protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters Class Reference

#include <StepWiseBasicWorkingParameters.hh>

Inheritance diagram for protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters:

Public Member Functions
	StepWiseBasicWorkingParameters ()
	~StepWiseBasicWorkingParameters () override
std::string const &	sequence () const
void	set_sequence (std::string const &setting)
std::string const &	full_sequence () const
void	set_full_sequence (std::string const &setting)
std::string const &	working_sequence () const
core::Size const &	moving_res () const
void	set_moving_res (core::Size const &setting)
core::Size const &	working_moving_res () const
core::Size const &	working_moving_suite () const
core::Size	actually_moving_res () const
utility::vector1< core::Size >	working_res_list () const
utility::vector1< core::Size > const &	working_moving_res_list () const
void	set_working_moving_res_list (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size > const &	working_moving_suite_list () const
utility::vector1< core::Size > const &	is_working_res () const
void	set_is_working_res (utility::vector1< core::Size > const &setting)
std::map< core::Size, core::Size > &	full_to_sub ()
void	set_full_to_sub (std::map< core::Size, core::Size > const &setting)
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::Size	full_to_sub (core::Size const i) const
core::Size	sub_to_full (core::Size const i) const
utility::vector1< core::Size >	apply_full_to_sub_mapping (utility::vector1< core::Size > const &res_vector)
core::Size	apply_full_to_sub_mapping (core::Size const res) const
std::map< core::Size, core::Size >	create_sub_to_full_map (std::map< core::Size, core::Size > const &full_to_sub) const
utility::vector1< core::Size > const &	cutpoint_closed_list () const
void	set_cutpoint_closed_list (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size > const &	cutpoint_open_list () const
void	set_cutpoint_open_list (utility::vector1< core::Size > const &setting)
utility::vector1< std::pair < core::Size, core::Size > > const &	chain_boundaries () const
void	set_chain_boundaries (utility::vector1< std::pair< core::Size, core::Size > > const &setting)
ObjexxFCL::FArray1D< bool > const &	partition_definition () const
void	set_partition_definition (ObjexxFCL::FArray1D< bool > const &setting)
void	set_partition_definition (utility::vector1< core::Size > const &partition_definition_vector)
bool const &	is_prepend () const
void	set_is_prepend (bool const &setting)
bool const &	is_internal () const
void	set_is_internal (bool const &setting)
core::Size const &	gap_size () const
void	set_gap_size (core::Size const &setting)
utility::vector1< core::Size > const &	fixed_res () const
void	set_fixed_res (utility::vector1< core::Size > const &fixed_res)
utility::vector1< core::Size > const &	working_fixed_res () const
void	set_working_fixed_res (utility::vector1< core::Size > const &working_fixed_res)
utility::vector1< core::Size > const &	calc_rms_res () const
void	set_calc_rms_res (utility::vector1< core::Size > const &calc_rms_res)
utility::vector1< core::Size > const &	working_calc_rms_res () const
void	set_working_calc_rms_res (utility::vector1< core::Size > const &working_calc_rms_res)
utility::vector1< core::Size > const &	working_moving_partition_res () const
void	set_working_moving_partition_res (utility::vector1< core::Size > const &working_moving_partition_res)
core::pose::PoseCOP	working_native_pose () const
void	set_working_native_pose (core::pose::PoseOP &pose)
void	set_working_native_pose (core::pose::PoseCOP pose)

Protected Attributes
std::string	full_sequence_
std::string	working_sequence_
core::Size	moving_res_
core::Size	working_moving_res_
core::Size	working_moving_suite_
utility::vector1< core::Size >	working_moving_res_list_
utility::vector1< core::Size >	working_moving_suite_list_
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_
utility::vector1< core::Size >	cutpoint_closed_list_
utility::vector1< core::Size >	cutpoint_open_list_
utility::vector1< std::pair < core::Size, core::Size > >	chain_boundaries_
ObjexxFCL::FArray1D< bool >	partition_definition_
bool	is_prepend_
bool	is_internal_
core::Size	gap_size_
core::pose::PoseCOP	working_native_pose_
utility::vector1< core::Size >	fixed_res_
utility::vector1< core::Size >	working_fixed_res_
utility::vector1< core::Size >	calc_rms_res_
utility::vector1< core::Size >	working_calc_rms_res_
utility::vector1< core::Size >	working_moving_partition_res_

Private Member Functions
void	update_working_moving_suite ()
void	update_working_sequence ()

Constructor & Destructor Documentation

protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::StepWiseBasicWorkingParameters

(

)

protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::~StepWiseBasicWorkingParameters ( )

overridedefault

Member Function Documentation

Size protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::actually_moving_res

(

)

const

References is_prepend_, and working_moving_suite_list_.

