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protocols::swa::StepWiseJobParameters Class Reference

#include <StepWiseJobParameters.hh>

Inheritance diagram for protocols::swa::StepWiseJobParameters:
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Public Member Functions

 StepWiseJobParameters ()
 
virtual ~StepWiseJobParameters ()
 
std::string const & sequence () const
 
std::string const & working_sequence () const
 
utility::vector1< core::Size >
const & 		working_res_list () const
 
utility::vector1< core::Size >
const & 		working_moving_res_list () const
 
utility::vector1< core::Size >
const & 		working_moving_suite_list () const
 
Size actually_moving_res () const
 
ObjexxFCL::FArray1D
< core::Size > const & 		is_working_res () const
 
ObjexxFCL::FArray1D
< core::Size > const & 		is_moving_res () const
 
std::map< core::Size,
core::Size > & 		full_to_sub ()
 
std::map< core::Size,
core::Size > & 		sub_to_full ()
 
utility::vector1< std::pair
< core::Size, core::Size >
> const & 		chain_boundaries () const
 
Size const & which_chain_has_moving_res () const
 
Size const & gap_size () const
 
Size const & first_chain_break_res () const
 
bool const & Is_prepend () const
 
bool const & Is_internal () const
 
ObjexxFCL::FArray1D< bool > const & partition_definition () const
 
utility::vector1< core::Size >
const & 		working_fixed_res () const
 
utility::vector1< core::Size >
const & 		working_terminal_res () const
 
utility::vector1< core::Size >
const & 		working_superimpose_res () const
 
utility::vector1< core::Size >
const & 		working_calc_rms_res () const
 
utility::vector1< core::Size >
const & 		working_bridge_res () const
 
utility::vector1< core::Size >
const & 		moving_pos () const
 
void set_sequence (std::string const &setting)
 
void set_working_sequence (std::string const &setting)
 
void set_working_res_list (utility::vector1< core::Size > const &setting)
 
void set_working_moving_res_list (utility::vector1< core::Size > const &setting)
 
void set_working_moving_suite_list (utility::vector1< core::Size > const &setting)
 
void set_is_working_res (ObjexxFCL::FArray1D< core::Size > const &setting)
 
void set_is_moving_res (ObjexxFCL::FArray1D< core::Size > const &setting)
 
void set_full_to_sub (std::map< core::Size, core::Size > const &setting)
 
std::map< core::Size, core::Size > create_sub_to_full_map (std::map< core::Size, core::Size > const &full_to_sub) const
 
void set_chain_boundaries (utility::vector1< std::pair< core::Size, core::Size > > const &setting)
 
void set_which_chain_has_moving_res (Size const &setting)
 
void set_gap_size (Size const &setting)
 
void set_first_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_working_terminal_res (utility::vector1< core::Size > const &working_terminal_res)
 
void set_working_superimpose_res (utility::vector1< core::Size > const &working_superimpose_res)
 
void set_working_calc_rms_res (utility::vector1< core::Size > const &working_calc_rms_res)
 
void set_working_bridge_res (utility::vector1< core::Size > const &working_bridge_res)
 
void set_moving_pos (utility::vector1< core::Size > const &moving_pos)
 
utility::vector1< bool > const is_pre_proline () const
 
core::pose::PoseCOP working_native_pose () const
 
utility::vector1< Size > apply_full_to_sub_mapping (utility::vector1< Size > const &res_vector)
 
Size apply_full_to_sub_mapping (Size const res) const
 

Private Attributes

std::string sequence_
 
std::string working_sequence_
 
utility::vector1< core::Size > working_res_list_
 
utility::vector1< core::Size > working_moving_res_list_
 
utility::vector1< core::Size > working_moving_suite_list_
 
ObjexxFCL::FArray1D< core::Size > is_working_res_
 
ObjexxFCL::FArray1D< core::Size > is_moving_res_
 
std::map< core::Size, core::Size > full_to_sub_
 
std::map< core::Size, core::Size > sub_to_full_
 
utility::vector1< std::pair
< core::Size, core::Size > > 		chain_boundaries_
 
Size which_chain_has_moving_res_
 
Size gap_size_
 
Size first_chain_break_res_
 
bool Is_prepend_
 
bool Is_internal_
 
ObjexxFCL::FArray1D< bool > partition_definition_
 
core::pose::PoseOP working_native_pose_
 
utility::vector1< core::Size > working_fixed_res_
 
utility::vector1< core::Size > working_terminal_res_
 
utility::vector1< core::Size > working_superimpose_res_
 
utility::vector1< core::Size > working_calc_rms_res_
 
utility::vector1< core::Size > working_bridge_res_
 
utility::vector1< core::Size > moving_pos_
 

Detailed Description

Definition at line 35 of file StepWiseJobParameters.hh.

