Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::optimize_weights::PNatRotOptEPositionData Class Reference

#include <OptEData.hh>

Public Member Functions

 PNatRotOptEPositionData ()
 
virtual ~PNatRotOptEPositionData ()
 
virtual Real get_score (Multivec const &component_weights, Multivec const &vars, Multivec &dE_dvars, Size const num_energy_dofs, int const num_ref_dofs, int const num_total_dofs, EnergyMap const &fixed_terms, ScoreTypes const &score_list, ScoreTypes const &fixed_score_list) const
 
virtual void print_score (std::ostream &ostr, Multivec const &component_weights, Multivec const &vars, Multivec &dE_dvars, Size const num_energy_dofs, int const num_ref_dofs, int const num_total_dofs, EnergyMap const &fixed_terms, ScoreTypes const &score_list, ScoreTypes const &fixed_score_list) const
 
Real process_score (std::ostream &ostr, bool print, Multivec const &component_weights, Multivec const &vars, Multivec &dE_dvars, Size const num_energy_dofs, int const, int const, EnergyMap const &fixed_terms, ScoreTypes const &, ScoreTypes const &fixed_score_list) const
 
virtual void range (ScoreTypes const &free_score_list, ScoreTypes const &fixed_score_list, EnergyMap &lower_bound, EnergyMap &upper_bound) const
 Return the upper and lower bound on the unweighted components at this position if they are larger (or smaller) than the unweighted values already in the two input EnergyMaps. More...
 
virtual Size size () const
 
virtual OptEPositionDataType type () const
 
virtual void write_to_file (std::ofstream &outfile) const
 
virtual void read_from_file (std::ifstream &infile)
 
virtual void write_to_binary_file (std::ofstream &outfile) const
 
virtual void read_from_binary_file (std::ifstream &infile)
 
virtual Size memory_use () const
 
void set_native_rotamer_index (utility::vector1< Size > const &native_rotamer_index)
 
void set_native_rotamer_chi (utility::vector1< Real > const &native_chi)
 
void set_native_chi_periodicity (utility::vector1< Real > const &native_chi_periodicity)
 
bool count_rotamer_as_native (PNatRotOptERotamerDataOP rotamer) const
 
void set_rotamer_well_counts (utility::vector1< Size > const &rotamer_well_counts)
 
void add_rotamer_line_data (PNatRotOptERotamerDataOP rot_in)
 
PNatRotOptERotamerDataOPsdata ()
 
PNatRotOptERotamerDataOPs const & data () const
 
PNatRotOptERotamerDataOPs::const_iterator rotamer_data_begin () const
 
PNatRotOptERotamerDataOPs::const_iterator rotamer_data_end () const
 
core::chemical::AA aa () const
 
core::chemical::AAaa ()
 
Real phi () const
 
Real psi () const
 
Realphi ()
 
Realpsi ()
 
- Public Member Functions inherited from protocols::optimize_weights::OptEPositionData
 OptEPositionData ()
 
virtual ~OptEPositionData ()
 
void tag (std::string const &tag_in)
 
std::string const & tag () const
 

Private Member Functions

Size rotamer_index_2_well_id (utility::vector1< Size > const &rotamer_index) const
 
Size rotamer_index_2_well_id (utility::LexicographicalIterator const &lexiter) const
 
bool is_native_rotamer_well (utility::vector1< Size > const &rotamer_index) const
 
bool is_native_rotamer_well (utility::LexicographicalIterator const &lexiter) const
 

Private Attributes

utility::vector1< Sizenative_rotamer_index_
 
utility::vector1< Sizerotamer_well_counts_
 
int n_wells_
 
core::chemical::AA aa_
 
Real phi_
 
Real psi_
 
PNatRotOptERotamerDataOPs data_
 
utility::vector1< Realnative_chi_
 
utility::vector1< Realnative_chi_periodicity_
 

Additional Inherited Members

- Public Types inherited from protocols::optimize_weights::OptEPositionData
typedef core::Real Real
 
typedef core::Size Size
 
typedef
core::optimization::Multivec 
Multivec
 
typedef core::scoring::EnergyMap EnergyMap
 
typedef core::scoring::ScoreTypes ScoreTypes
 
- Protected Member Functions inherited from protocols::optimize_weights::OptEPositionData
void update_range (SingleStructureDataCOP structure, ScoreTypes const &free_score_list, ScoreTypes const &fixed_score_list, EnergyMap &lower_bound, EnergyMap &upper_bound) const
 Helper function for range(); updates lower/upper_bound as needed so that score_list scores from structure are included in the range. More...
 