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::apply_full_to_sub_mapping

(

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

res_vector

)

References full_to_sub_, and is_working_res_.

Referenced by protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_block_stack_above_res(), protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_block_stack_below_res(), protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_force_anti_chi_res_list(), protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_force_north_sugar_list(), protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_force_south_sugar_list(), protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_force_syn_chi_res_list(), protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_global_sample_res_list(), protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_protonated_H1_adenosine_list(), and protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::set_terminal_res().

Size protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::apply_full_to_sub_mapping

(

core::Size const

res

)

const

References full_to_sub_.

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::calc_rms_res ( ) const

inline

References calc_rms_res_.

Referenced by set_calc_rms_res().

utility::vector1< std::pair< core::Size, core::Size > > const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::chain_boundaries ( ) const

inline

References chain_boundaries_.

std::map< core::Size, core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::const_full_to_sub ( ) const

inline

References full_to_sub_.

std::map< core::Size, core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::const_sub_to_full ( ) const

inline

References sub_to_full_.

std::map< core::Size, core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::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().

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::cutpoint_closed_list ( ) const

inline

References cutpoint_closed_list_.

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::cutpoint_open_list ( ) const

inline

References cutpoint_open_list_.

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::fixed_res ( ) const

inline

References fixed_res_.

Referenced by set_fixed_res().

std::string const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::full_sequence ( ) const

inline

References full_sequence_.

Referenced by protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::is_pre_proline(), and sequence().

std::map< core::Size, core::Size >& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::full_to_sub ( )

inline

References full_to_sub_.

core::Size protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::full_to_sub ( core::Size const  i ) const

inline

References full_to_sub_.

core::Size const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::gap_size ( ) const

inline

References gap_size_.

bool const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::is_internal ( ) const

inline

References is_internal_.

bool const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::is_prepend ( ) const

inline

References is_prepend_.

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::is_working_res ( ) const

inline

References is_working_res_.

core::Size const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::moving_res ( ) const

inline

References moving_res_.

ObjexxFCL::FArray1D< bool > const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::partition_definition ( ) const

inline

References partition_definition_.

std::string const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::sequence ( ) const

inline

References full_sequence().

Referenced by protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::is_pre_proline().

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_calc_rms_res ( utility::vector1< core::Size > const &  calc_rms_res )

inline

References calc_rms_res(), and calc_rms_res_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_chain_boundaries ( utility::vector1< std::pair< core::Size, core::Size > > const &  setting )

inline

References chain_boundaries_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_cutpoint_closed_list ( utility::vector1< core::Size > const &  setting )

inline

References cutpoint_closed_list_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_cutpoint_open_list ( utility::vector1< core::Size > const &  setting )

inline

References cutpoint_open_list_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_fixed_res ( utility::vector1< core::Size > const &  fixed_res )

inline

References fixed_res(), and fixed_res_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_full_sequence ( std::string const &  setting )

inline

References full_sequence_, and update_working_sequence().

Referenced by set_sequence().

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::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_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_gap_size ( core::Size const &  setting )

inline

References gap_size_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_is_internal ( bool const &  setting )

inline

References is_internal_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_is_prepend ( bool const &  setting )

inline

References is_prepend_, and update_working_moving_suite().

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_is_working_res ( utility::vector1< core::Size > const &  setting )

inline

References is_working_res_, and update_working_sequence().

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_moving_res ( core::Size const &  setting )

inline

References moving_res_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_partition_definition ( ObjexxFCL::FArray1D< bool > const &  setting )

inline

References partition_definition_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_partition_definition

(

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

partition_definition_vector

)

References partition_definition_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_sequence ( std::string const &  setting )

inline

References set_full_sequence().

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_working_calc_rms_res ( utility::vector1< core::Size > const &  working_calc_rms_res )

inline

References working_calc_rms_res(), and working_calc_rms_res_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_working_fixed_res ( utility::vector1< core::Size > const &  working_fixed_res )

inline

References working_fixed_res(), and working_fixed_res_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_working_moving_partition_res ( utility::vector1< core::Size > const &  working_moving_partition_res )

inline

References working_moving_partition_res(), and working_moving_partition_res_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_working_moving_res_list

(

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

setting

)

References update_working_moving_suite(), working_moving_res_, and working_moving_res_list_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_working_native_pose

(

core::pose::PoseOP &

pose

)

References working_native_pose_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_working_native_pose

(

core::pose::PoseCOP

pose

)

References working_native_pose_.

std::map< core::Size, core::Size >& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::sub_to_full ( )

inline

References sub_to_full_.