Constructor & Destructor Documentation

protocols::swa::StepWiseJobParameters::StepWiseJobParameters ( )

Definition at line 34 of file StepWiseJobParameters.cc.

protocols::swa::StepWiseJobParameters::~StepWiseJobParameters ( )
virtual

Definition at line 45 of file StepWiseJobParameters.cc.

Member Function Documentation

Size protocols::swa::StepWiseJobParameters::actually_moving_res ( ) const

Definition at line 256 of file StepWiseJobParameters.cc.

References Is_prepend_, and working_moving_suite_list_.

utility::vector1< Size > protocols::swa::StepWiseJobParameters::apply_full_to_sub_mapping ( utility::vector1< Size > const &  res_vector)

Definition at line 293 of file StepWiseJobParameters.cc.

References full_to_sub_, and is_working_res_.

Size protocols::swa::StepWiseJobParameters::apply_full_to_sub_mapping ( Size const  res) const

Definition at line 306 of file StepWiseJobParameters.cc.

References full_to_sub_.

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

Definition at line 88 of file StepWiseJobParameters.cc.

References chain_boundaries_.

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

Definition at line 171 of file StepWiseJobParameters.cc.

References sub_to_full().

Referenced by set_full_to_sub().

Size const & protocols::swa::StepWiseJobParameters::first_chain_break_res ( ) const

Definition at line 100 of file StepWiseJobParameters.cc.

References first_chain_break_res_.

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

Definition at line 80 of file StepWiseJobParameters.cc.

References full_to_sub_.

Size const & protocols::swa::StepWiseJobParameters::gap_size ( ) const

Definition at line 96 of file StepWiseJobParameters.cc.

References gap_size_.

bool const & protocols::swa::StepWiseJobParameters::Is_internal ( ) const

Definition at line 108 of file StepWiseJobParameters.cc.

References Is_internal_.

ObjexxFCL::FArray1D< Size > const & protocols::swa::StepWiseJobParameters::is_moving_res ( ) const

Definition at line 76 of file StepWiseJobParameters.cc.

References is_moving_res_.

utility::vector1< bool > const protocols::swa::StepWiseJobParameters::is_pre_proline ( ) const

Definition at line 197 of file StepWiseJobParameters.cc.

References sequence_, and working_res_list_.

bool const & protocols::swa::StepWiseJobParameters::Is_prepend ( ) const

Definition at line 104 of file StepWiseJobParameters.cc.

References Is_prepend_.

ObjexxFCL::FArray1D< Size > const & protocols::swa::StepWiseJobParameters::is_working_res ( ) const

Definition at line 72 of file StepWiseJobParameters.cc.

References is_working_res_.

utility::vector1< core::Size > const & protocols::swa::StepWiseJobParameters::moving_pos ( ) const

Definition at line 132 of file StepWiseJobParameters.cc.

References moving_pos_.

Referenced by set_moving_pos().

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

Definition at line 112 of file StepWiseJobParameters.cc.

References partition_definition_.

std::string const & protocols::swa::StepWiseJobParameters::sequence ( ) const

Definition at line 48 of file StepWiseJobParameters.cc.

References sequence_.

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

Definition at line 215 of file StepWiseJobParameters.cc.

References chain_boundaries_.

void protocols::swa::StepWiseJobParameters::set_first_chain_break_res ( Size const &  setting)

Definition at line 227 of file StepWiseJobParameters.cc.

References first_chain_break_res_.

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

Definition at line 164 of file StepWiseJobParameters.cc.

References create_sub_to_full_map(), full_to_sub_, and sub_to_full_.

void protocols::swa::StepWiseJobParameters::set_gap_size ( Size const &  setting)

Definition at line 223 of file StepWiseJobParameters.cc.

References gap_size_.

void protocols::swa::StepWiseJobParameters::set_Is_internal ( bool const &  setting)

Definition at line 235 of file StepWiseJobParameters.cc.

References Is_internal_.

void protocols::swa::StepWiseJobParameters::set_is_moving_res ( ObjexxFCL::FArray1D< core::Size > const &  setting)

Definition at line 160 of file StepWiseJobParameters.cc.

References is_moving_res_.

void protocols::swa::StepWiseJobParameters::set_Is_prepend ( bool const &  setting)

Definition at line 231 of file StepWiseJobParameters.cc.

