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Public Member Functions | Private Attributes | List of all members
protocols::loop_grower::LoopPartialSolution Class Reference

#include <LoopGrower.hh>

Public Member Functions

 LoopPartialSolution (core::pose::Pose const &pose, int reslow, int reshigh, core::Real score)
 
 LoopPartialSolution ()
 
void store_coordinates (core::pose::Pose const &pose, int reslow, int reshigh, core::Size lower_fasta)
 
void set_centerofmass ()
 
void set_coordinates (core::pose::Pose &pose)
 
void store_sheetpositions (core::pose::Pose &pose, core::Size rangelo, core::Size rangehi, core::Size jumpid, core::Size basres)
 
void write_beam_lps (std::ostream &lpsfile)
 
void write_beam (std::ostream &outbeam)
 
void apply (core::pose::Pose &pose, int range1lo, int range1hi, int range2lo, int range2hi)
 
void apply_sheets (core::pose::Pose &pose)
 
void add_sheets (core::pose::Pose &pose, core::Size takeoffres, core::Size totalres)
 
void set_rms (core::Real RMS)
 
void set_gdt (core::Real GDT)
 
void set_bonus_score (core::Real bonus)
 
core::Real get_bonus_score () const
 
core::Real get_rms () const
 
core::Real get_gdt () const
 
void apply (core::pose::Pose &pose, int range1lo, int range1hi)
 
void set_id (std::string id)
 
std::string get_id ()
 
core::Real size ()
 
void push_back_restorsions (ResTorsions restorsions)
 
void push_back_backbone (utility::vector1< core::Vector > backbone)
 
void push_back_sheet (SheetPositions sheet)
 
void set_positions (utility::vector1< numeric::xyzVector< core::Real > > positions)
 
void set_ids (utility::vector1< core::id::AtomID > ids)
 
void set_score (core::Real score)
 
void set_history (utility::vector1< std::pair< core::Size, core::Size > > history, std::pair< core::Size, core::Size > newfrag)
 
void set_history (utility::vector1< std::pair< core::Size, core::Size > > history)
 
utility::vector1< std::pair
< core::Size, core::Size > > 
get_history ()
 
utility::vector1< core::Vectorget_calphas () const
 
utility::vector1
< utility::vector1
< core::Vector > > 
get_backbone () const
 
core::Real get_score () const
 
core::Real partialrms (const LoopPartialSolution &, int fragmelt, int total_lower, bool takeoffonly, int rmswindow) const
 
core::Real max_calpha_distance (const LoopPartialSolution &, core::Size fragmelt, core::Size total_lower, bool takeoffonly, bool full_loop, bool lower) const
 
bool operator< (const LoopPartialSolution &lps1) const
 

Private Attributes

utility::vector1< ResTorsionsresidues_
 
utility::vector1< SheetPositionssheets_
 
utility::vector1< core::Vectorcalphas_
 
utility::vector1
< core::id::AtomID
ids_
 
utility::vector1
< numeric::xyzVector
< core::Real > > 
positions_
 
utility::vector1
< utility::vector1
< core::Vector > > 
backbones_
 
utility::vector1< std::pair
< core::Size, core::Size > > 
fragmenthistory_
 
numeric::xyzVector< core::Realcenterofmass_
 
core::Real score_
 
core::Real bonus_score_ = 0
 
core::Real RMS_ = 0
 
core::Real GDT_ = 0
 
std::string id_
 

Constructor & Destructor Documentation

protocols::loop_grower::LoopPartialSolution::LoopPartialSolution ( core::pose::Pose const &  pose,
int  reslow,
int  reshigh,
core::Real  score 
)
inline
protocols::loop_grower::LoopPartialSolution::LoopPartialSolution ( )
inline

Member Function Documentation

void protocols::loop_grower::LoopPartialSolution::add_sheets ( core::pose::Pose pose,
core::Size  takeoffres,
core::Size  totalres 
)
void protocols::loop_grower::LoopPartialSolution::apply ( core::pose::Pose pose,
int  range1lo,
int  range1hi,
int  range2lo,
int  range2hi 
)
inline
void protocols::loop_grower::LoopPartialSolution::apply ( core::pose::Pose pose,
int  range1lo,
int  range1hi 
)
inline

References apply().

void protocols::loop_grower::LoopPartialSolution::apply_sheets ( core::pose::Pose pose)
utility::vector1< utility::vector1< core::Vector > > protocols::loop_grower::LoopPartialSolution::get_backbone ( ) const
inline

References backbones_.

Referenced by max_calpha_distance(), and partialrms().

core::Real protocols::loop_grower::LoopPartialSolution::get_bonus_score ( ) const
inline
utility::vector1< core::Vector > protocols::loop_grower::LoopPartialSolution::get_calphas ( ) const
inline

References calphas_.

