protocols::stepwise::sampling::protein::StepWiseProteinJobParameters Class Reference

#include <StepWiseProteinJobParameters.hh>

Public Member Functions
	StepWiseProteinJobParameters ()
virtual	~StepWiseProteinJobParameters ()
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::PoseCOP 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::PoseCOP	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_

Constructor & Destructor Documentation

protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::StepWiseProteinJobParameters

(

)

protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::~StepWiseProteinJobParameters ( )

virtual

Member Function Documentation

Size protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::actually_moving_res

(

)

const

References is_prepend_, and working_moving_suite_list_.

utility::vector1< Size > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::apply_full_to_sub_mapping

(

utility::vector1< Size > const &

res_vector

)

References full_to_sub_, and is_working_res_.

Size protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::apply_full_to_sub_mapping

(

Size const

res

)

const

References full_to_sub_.

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

(

)

const

References chain_boundaries_.

std::map< core::Size, core::Size > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::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::stepwise::sampling::protein::StepWiseProteinJobParameters::first_chain_break_res

(

)

const

References first_chain_break_res_.

std::map< core::Size, core::Size > & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::full_to_sub

(

)

References full_to_sub_.

Size const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::gap_size

(

)

const

References gap_size_.

bool const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::is_internal

(

)

const

References is_internal_.

ObjexxFCL::FArray1D< Size > const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::is_moving_res

(

)

const

References is_moving_res_.

utility::vector1< bool > const protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::is_pre_proline

(

)

const

References sequence_, and working_res_list_.

bool const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::is_prepend

(

)

const

References is_prepend_.

ObjexxFCL::FArray1D< Size > const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::is_working_res

(

)

const

References is_working_res_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::moving_pos

(

)

const

References moving_pos_.

Referenced by set_moving_pos().

ObjexxFCL::FArray1D< bool > const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::partition_definition

(

)

const

References partition_definition_.

std::string const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::sequence

(

)

const

References sequence_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_chain_boundaries

(

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

setting

)

References chain_boundaries_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_first_chain_break_res

(

Size const &

setting

)

References first_chain_break_res_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_full_to_sub

(

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

setting

)

References create_sub_to_full_map(), full_to_sub_, and sub_to_full_.

Referenced by protocols::stepwise::sampling::protein::setup_job_parameters_for_protein_swa().

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_gap_size

(

Size const &

setting

)

References gap_size_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_is_internal

(

bool const &

setting

)

References is_internal_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_is_moving_res

(

ObjexxFCL::FArray1D< core::Size > const &

setting

)

References is_moving_res_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_is_prepend

(

bool const &

setting

)

References is_prepend_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_is_working_res

(

ObjexxFCL::FArray1D< core::Size > const &

setting

)

References is_working_res_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_moving_pos

(

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

moving_pos

)

References moving_pos(), and moving_pos_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_partition_definition

(

ObjexxFCL::FArray1D< bool > const &

setting

)

References partition_definition_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_sequence

(

std::string const &

setting

)

References sequence_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_which_chain_has_moving_res

(

Size const &

setting

)

References which_chain_has_moving_res_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_working_bridge_res

(

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

working_bridge_res

)

References working_bridge_res_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_working_calc_rms_res

(

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

working_calc_rms_res

)

References working_calc_rms_res(), and working_calc_rms_res_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_working_fixed_res

(

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

working_fixed_res

)

References working_fixed_res(), and working_fixed_res_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_working_moving_res_list

(

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

setting

)

References working_moving_res_list_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_working_moving_suite_list

(

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

setting

)

References working_moving_suite_list_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_working_native_pose

(

core::pose::PoseCOP

pose

)

References working_native_pose_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_working_res_list

(

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

setting

)

References working_res_list_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_working_sequence

(

std::string const &

setting

)

References working_sequence_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_working_superimpose_res

(

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

working_superimpose_res

)

References working_superimpose_res(), and working_superimpose_res_.

void protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::set_working_terminal_res

(

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

working_terminal_res

)

References working_terminal_res(), and working_terminal_res_.

std::map< core::Size, core::Size > & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::sub_to_full

(

)

References sub_to_full_.