References Is_prepend_.

void protocols::swa::StepWiseJobParameters::set_is_working_res ( ObjexxFCL::FArray1D< core::Size > const &  setting)

Definition at line 156 of file StepWiseJobParameters.cc.

References is_working_res_.

void protocols::swa::StepWiseJobParameters::set_moving_pos ( utility::vector1< core::Size > const &  moving_pos)

Definition at line 287 of file StepWiseJobParameters.cc.

References moving_pos(), and moving_pos_.

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

Definition at line 239 of file StepWiseJobParameters.cc.

References partition_definition_.

void protocols::swa::StepWiseJobParameters::set_sequence ( std::string const &  setting)

Definition at line 136 of file StepWiseJobParameters.cc.

References sequence_.

void protocols::swa::StepWiseJobParameters::set_which_chain_has_moving_res ( Size const &  setting)

Definition at line 219 of file StepWiseJobParameters.cc.

References which_chain_has_moving_res_.

void protocols::swa::StepWiseJobParameters::set_working_bridge_res ( utility::vector1< core::Size > const &  working_bridge_res)

Definition at line 282 of file StepWiseJobParameters.cc.

References working_bridge_res_.

void protocols::swa::StepWiseJobParameters::set_working_calc_rms_res ( utility::vector1< core::Size > const &  working_calc_rms_res)

Definition at line 278 of file StepWiseJobParameters.cc.

References working_calc_rms_res(), and working_calc_rms_res_.

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

Definition at line 263 of file StepWiseJobParameters.cc.

References working_fixed_res(), and working_fixed_res_.

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

Definition at line 148 of file StepWiseJobParameters.cc.

References working_moving_res_list_.

void protocols::swa::StepWiseJobParameters::set_working_moving_suite_list ( utility::vector1< core::Size > const &  setting)

Definition at line 152 of file StepWiseJobParameters.cc.

References working_moving_suite_list_.

void protocols::swa::StepWiseJobParameters::set_working_native_pose ( core::pose::PoseOP &  pose)

Definition at line 250 of file StepWiseJobParameters.cc.

References working_native_pose_.

void protocols::swa::StepWiseJobParameters::set_working_res_list ( utility::vector1< core::Size > const &  setting)

Definition at line 144 of file StepWiseJobParameters.cc.

References working_res_list_.

void protocols::swa::StepWiseJobParameters::set_working_sequence ( std::string const &  setting)

Definition at line 140 of file StepWiseJobParameters.cc.

References working_sequence_.

void protocols::swa::StepWiseJobParameters::set_working_superimpose_res ( utility::vector1< core::Size > const &  working_superimpose_res)

Definition at line 273 of file StepWiseJobParameters.cc.

References working_superimpose_res(), and working_superimpose_res_.

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

Definition at line 268 of file StepWiseJobParameters.cc.

References working_terminal_res(), and working_terminal_res_.

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

Definition at line 84 of file StepWiseJobParameters.cc.

References sub_to_full_.

Referenced by create_sub_to_full_map().

Size const & protocols::swa::StepWiseJobParameters::which_chain_has_moving_res ( ) const

Definition at line 92 of file StepWiseJobParameters.cc.

References which_chain_has_moving_res_.

utility::vector1< core::Size > const & protocols::swa::StepWiseJobParameters::working_bridge_res ( ) const

Definition at line 64 of file StepWiseJobParameters.cc.

References working_bridge_res_.

utility::vector1< core::Size > const & protocols::swa::StepWiseJobParameters::working_calc_rms_res ( ) const

Definition at line 128 of file StepWiseJobParameters.cc.

References working_calc_rms_res_.

Referenced by set_working_calc_rms_res().

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

Definition at line 116 of file StepWiseJobParameters.cc.

References working_fixed_res_.

Referenced by set_working_fixed_res().

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

Definition at line 60 of file StepWiseJobParameters.cc.

References working_moving_res_list_.

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

Definition at line 68 of file StepWiseJobParameters.cc.

References working_moving_suite_list_.

core::pose::PoseCOP protocols::swa::StepWiseJobParameters::working_native_pose ( ) const

Definition at line 244 of file StepWiseJobParameters.cc.

References working_native_pose_.

utility::vector1< core::Size > const & protocols::swa::StepWiseJobParameters::working_res_list ( ) const

Definition at line 56 of file StepWiseJobParameters.cc.

References working_res_list_.

std::string const & protocols::swa::StepWiseJobParameters::working_sequence ( ) const

Definition at line 52 of file StepWiseJobParameters.cc.

References working_sequence_.

utility::vector1< core::Size > const & protocols::swa::StepWiseJobParameters::working_superimpose_res ( ) const

Definition at line 124 of file StepWiseJobParameters.cc.

