, and update_working_sequence().

void protocols::swa::rna::StepWiseRNA_JobParameters::set_moving_res ( Size const &  setting)

Definition at line 311 of file StepWiseRNA_JobParameters.cc.

References moving_res_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_native_alignment ( utility::vector1< core::Size > const &  setting)

Definition at line 441 of file StepWiseRNA_JobParameters.cc.

References native_alignment_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_output_extra_RMSDs ( bool const &  setting)

Definition at line 292 of file StepWiseRNA_JobParameters.cc.

References output_extra_RMSDs_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_partition_definition ( ObjexxFCL::FArray1D< bool > const &  setting)

Definition at line 382 of file StepWiseRNA_JobParameters.cc.

References partition_definition_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_protonated_H1_adenosine_list ( utility::vector1< core::Size > const &  setting)

Definition at line 489 of file StepWiseRNA_JobParameters.cc.

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

void protocols::swa::rna::StepWiseRNA_JobParameters::set_rmsd_res_list ( utility::vector1< core::Size > const &  rmsd_res_list)

Definition at line 410 of file StepWiseRNA_JobParameters.cc.

References rmsd_res_list(), rmsd_res_list_, and protocols::swa::rna::sort_seq_num_list().

void protocols::swa::rna::StepWiseRNA_JobParameters::set_working_best_alignment ( utility::vector1< core::Size > const &  setting)

Definition at line 436 of file StepWiseRNA_JobParameters.cc.

References working_best_alignment_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_working_fixed_res ( utility::vector1< core::Size > const &  working_fixed_res)

Definition at line 405 of file StepWiseRNA_JobParameters.cc.

References working_fixed_res(), and working_fixed_res_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_working_moving_partition_pos ( utility::vector1< core::Size > const &  working_moving_partition_pos)

Definition at line 421 of file StepWiseRNA_JobParameters.cc.

References working_moving_partition_pos(), and working_moving_partition_pos_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_working_moving_res_list ( utility::vector1< core::Size > const &  setting)

Definition at line 315 of file StepWiseRNA_JobParameters.cc.

References update_working_moving_suite(), working_moving_res_, and working_moving_res_list_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_working_native_alignment ( utility::vector1< core::Size > const &  setting)

Definition at line 446 of file StepWiseRNA_JobParameters.cc.

References working_native_alignment_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_working_native_pose ( core::pose::PoseOP &  pose)

Definition at line 393 of file StepWiseRNA_JobParameters.cc.

References working_native_pose_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_working_terminal_res ( utility::vector1< core::Size > const &  working_terminal_res)

Definition at line 416 of file StepWiseRNA_JobParameters.cc.

References working_terminal_res(), and working_terminal_res_.

std::map< core::Size, core::Size > & protocols::swa::rna::StepWiseRNA_JobParameters::sub_to_full ( )

Definition at line 152 of file StepWiseRNA_JobParameters.cc.

References sub_to_full_.

Referenced by create_sub_to_full_map().

void protocols::swa::rna::StepWiseRNA_JobParameters::update_working_moving_suite ( )
private

Definition at line 495 of file StepWiseRNA_JobParameters.cc.

References Is_prepend_, 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::swa::rna::StepWiseRNA_JobParameters::update_working_sequence ( )
private

Definition at line 560 of file StepWiseRNA_JobParameters.cc.

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::swa::rna::StepWiseRNA_JobParameters::working_best_alignment ( ) const

Definition at line 236 of file StepWiseRNA_JobParameters.cc.

References working_best_alignment_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::working_fixed_res ( ) const

Definition at line 210 of file StepWiseRNA_JobParameters.cc.

References working_fixed_res_.

Referenced by set_working_fixed_res().

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::working_force_north_ribose_list ( ) const

Definition at line 272 of file StepWiseRNA_JobParameters.cc.

References working_force_north_ribose_list_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::working_force_south_ribose_list ( ) const

Definition at line 280 of file StepWiseRNA_JobParameters.cc.

References working_force_south_ribose_list_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::working_force_syn_chi_res_list ( ) const

Definition at line 264 of file StepWiseRNA_JobParameters.cc.

References working_force_syn_chi_res_list_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::working_global_sample_res_list ( ) const

Definition at line 256 of file StepWiseRNA_JobParameters.cc.

References working_global_sample_res_list_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::working_moving_partition_pos ( ) const

Definition at line 223 of file StepWiseRNA_JobParameters.cc.

References working_moving_partition_pos_.

Referenced by set_working_moving_partition_pos().

Size const & protocols::swa::rna::StepWiseRNA_JobParameters::working_moving_res ( ) const

Definition at line 110 of file StepWiseRNA_JobParameters.cc.

References working_moving_res_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::working_moving_res_list ( ) const

Definition at line 114 of file StepWiseRNA_JobParameters.cc.