Referenced by max_calpha_distance(), and partialrms().

core::Real protocols::loop_grower::LoopPartialSolution::get_gdt ( ) const
inline
utility::vector1< std::pair<core::Size,core::Size> > protocols::loop_grower::LoopPartialSolution::get_history ( )
inline
std::string protocols::loop_grower::LoopPartialSolution::get_id ( )
inline
core::Real protocols::loop_grower::LoopPartialSolution::get_rms ( ) const
inline
core::Real protocols::loop_grower::LoopPartialSolution::get_score ( ) const
inline
Real protocols::loop_grower::LoopPartialSolution::max_calpha_distance ( const LoopPartialSolution newlps,
core::Size  fragmelt,
core::Size  total_lower,
bool  takeoffonly,
bool  full_loop,
bool  lower 
) const
bool protocols::loop_grower::LoopPartialSolution::operator< ( const LoopPartialSolution lps1) const
inline

References score_.

Real protocols::loop_grower::LoopPartialSolution::partialrms ( const LoopPartialSolution newlps,
int  fragmelt,
int  total_lower,
bool  takeoffonly,
int  rmswindow 
) const
void protocols::loop_grower::LoopPartialSolution::push_back_backbone ( utility::vector1< core::Vector backbone)
inline
void protocols::loop_grower::LoopPartialSolution::push_back_restorsions ( ResTorsions  restorsions)
inline
void protocols::loop_grower::LoopPartialSolution::push_back_sheet ( SheetPositions  sheet)
inline
void protocols::loop_grower::LoopPartialSolution::set_bonus_score ( core::Real  bonus)
inline
void protocols::loop_grower::LoopPartialSolution::set_centerofmass ( )

Referenced by LoopPartialSolution().

void protocols::loop_grower::LoopPartialSolution::set_coordinates ( core::pose::Pose pose)
inline
void protocols::loop_grower::LoopPartialSolution::set_gdt ( core::Real  GDT)
inline
void protocols::loop_grower::LoopPartialSolution::set_history ( utility::vector1< std::pair< core::Size, core::Size > >  history,
std::pair< core::Size, core::Size newfrag 
)
inline
void protocols::loop_grower::LoopPartialSolution::set_history ( utility::vector1< std::pair< core::Size, core::Size > >  history)
inline

References fragmenthistory_.

void protocols::loop_grower::LoopPartialSolution::set_id ( std::string  id)
inline
void protocols::loop_grower::LoopPartialSolution::set_ids ( utility::vector1< core::id::AtomID ids)
inline
void protocols::loop_grower::LoopPartialSolution::set_positions ( utility::vector1< numeric::xyzVector< core::Real > >  positions)
inline
void protocols::loop_grower::LoopPartialSolution::set_rms ( core::Real  RMS)
inline
void protocols::loop_grower::LoopPartialSolution::set_score ( core::Real  score)
inline
core::Real protocols::loop_grower::LoopPartialSolution::size ( )
inline
void protocols::loop_grower::LoopPartialSolution::store_coordinates ( core::pose::Pose const &  pose,
int  reslow,
int  reshigh,
core::Size  lower_fasta 
)
inline
void protocols::loop_grower::LoopPartialSolution::store_sheetpositions ( core::pose::Pose pose,
core::Size  rangelo,
core::Size  rangehi,
core::Size  jumpid,
core::Size  basres 
)
inline
void protocols::loop_grower::LoopPartialSolution::write_beam ( std::ostream &  outbeam)
void protocols::loop_grower::LoopPartialSolution::write_beam_lps ( std::ostream &  lpsfile)

Member Data Documentation

utility::vector1< utility::vector1< core::Vector > > protocols::loop_grower::LoopPartialSolution::backbones_
private
core::Real protocols::loop_grower::LoopPartialSolution::bonus_score_ = 0
private
utility::vector1< core::Vector > protocols::loop_grower::LoopPartialSolution::calphas_
private
numeric::xyzVector<core::Real> protocols::loop_grower::LoopPartialSolution::centerofmass_
private
utility::vector1< std::pair<core::Size,core::Size> > protocols::loop_grower::LoopPartialSolution::fragmenthistory_
private

Referenced by get_history(), and set_history().

core::Real protocols::loop_grower::LoopPartialSolution::GDT_ = 0
private

Referenced by get_gdt(), and set_gdt().

std::string protocols::loop_grower::LoopPartialSolution::id_
private

Referenced by get_id(), and set_id().

utility::vector1< core::id::AtomID > protocols::loop_grower::LoopPartialSolution::ids_
private
utility::vector1< numeric::xyzVector<core::Real> > protocols::loop_grower::LoopPartialSolution::positions_
private
utility::vector1< ResTorsions > protocols::loop_grower::LoopPartialSolution::residues_
private
core::Real protocols::loop_grower::LoopPartialSolution::RMS_ = 0
private

Referenced by get_rms(), and set_rms().

core::Real protocols::loop_grower::LoopPartialSolution::score_
private
utility::vector1< SheetPositions > protocols::loop_grower::LoopPartialSolution::sheets_
private

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