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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::Sizecreate_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::Sizeworking_moving_res_list_
 
utility::vector1< core::Sizeworking_moving_suite_list_
 
Size working_moving_res_
 
Size working_moving_suite_
 
utility::vector1< core::Sizeis_working_res_
 
std::map< core::Size, core::Sizefull_to_sub_
 
std::map< core::Size, core::Sizesub_to_full_
 
std::map< core::Size, boolIs_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< boolpartition_definition_
 
core::pose::PoseOP working_native_pose_
 
utility::vector1< core::Sizeworking_fixed_res_
 
utility::vector1< core::Sizermsd_res_list_
 
utility::vector1< core::Sizeworking_terminal_res_
 
utility::vector1< core::Sizeworking_moving_partition_pos_
 
core::kinematics::FoldTree fold_tree_
 
utility::vector1
< utility::vector1< core::Size > > 
input_res_vectors_
 
utility::vector1< core::Sizecutpoint_closed_list_
 
utility::vector1< core::Sizeworking_best_alignment_
 
utility::vector1< core::Sizenative_alignment_
 
utility::vector1< core::Sizeworking_native_alignment_
 
utility::vector1< core::Sizeglobal_sample_res_list_
 
utility::vector1< core::Sizeworking_global_sample_res_list_
 
utility::vector1< core::Sizeforce_syn_chi_res_list_
 
utility::vector1< core::Sizeworking_force_syn_chi_res_list_
 
utility::vector1< core::Sizeforce_north_ribose_list_
 
utility::vector1< core::Sizeworking_force_north_ribose_list_
 
utility::vector1< core::Sizeforce_south_ribose_list_
 
utility::vector1< core::Sizeworking_force_south_ribose_list_
 
utility::vector1< core::Sizeprotonated_H1_adenosine_list_
 
utility::vector1< core::Sizeworking_protonated_H1_adenosine_list_
 

Constructor & Destructor Documentation

protocols::swa::rna::StepWiseRNA_JobParameters::StepWiseRNA_JobParameters ( )
protocols::swa::rna::StepWiseRNA_JobParameters::~StepWiseRNA_JobParameters ( )
virtual

Member Function Documentation

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

References working_moving_res_.

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

References add_virt_res_as_root_.

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

References chain_boundaries_.

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

References full_to_sub_.

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

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

References sub_to_full().

Referenced by set_full_to_sub().

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

References cutpoint_closed_list_.

Size const & protocols::swa::rna::StepWiseRNA_JobParameters::five_prime_chain_break_res ( ) const
core::kinematics::FoldTree const & protocols::swa::rna::StepWiseRNA_JobParameters::fold_tree ( ) const
utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::force_north_ribose_list ( ) const
utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::force_south_ribose_list ( ) const
utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::force_syn_chi_res_list ( ) const
std::string const & protocols::swa::rna::StepWiseRNA_JobParameters::full_sequence ( ) const

References full_sequence_.

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

References full_to_sub_.

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

References gap_size_.

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

References input_res_vectors_.

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

References Is_internal_.

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

References Is_prepend_.

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

References Is_prepend_map_.

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

References is_working_res_.

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

References moving_res_.

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

References native_alignment_.

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

References output_extra_RMSDs_.

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

References partition_definition_.

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

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

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)

References chain_boundaries_.

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

References cutpoint_closed_list_.

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

References fold_tree_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_force_north_ribose_list ( utility::vector1< core::Size > const &  setting)
void protocols::swa::rna::StepWiseRNA_JobParameters::set_force_south_ribose_list ( utility::vector1< core::Size > const &  setting)
void protocols::swa::rna::StepWiseRNA_JobParameters::set_force_syn_chi_res_list ( utility::vector1< core::Size > const &  setting)
void protocols::swa::rna::StepWiseRNA_JobParameters::set_full_sequence ( std::string const &  setting)
void protocols::swa::rna::StepWiseRNA_JobParameters::set_full_to_sub ( std::map< core::Size, core::Size > const &  setting)
void protocols::swa::rna::StepWiseRNA_JobParameters::set_gap_size ( Size const &  setting)

References gap_size_.

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

References input_res_vectors_.

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

References Is_internal_.

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

References Is_prepend_map_.

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

References moving_res_.

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

References native_alignment_.

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

References output_extra_RMSDs_.