References working_moving_res_list_.

Size const & protocols::swa::rna::StepWiseRNA_JobParameters::working_moving_suite ( ) const

Definition at line 133 of file StepWiseRNA_JobParameters.cc.

References working_moving_suite_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::working_moving_suite_list ( ) const

Definition at line 137 of file StepWiseRNA_JobParameters.cc.

References working_moving_suite_list_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::working_native_alignment ( ) const

Definition at line 247 of file StepWiseRNA_JobParameters.cc.

References working_native_alignment_.

core::pose::PoseCOP protocols::swa::rna::StepWiseRNA_JobParameters::working_native_pose ( ) const

Definition at line 387 of file StepWiseRNA_JobParameters.cc.

References working_native_pose_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::working_protonated_H1_adenosine_list ( ) const

Definition at line 288 of file StepWiseRNA_JobParameters.cc.

References working_protonated_H1_adenosine_list_.

Size protocols::swa::rna::StepWiseRNA_JobParameters::working_reference_res ( ) const

Definition at line 119 of file StepWiseRNA_JobParameters.cc.

References Is_prepend_, working_moving_res_, and working_moving_res_list_.

std::string const & protocols::swa::rna::StepWiseRNA_JobParameters::working_sequence ( ) const

Definition at line 100 of file StepWiseRNA_JobParameters.cc.

References working_sequence_.

utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::working_terminal_res ( ) const

Definition at line 219 of file StepWiseRNA_JobParameters.cc.

References working_terminal_res_.

Referenced by set_working_terminal_res().

Member Data Documentation

bool protocols::swa::rna::StepWiseRNA_JobParameters::add_virt_res_as_root_
private

Definition at line 199 of file StepWiseRNA_JobParameters.hh.

Referenced by add_virt_res_as_root(), and set_add_virt_res_as_root().

utility::vector1< std::pair< core::Size, core::Size > > protocols::swa::rna::StepWiseRNA_JobParameters::chain_boundaries_
private

Definition at line 192 of file StepWiseRNA_JobParameters.hh.

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

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::cutpoint_closed_list_
private

Definition at line 211 of file StepWiseRNA_JobParameters.hh.

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

Size protocols::swa::rna::StepWiseRNA_JobParameters::five_prime_chain_break_res_
private

Definition at line 195 of file StepWiseRNA_JobParameters.hh.

Referenced by five_prime_chain_break_res(), and set_five_prime_chain_break_res().

core::kinematics::FoldTree protocols::swa::rna::StepWiseRNA_JobParameters::fold_tree_
private

Definition at line 209 of file StepWiseRNA_JobParameters.hh.

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

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::force_north_ribose_list_
private

Definition at line 223 of file StepWiseRNA_JobParameters.hh.

Referenced by force_north_ribose_list(), set_force_north_ribose_list(), set_force_south_ribose_list(), and StepWiseRNA_JobParameters().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::force_south_ribose_list_
private

Definition at line 226 of file StepWiseRNA_JobParameters.hh.

Referenced by force_south_ribose_list(), set_force_north_ribose_list(), set_force_south_ribose_list(), and StepWiseRNA_JobParameters().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::force_syn_chi_res_list_
private

Definition at line 220 of file StepWiseRNA_JobParameters.hh.

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

std::string protocols::swa::rna::StepWiseRNA_JobParameters::full_sequence_
private

Definition at line 178 of file StepWiseRNA_JobParameters.hh.

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

std::map< core::Size, core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::full_to_sub_
private

Definition at line 188 of file StepWiseRNA_JobParameters.hh.

Referenced by const_full_to_sub(), full_to_sub(), set_force_north_ribose_list(), set_force_south_ribose_list(), set_force_syn_chi_res_list(), set_full_to_sub(), set_global_sample_res_list(), set_protonated_H1_adenosine_list(), and StepWiseRNA_JobParameters().

Size protocols::swa::rna::StepWiseRNA_JobParameters::gap_size_
private

Definition at line 194 of file StepWiseRNA_JobParameters.hh.

Referenced by gap_size(), and set_gap_size().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::global_sample_res_list_
private

Definition at line 217 of file StepWiseRNA_JobParameters.hh.

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

utility::vector1< utility::vector1< core::Size > > protocols::swa::rna::StepWiseRNA_JobParameters::input_res_vectors_
private

Definition at line 210 of file StepWiseRNA_JobParameters.hh.

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

bool protocols::swa::rna::StepWiseRNA_JobParameters::Is_internal_
private

Definition at line 198 of file StepWiseRNA_JobParameters.hh.

Referenced by Is_internal(), and set_Is_internal().

bool protocols::swa::rna::StepWiseRNA_JobParameters::Is_prepend_
private

Definition at line 197 of file StepWiseRNA_JobParameters.hh.