Referenced by create_sub_to_full_map().

Size const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::which_chain_has_moving_res

(

)

const

References which_chain_has_moving_res_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_bridge_res

(

)

const

References working_bridge_res_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_calc_rms_res

(

)

const

References working_calc_rms_res_.

Referenced by set_working_calc_rms_res().

utility::vector1< core::Size > const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_fixed_res

(

)

const

References working_fixed_res_.

Referenced by set_working_fixed_res().

utility::vector1< core::Size > const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_moving_res_list

(

)

const

References working_moving_res_list_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_moving_suite_list

(

)

const

References working_moving_suite_list_.

core::pose::PoseCOP protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_native_pose

(

)

const

References working_native_pose_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_res_list

(

)

const

References working_res_list_.

std::string const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_sequence

(

)

const

References working_sequence_.

utility::vector1< core::Size > const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_superimpose_res

(

)

const

References working_superimpose_res_.

Referenced by set_working_superimpose_res().

utility::vector1< core::Size > const & protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_terminal_res

(

)

const

References working_terminal_res_.

Referenced by set_working_terminal_res().

Member Data Documentation

utility::vector1< std::pair< core::Size, core::Size > > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::chain_boundaries_

private

Referenced by chain_boundaries(), and set_chain_boundaries().

Size protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::first_chain_break_res_

private

Referenced by first_chain_break_res(), and set_first_chain_break_res().

std::map< core::Size, core::Size > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::full_to_sub_

private

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

Size protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::gap_size_

private

Referenced by gap_size(), and set_gap_size().

bool protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::is_internal_

private

Referenced by is_internal(), and set_is_internal().

ObjexxFCL::FArray1D< core::Size > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::is_moving_res_

private

Referenced by is_moving_res(), and set_is_moving_res().

bool protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::is_prepend_

private

Referenced by actually_moving_res(), is_prepend(), and set_is_prepend().

ObjexxFCL::FArray1D< core::Size > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::is_working_res_

private

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

utility::vector1< core::Size > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::moving_pos_

private

Referenced by moving_pos(), and set_moving_pos().

ObjexxFCL::FArray1D< bool > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::partition_definition_

private

Referenced by partition_definition(), and set_partition_definition().

std::string protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::sequence_

private

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

std::map< core::Size, core::Size > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::sub_to_full_

private

Referenced by set_full_to_sub(), and sub_to_full().

Size protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::which_chain_has_moving_res_

private

Referenced by set_which_chain_has_moving_res(), and which_chain_has_moving_res().

utility::vector1< core::Size > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_bridge_res_

private

Referenced by set_working_bridge_res(), and working_bridge_res().

utility::vector1< core::Size > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_calc_rms_res_

private

Referenced by set_working_calc_rms_res(), and working_calc_rms_res().

utility::vector1< core::Size > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_fixed_res_

private

Referenced by set_working_fixed_res(), and working_fixed_res().

utility::vector1< core::Size > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_moving_res_list_

private

Referenced by set_working_moving_res_list(), and working_moving_res_list().

utility::vector1< core::Size > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_moving_suite_list_

private

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

core::pose::PoseCOP protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_native_pose_

private

Referenced by set_working_native_pose(), and working_native_pose().

utility::vector1< core::Size > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_res_list_

private

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

std::string protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_sequence_

private

Referenced by set_working_sequence(), and working_sequence().

utility::vector1< core::Size > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_superimpose_res_

private

Referenced by set_working_superimpose_res(), and working_superimpose_res().

utility::vector1< core::Size > protocols::stepwise::sampling::protein::StepWiseProteinJobParameters::working_terminal_res_

private

Referenced by set_working_terminal_res(), and working_terminal_res().

---

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

• symlinks/rosetta/src/protocols/stepwise/sampling/protein/StepWiseProteinJobParameters.hh
• symlinks/rosetta/src/protocols/stepwise/sampling/protein/StepWiseProteinJobParameters.cc