Rosetta Protocols  2014.35
Public Member Functions | Protected Attributes | Private Member Functions | List of all members
protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters Class Reference

#include <StepWiseBasicWorkingParameters.hh>

Public Member Functions

 StepWiseBasicWorkingParameters ()
 
 ~StepWiseBasicWorkingParameters ()
 
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
 
Size const & moving_res () const
 
void set_moving_res (Size const &setting)
 
Size const & working_moving_res () const
 
Size const & working_moving_suite () const
 
Size actually_moving_res () const
 
utility::vector1< core::Sizeworking_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 (Size const i) const
 
utility::vector1< Sizeapply_full_to_sub_mapping (utility::vector1< Size > const &res_vector)
 
Size apply_full_to_sub_mapping (Size const res) const
 
std::map< core::Size, core::Sizecreate_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< 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)
 
Size const & gap_size () const
 
void set_gap_size (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 & 
terminal_res () const
 
void set_terminal_res (utility::vector1< core::Size > const &terminal_res)
 
utility::vector1< core::Size >
const & 
working_terminal_res () const
 
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_
 
Size moving_res_
 
Size working_moving_res_
 
Size working_moving_suite_
 
utility::vector1< core::Sizeworking_moving_res_list_
 
utility::vector1< core::Sizeworking_moving_suite_list_
 
utility::vector1< core::Sizeis_working_res_
 
std::map< core::Size, core::Sizefull_to_sub_
 
std::map< core::Size, core::Sizesub_to_full_
 
utility::vector1< core::Sizecutpoint_closed_list_
 
utility::vector1< core::Sizecutpoint_open_list_
 
utility::vector1< std::pair
< core::Size, core::Size > > 
chain_boundaries_
 
ObjexxFCL::FArray1D< boolpartition_definition_
 
bool is_prepend_
 
bool is_internal_
 
Size gap_size_
 
core::pose::PoseCOP working_native_pose_
 
utility::vector1< core::Sizefixed_res_
 
utility::vector1< core::Sizeworking_fixed_res_
 
utility::vector1< core::Sizecalc_rms_res_
 
utility::vector1< core::Sizeworking_calc_rms_res_
 
utility::vector1< core::Sizeterminal_res_
 
utility::vector1< core::Sizeworking_terminal_res_
 
utility::vector1< core::Sizeworking_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 ( )

Member Function Documentation

Size protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::actually_moving_res ( ) const
utility::vector1< Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::apply_full_to_sub_mapping ( utility::vector1< Size > const &  res_vector)
Size protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::apply_full_to_sub_mapping ( 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
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 ( Size const  i) const
inline

References full_to_sub_.

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_.

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
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)
void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_gap_size ( 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
void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_is_working_res ( utility::vector1< core::Size > const &  setting)
inline
void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_moving_res ( 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< 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_terminal_res ( utility::vector1< core::Size > const &  terminal_res)
inline

References terminal_res(), and terminal_res_.

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_working_calc_rms_res ( utility::vector1< core::Size > const &  working_calc_rms_res)
inline
void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_working_fixed_res ( utility::vector1< core::Size > const &  working_fixed_res)
inline
void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_working_moving_partition_res ( utility::vector1< core::Size > const &  working_moving_partition_res)
inline
void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::set_working_moving_res_list ( utility::vector1< core::Size > const &  setting)
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().

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

References terminal_res_.

Referenced by set_terminal_res().

void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::update_working_moving_suite ( )
private
void protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::update_working_sequence ( )
private
utility::vector1< core::Size > const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_calc_rms_res ( ) const
inline
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
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
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
core::pose::PoseCOP protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_native_pose ( ) const

References working_native_pose_.

utility::vector1< Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_res_list ( ) const
std::string const& protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_sequence ( ) const
inline

References working_sequence_.

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

References working_terminal_res_.

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
utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::cutpoint_closed_list_
protected
utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::cutpoint_open_list_
protected
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
std::map< core::Size, core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::full_to_sub_
protected
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
utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::is_working_res_
protected
Size protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::moving_res_
protected
ObjexxFCL::FArray1D< bool > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::partition_definition_
protected
std::map< core::Size, core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::sub_to_full_
protected
utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::terminal_res_
protected

Referenced by set_terminal_res(), and terminal_res().

utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_calc_rms_res_
protected
utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_fixed_res_
protected
utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_partition_res_
protected
Size protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_res_
protected
utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_res_list_
protected
Size protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_suite_
protected
utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_moving_suite_list_
protected
core::pose::PoseCOP protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_native_pose_
protected
std::string protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_sequence_
protected
utility::vector1< core::Size > protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters::working_terminal_res_
protected

Referenced by working_terminal_res().


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