Referenced by Is_prepend(), set_Is_prepend(), update_working_moving_suite(), and working_reference_res().

std::map< core::Size, bool > protocols::swa::rna::StepWiseRNA_JobParameters::Is_prepend_map_
private

Definition at line 190 of file StepWiseRNA_JobParameters.hh.

Referenced by Is_prepend_map(), set_Is_prepend_map(), and StepWiseRNA_JobParameters().

bool protocols::swa::rna::StepWiseRNA_JobParameters::Is_simple_full_length_job_params_
private

Definition at line 176 of file StepWiseRNA_JobParameters.hh.

Referenced by Is_simple_full_length_job_params(), and set_Is_simple_full_length_job_params().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::is_working_res_
private

Definition at line 187 of file StepWiseRNA_JobParameters.hh.

Referenced by is_working_res(), set_force_north_ribose_list(), set_force_south_ribose_list(), set_force_syn_chi_res_list(), set_global_sample_res_list(), set_is_working_res(), set_protonated_H1_adenosine_list(), StepWiseRNA_JobParameters(), and update_working_sequence().

Size protocols::swa::rna::StepWiseRNA_JobParameters::moving_res_
private

Definition at line 181 of file StepWiseRNA_JobParameters.hh.

Referenced by moving_res(), and set_moving_res().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::native_alignment_
private

Definition at line 214 of file StepWiseRNA_JobParameters.hh.

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

bool protocols::swa::rna::StepWiseRNA_JobParameters::output_extra_RMSDs_
private

Definition at line 175 of file StepWiseRNA_JobParameters.hh.

Referenced by output_extra_RMSDs(), and set_output_extra_RMSDs().

ObjexxFCL::FArray1D< bool > protocols::swa::rna::StepWiseRNA_JobParameters::partition_definition_
private

Definition at line 201 of file StepWiseRNA_JobParameters.hh.

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

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::protonated_H1_adenosine_list_
private

Definition at line 230 of file StepWiseRNA_JobParameters.hh.

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

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::rmsd_res_list_
private

Definition at line 206 of file StepWiseRNA_JobParameters.hh.

Referenced by rmsd_res_list(), set_rmsd_res_list(), and StepWiseRNA_JobParameters().

std::map< core::Size, core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::sub_to_full_
private

Definition at line 189 of file StepWiseRNA_JobParameters.hh.

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

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_best_alignment_
private

Definition at line 212 of file StepWiseRNA_JobParameters.hh.

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

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_fixed_res_
private

Definition at line 205 of file StepWiseRNA_JobParameters.hh.

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

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_force_north_ribose_list_
private

Definition at line 224 of file StepWiseRNA_JobParameters.hh.

Referenced by set_force_north_ribose_list(), StepWiseRNA_JobParameters(), and working_force_north_ribose_list().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_force_south_ribose_list_
private

Definition at line 227 of file StepWiseRNA_JobParameters.hh.

Referenced by set_force_south_ribose_list(), StepWiseRNA_JobParameters(), and working_force_south_ribose_list().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_force_syn_chi_res_list_
private

Definition at line 221 of file StepWiseRNA_JobParameters.hh.

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

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_global_sample_res_list_
private

Definition at line 218 of file StepWiseRNA_JobParameters.hh.

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

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_moving_partition_pos_
private

Definition at line 208 of file StepWiseRNA_JobParameters.hh.

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

Size protocols::swa::rna::StepWiseRNA_JobParameters::working_moving_res_
private

Definition at line 184 of file StepWiseRNA_JobParameters.hh.

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::swa::rna::StepWiseRNA_JobParameters::working_moving_res_list_
private

Definition at line 182 of file StepWiseRNA_JobParameters.hh.

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

Size protocols::swa::rna::StepWiseRNA_JobParameters::working_moving_suite_
private

Definition at line 185 of file StepWiseRNA_JobParameters.hh.

Referenced by update_working_moving_suite(), and working_moving_suite().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_moving_suite_list_
private

Definition at line 183 of file StepWiseRNA_JobParameters.hh.

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

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_native_alignment_
private

Definition at line 215 of file StepWiseRNA_JobParameters.hh.

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

core::pose::PoseOP protocols::swa::rna::StepWiseRNA_JobParameters::working_native_pose_
private

Definition at line 203 of file StepWiseRNA_JobParameters.hh.

Referenced by set_working_native_pose(), and working_native_pose().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_protonated_H1_adenosine_list_
private

Definition at line 231 of file StepWiseRNA_JobParameters.hh.

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

std::string protocols::swa::rna::StepWiseRNA_JobParameters::working_sequence_
private

Definition at line 179 of file StepWiseRNA_JobParameters.hh.

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

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_terminal_res_
private

Definition at line 207 of file StepWiseRNA_JobParameters.hh.

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

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