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Public Member Functions | Private Attributes | List of all members
protocols::swa::StepWiseJobParameters Class Reference

#include <StepWiseJobParameters.hh>

Inheritance diagram for protocols::swa::StepWiseJobParameters:
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Collaboration 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::Sizecreate_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< Sizeapply_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::Sizeworking_res_list_
 
utility::vector1< core::Sizeworking_moving_res_list_
 
utility::vector1< core::Sizeworking_moving_suite_list_
 
ObjexxFCL::FArray1D< core::Sizeis_working_res_
 
ObjexxFCL::FArray1D< core::Sizeis_moving_res_
 
std::map< core::Size, core::Sizefull_to_sub_
 
std::map< core::Size, core::Sizesub_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< boolpartition_definition_
 
core::pose::PoseOP working_native_pose_
 
utility::vector1< core::Sizeworking_fixed_res_
 
utility::vector1< core::Sizeworking_terminal_res_
 
utility::vector1< core::Sizeworking_superimpose_res_
 
utility::vector1< core::Sizeworking_calc_rms_res_
 
utility::vector1< core::Sizeworking_bridge_res_
 
utility::vector1< core::Sizemoving_pos_
 

Constructor & Destructor Documentation

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

Member Function Documentation

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

References full_to_sub_, and is_working_res_.

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

References full_to_sub_.

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

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

References sub_to_full().

Referenced by set_full_to_sub().

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

References full_to_sub_.

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

References gap_size_.

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

References Is_internal_.

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

References is_moving_res_.

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

References sequence_, and working_res_list_.

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

References Is_prepend_.

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

References is_working_res_.

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

References moving_pos_.

Referenced by set_moving_pos().

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

References partition_definition_.

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

References sequence_.

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

References chain_boundaries_.

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

References gap_size_.

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

References Is_internal_.

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

References is_moving_res_.

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

References Is_prepend_.

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

References is_working_res_.

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

References moving_pos(), and moving_pos_.

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

References partition_definition_.

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

References sequence_.

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

References working_bridge_res_.

void protocols::swa::StepWiseJobParameters::set_working_calc_rms_res ( utility::vector1< core::Size > const &  working_calc_rms_res)
void protocols::swa::StepWiseJobParameters::set_working_fixed_res ( utility::vector1< core::Size > const &  working_fixed_res)
void protocols::swa::StepWiseJobParameters::set_working_moving_res_list ( utility::vector1< core::Size > const &  setting)
void protocols::swa::StepWiseJobParameters::set_working_moving_suite_list ( utility::vector1< core::Size > const &  setting)
void protocols::swa::StepWiseJobParameters::set_working_native_pose ( core::pose::PoseOP pose)

References working_native_pose_.

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

References working_res_list_.

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

References working_sequence_.

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

References sub_to_full_.

Referenced by create_sub_to_full_map().

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

References working_bridge_res_.

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

References working_fixed_res_.

Referenced by set_working_fixed_res().

utility::vector1< core::Size > const & protocols::swa::StepWiseJobParameters::working_moving_res_list ( ) const
utility::vector1< core::Size > const & protocols::swa::StepWiseJobParameters::working_moving_suite_list ( ) const
core::pose::PoseCOP protocols::swa::StepWiseJobParameters::working_native_pose ( ) const

References working_native_pose_.

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

References working_res_list_.

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

References working_sequence_.

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

Member Data Documentation

utility::vector1< std::pair< core::Size, core::Size > > protocols::swa::StepWiseJobParameters::chain_boundaries_
private
Size protocols::swa::StepWiseJobParameters::first_chain_break_res_
private
std::map< core::Size, core::Size > protocols::swa::StepWiseJobParameters::full_to_sub_
private
Size protocols::swa::StepWiseJobParameters::gap_size_
private

Referenced by gap_size(), and set_gap_size().

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

Referenced by Is_internal(), and set_Is_internal().

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

Referenced by is_moving_res(), and set_is_moving_res().

bool protocols::swa::StepWiseJobParameters::Is_prepend_
private
ObjexxFCL::FArray1D< core::Size > protocols::swa::StepWiseJobParameters::is_working_res_
private
utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::moving_pos_
private

Referenced by moving_pos(), and set_moving_pos().

ObjexxFCL::FArray1D< bool > protocols::swa::StepWiseJobParameters::partition_definition_
private
std::string protocols::swa::StepWiseJobParameters::sequence_
private
std::map< core::Size, core::Size > protocols::swa::StepWiseJobParameters::sub_to_full_
private

Referenced by set_full_to_sub(), and sub_to_full().

Size protocols::swa::StepWiseJobParameters::which_chain_has_moving_res_
private
utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_bridge_res_
private
utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_calc_rms_res_
private
utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_fixed_res_
private
utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_moving_res_list_
private
utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_moving_suite_list_
private
core::pose::PoseOP protocols::swa::StepWiseJobParameters::working_native_pose_
private
utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_res_list_
private
std::string protocols::swa::StepWiseJobParameters::working_sequence_
private
utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_superimpose_res_
private
utility::vector1< core::Size > protocols::swa::StepWiseJobParameters::working_terminal_res_
private

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