References working_superimpose_res_.

Referenced by set_working_superimpose_res().

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

Definition at line 120 of file StepWiseJobParameters.cc.

References working_terminal_res_.

Referenced by set_working_terminal_res().

Member Data Documentation

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

Definition at line 131 of file StepWiseJobParameters.hh.

Referenced by chain_boundaries(), and set_chain_boundaries().

Size protocols::swa::StepWiseJobParameters::first_chain_break_res_
private

Definition at line 134 of file StepWiseJobParameters.hh.

Referenced by first_chain_break_res(), and set_first_chain_break_res().

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

Definition at line 128 of file StepWiseJobParameters.hh.

Referenced by apply_full_to_sub_mapping(), full_to_sub(), and set_full_to_sub().

Size protocols::swa::StepWiseJobParameters::gap_size_
private

Definition at line 133 of file StepWiseJobParameters.hh.

Referenced by gap_size(), and set_gap_size().

bool protocols::swa::StepWiseJobParameters::Is_internal_
private

Definition at line 137 of file StepWiseJobParameters.hh.

Referenced by Is_internal(), and set_Is_internal().

ObjexxFCL::FArray1D< core::Size > protocols::swa::StepWiseJobParameters::is_moving_res_
private

Definition at line 127 of file StepWiseJobParameters.hh.

Referenced by is_moving_res(), and set_is_moving_res().

bool protocols::swa::StepWiseJobParameters::Is_prepend_
private

Definition at line 136 of file StepWiseJobParameters.hh.

Referenced by actually_moving_res(), Is_prepend(), and set_Is_prepend().

ObjexxFCL::FArray1D< core::Size > protocols::swa::StepWiseJobParameters::is_working_res_
private

Definition at line 126 of file StepWiseJobParameters.hh.

Referenced by apply_full_to_sub_mapping(), is_working_res(), and set_is_working_res().

utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::moving_pos_
private

Definition at line 148 of file StepWiseJobParameters.hh.

Referenced by moving_pos(), and set_moving_pos().

ObjexxFCL::FArray1D< bool > protocols::swa::StepWiseJobParameters::partition_definition_
private

Definition at line 139 of file StepWiseJobParameters.hh.

Referenced by partition_definition(), and set_partition_definition().

std::string protocols::swa::StepWiseJobParameters::sequence_
private

Definition at line 118 of file StepWiseJobParameters.hh.

Referenced by is_pre_proline(), sequence(), and set_sequence().

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

Definition at line 129 of file StepWiseJobParameters.hh.

Referenced by set_full_to_sub(), and sub_to_full().

Size protocols::swa::StepWiseJobParameters::which_chain_has_moving_res_
private

Definition at line 132 of file StepWiseJobParameters.hh.

Referenced by set_which_chain_has_moving_res(), and which_chain_has_moving_res().

utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_bridge_res_
private

Definition at line 147 of file StepWiseJobParameters.hh.

Referenced by set_working_bridge_res(), and working_bridge_res().

utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_calc_rms_res_
private

Definition at line 146 of file StepWiseJobParameters.hh.

Referenced by set_working_calc_rms_res(), and working_calc_rms_res().

utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_fixed_res_
private

Definition at line 143 of file StepWiseJobParameters.hh.

Referenced by set_working_fixed_res(), and working_fixed_res().

utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_moving_res_list_
private

Definition at line 123 of file StepWiseJobParameters.hh.

Referenced by set_working_moving_res_list(), and working_moving_res_list().

utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_moving_suite_list_
private

Definition at line 124 of file StepWiseJobParameters.hh.

Referenced by actually_moving_res(), set_working_moving_suite_list(), and working_moving_suite_list().

core::pose::PoseOP protocols::swa::StepWiseJobParameters::working_native_pose_
private

Definition at line 141 of file StepWiseJobParameters.hh.

Referenced by set_working_native_pose(), and working_native_pose().

utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_res_list_
private

Definition at line 121 of file StepWiseJobParameters.hh.

Referenced by is_pre_proline(), set_working_res_list(), and working_res_list().

std::string protocols::swa::StepWiseJobParameters::working_sequence_
private

Definition at line 119 of file StepWiseJobParameters.hh.

Referenced by set_working_sequence(), and working_sequence().

utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_superimpose_res_
private

Definition at line 145 of file StepWiseJobParameters.hh.

Referenced by set_working_superimpose_res(), and working_superimpose_res().

utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_terminal_res_
private

Definition at line 144 of file StepWiseJobParameters.hh.

Referenced by set_working_terminal_res(), and working_terminal_res().

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