Referenced by create_sub_to_full_map().

core::Size protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::sub_to_full ( core::Size const  i ) const

inline

References sub_to_full_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::update_working_moving_suite ( )

private

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::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::update_working_sequence ( )

private

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::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_calc_rms_res ( ) const

inline

References working_calc_rms_res_.

Referenced by set_working_calc_rms_res().

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_fixed_res ( ) const

inline

References working_fixed_res_.

Referenced by set_working_fixed_res().

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_partition_res ( ) const

inline

References working_moving_partition_res_.

Referenced by set_working_moving_partition_res().

core::Size const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_res ( ) const

inline

References working_moving_res_.

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_res_list ( ) const

inline

References working_moving_res_list_.

core::Size const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_suite ( ) const

inline

References working_moving_suite_.

utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_suite_list ( ) const

inline

References working_moving_suite_list_.

core::pose::PoseCOP protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_native_pose

(

)

const

References working_native_pose_.

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_res_list

(

)

const

References sub_to_full_.

Referenced by protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::is_pre_proline().

std::string const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_sequence ( ) const

inline

References working_sequence_.

Member Data Documentation

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::calc_rms_res_

protected

Referenced by calc_rms_res(), and set_calc_rms_res().

utility::vector1< std::pair< core::Size, core::Size > > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::chain_boundaries_

protected

Referenced by chain_boundaries(), and set_chain_boundaries().

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::cutpoint_closed_list_

protected

Referenced by cutpoint_closed_list(), and set_cutpoint_closed_list().

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::cutpoint_open_list_

protected

Referenced by cutpoint_open_list(), protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::gap_size_to_anchor(), and set_cutpoint_open_list().

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::fixed_res_

protected

Referenced by fixed_res(), and set_fixed_res().

std::string protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::full_sequence_

protected

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

std::map< core::Size, core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::full_to_sub_

protected

Referenced by apply_full_to_sub_mapping(), const_full_to_sub(), full_to_sub(), set_full_to_sub(), and protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_floating_base_anchor_res().

core::Size protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::gap_size_

protected

Referenced by gap_size(), and set_gap_size().

bool protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::is_internal_

protected

Referenced by is_internal(), and set_is_internal().

bool protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::is_prepend_

protected

Referenced by actually_moving_res(), is_prepend(), set_is_prepend(), update_working_moving_suite(), and protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_reference_res().

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::is_working_res_

protected

Referenced by apply_full_to_sub_mapping(), is_working_res(), set_is_working_res(), update_working_sequence(), and protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_floating_base_anchor_res().

core::Size protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::moving_res_

protected

Referenced by protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::gap_size_to_anchor(), moving_res(), and set_moving_res().

ObjexxFCL::FArray1D< bool > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::partition_definition_

protected

Referenced by partition_definition(), and set_partition_definition().

std::map< core::Size, core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::sub_to_full_

protected

Referenced by const_sub_to_full(), protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::gap_size_to_anchor(), set_full_to_sub(), sub_to_full(), and working_res_list().

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_calc_rms_res_

protected

Referenced by set_working_calc_rms_res(), and working_calc_rms_res().

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_fixed_res_

protected

Referenced by set_working_fixed_res(), and working_fixed_res().

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_partition_res_

protected

Referenced by set_working_moving_partition_res(), and working_moving_partition_res().

core::Size protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_res_

protected

Referenced by protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::actually_moving_res(), set_working_moving_res_list(), update_working_moving_suite(), working_moving_res(), and protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_reference_res().

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_res_list_

protected

Referenced by set_working_moving_res_list(), update_working_moving_suite(), working_moving_res_list(), and protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::working_reference_res().

core::Size protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_suite_

protected

Referenced by update_working_moving_suite(), and working_moving_suite().

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_suite_list_

protected

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

core::pose::PoseCOP protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_native_pose_

protected

Referenced by set_working_native_pose(), and working_native_pose().

std::string protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_sequence_

protected

Referenced by update_working_sequence(), and working_sequence().

---

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

• src/protocols/stepwise/modeler/working_parameters/StepWiseBasicWorkingParameters.hh
• src/protocols/stepwise/modeler/working_parameters/StepWiseBasicWorkingParameters.cc