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

References partition_definition_.

void protocols::swa::rna::StepWiseRNA_JobParameters::set_protonated_H1_adenosine_list ( utility::vector1< core::Size > const &  setting)
void protocols::swa::rna::StepWiseRNA_JobParameters::set_rmsd_res_list ( utility::vector1< core::Size > const &  rmsd_res_list)
void protocols::swa::rna::StepWiseRNA_JobParameters::set_working_best_alignment ( utility::vector1< core::Size > const &  setting)
void protocols::swa::rna::StepWiseRNA_JobParameters::set_working_fixed_res ( utility::vector1< core::Size > const &  working_fixed_res)
void protocols::swa::rna::StepWiseRNA_JobParameters::set_working_moving_partition_pos ( utility::vector1< core::Size > const &  working_moving_partition_pos)
void protocols::swa::rna::StepWiseRNA_JobParameters::set_working_moving_res_list ( utility::vector1< core::Size > const &  setting)
void protocols::swa::rna::StepWiseRNA_JobParameters::set_working_native_alignment ( utility::vector1< core::Size > const &  setting)
void protocols::swa::rna::StepWiseRNA_JobParameters::set_working_native_pose ( core::pose::PoseOP pose)

References working_native_pose_.

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

References sub_to_full_.

Referenced by create_sub_to_full_map().

void protocols::swa::rna::StepWiseRNA_JobParameters::update_working_moving_suite ( )
private
void protocols::swa::rna::StepWiseRNA_JobParameters::update_working_sequence ( )
private
utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::working_best_alignment ( ) const
utility::vector1< core::Size > const & protocols::swa::rna::StepWiseRNA_JobParameters::working_fixed_res ( ) const

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

References working_moving_res_.

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

References working_moving_suite_.

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

References working_native_pose_.

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

References working_sequence_.

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

Member Data Documentation

bool protocols::swa::rna::StepWiseRNA_JobParameters::add_virt_res_as_root_
private
utility::vector1< std::pair< core::Size, core::Size > > protocols::swa::rna::StepWiseRNA_JobParameters::chain_boundaries_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::cutpoint_closed_list_
private
Size protocols::swa::rna::StepWiseRNA_JobParameters::five_prime_chain_break_res_
private
core::kinematics::FoldTree protocols::swa::rna::StepWiseRNA_JobParameters::fold_tree_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::force_north_ribose_list_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::force_south_ribose_list_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::force_syn_chi_res_list_
private
std::string protocols::swa::rna::StepWiseRNA_JobParameters::full_sequence_
private
std::map< core::Size, core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::full_to_sub_
private
Size protocols::swa::rna::StepWiseRNA_JobParameters::gap_size_
private

Referenced by gap_size(), and set_gap_size().

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

Referenced by Is_internal(), and set_Is_internal().

bool protocols::swa::rna::StepWiseRNA_JobParameters::Is_prepend_
private
std::map< core::Size, bool > protocols::swa::rna::StepWiseRNA_JobParameters::Is_prepend_map_
private
bool protocols::swa::rna::StepWiseRNA_JobParameters::Is_simple_full_length_job_params_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::is_working_res_
private
Size protocols::swa::rna::StepWiseRNA_JobParameters::moving_res_
private

Referenced by moving_res(), and set_moving_res().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::native_alignment_
private
bool protocols::swa::rna::StepWiseRNA_JobParameters::output_extra_RMSDs_
private
ObjexxFCL::FArray1D< bool > protocols::swa::rna::StepWiseRNA_JobParameters::partition_definition_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::protonated_H1_adenosine_list_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::rmsd_res_list_
private
std::map< core::Size, core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::sub_to_full_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_best_alignment_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_fixed_res_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_force_north_ribose_list_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_force_south_ribose_list_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_force_syn_chi_res_list_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_global_sample_res_list_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_moving_partition_pos_
private
Size protocols::swa::rna::StepWiseRNA_JobParameters::working_moving_res_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_moving_res_list_
private
Size protocols::swa::rna::StepWiseRNA_JobParameters::working_moving_suite_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_moving_suite_list_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_native_alignment_
private
core::pose::PoseOP protocols::swa::rna::StepWiseRNA_JobParameters::working_native_pose_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_protonated_H1_adenosine_list_
private
std::string protocols::swa::rna::StepWiseRNA_JobParameters::working_sequence_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters::working_terminal_res_
private

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