Constructor & Destructor Documentation

protocols::optimize_weights::PNatRotOptEPositionData::PNatRotOptEPositionData ( )

Referenced by memory_use().

protocols::optimize_weights::PNatRotOptEPositionData::~PNatRotOptEPositionData ( )
virtual

Member Function Documentation

core::chemical::AA protocols::optimize_weights::PNatRotOptEPositionData::aa ( ) const

References aa_.

core::chemical::AA & protocols::optimize_weights::PNatRotOptEPositionData::aa ( )

References aa_.

void protocols::optimize_weights::PNatRotOptEPositionData::add_rotamer_line_data ( PNatRotOptERotamerDataOP  rot_in)

References data_.

bool protocols::optimize_weights::PNatRotOptEPositionData::count_rotamer_as_native ( PNatRotOptERotamerDataOP  rotamer) const
PNatRotOptERotamerDataOPs & protocols::optimize_weights::PNatRotOptEPositionData::data ( )

References data_.

PNatRotOptERotamerDataOPs const & protocols::optimize_weights::PNatRotOptEPositionData::data ( ) const

References data_.

Real protocols::optimize_weights::PNatRotOptEPositionData::get_score ( optimization::Multivec const &  component_weights,
optimization::Multivec const &  vars,
optimization::Multivec dE_dvars,
Size const  num_energy_dofs,
int const  num_ref_dofs,
int const  num_total_dofs,
EnergyMap const &  fixed_terms,
ScoreTypes const &  score_list,
ScoreTypes const &  fixed_score_list 
) const
virtual
Parameters
num_energy_dofsBasically, turn over all the private data from OptEMultiFunc

Implements protocols::optimize_weights::OptEPositionData.

References process_score(), and protocols::optimize_weights::TR.

bool protocols::optimize_weights::PNatRotOptEPositionData::is_native_rotamer_well ( utility::vector1< Size > const &  rotamer_index) const
private

References native_rotamer_index_.

Referenced by process_score().

bool protocols::optimize_weights::PNatRotOptEPositionData::is_native_rotamer_well ( utility::LexicographicalIterator const &  lexiter) const
private

References native_rotamer_index_.

Size protocols::optimize_weights::PNatRotOptEPositionData::memory_use ( ) const
virtual
Real protocols::optimize_weights::PNatRotOptEPositionData::phi ( ) const

References phi_.

Real & protocols::optimize_weights::PNatRotOptEPositionData::phi ( )

References phi_.

void protocols::optimize_weights::PNatRotOptEPositionData::print_score ( std::ostream &  ostr,
optimization::Multivec const &  component_weights,
optimization::Multivec const &  vars,
optimization::Multivec dE_dvars,
Size const  num_energy_dofs,
int const  num_ref_dofs,
int const  num_total_dofs,
EnergyMap const &  fixed_terms,
ScoreTypes const &  score_list,
ScoreTypes const &  fixed_score_list 
) const
virtual
Parameters
num_energy_dofsBasically, turn over all the private data from OptEMultiFunc

Implements protocols::optimize_weights::OptEPositionData.

References process_score().

Real protocols::optimize_weights::PNatRotOptEPositionData::process_score ( std::ostream &  ostr,
bool  print,
optimization::Multivec const &  component_weights,
optimization::Multivec const &  vars,
optimization::Multivec dE_dvars,
Size const  num_energy_dofs,
int const  ,
int const  ,
EnergyMap const &  fixed_terms,
ScoreTypes const &  score_list,
ScoreTypes const &  fixed_score_list 
) const
Real protocols::optimize_weights::PNatRotOptEPositionData::psi ( ) const

References psi_.

Real & protocols::optimize_weights::PNatRotOptEPositionData::psi ( )

References psi_.

void protocols::optimize_weights::PNatRotOptEPositionData::range ( ScoreTypes const &  free_score_list,
ScoreTypes const &  fixed_score_list,
EnergyMap lower_bound,
EnergyMap upper_bound 
) const
virtual

Return the upper and lower bound on the unweighted components at this position if they are larger (or smaller) than the unweighted values already in the two input EnergyMaps.

Implements protocols::optimize_weights::OptEPositionData.

References rotamer_data_begin(), and rotamer_data_end().

void protocols::optimize_weights::PNatRotOptEPositionData::read_from_binary_file ( std::ifstream &  infile)
virtual
void protocols::optimize_weights::PNatRotOptEPositionData::read_from_file ( std::ifstream &  infile)
virtual
PNatRotOptERotamerDataOPs::const_iterator protocols::optimize_weights::PNatRotOptEPositionData::rotamer_data_begin ( ) const

References data_.

Referenced by process_score(), and range().

PNatRotOptERotamerDataOPs::const_iterator protocols::optimize_weights::PNatRotOptEPositionData::rotamer_data_end ( ) const

References data_.

Referenced by process_score(), and range().

Size protocols::optimize_weights::PNatRotOptEPositionData::rotamer_index_2_well_id ( utility::vector1< Size > const &  rotamer_index) const
private

References rotamer_well_counts_.

Referenced by process_score().

Size protocols::optimize_weights::PNatRotOptEPositionData::rotamer_index_2_well_id ( utility::LexicographicalIterator const &  lexiter) const
private

References rotamer_well_counts_.

void protocols::optimize_weights::PNatRotOptEPositionData::set_native_chi_periodicity ( utility::vector1< Real > const &  native_chi_periodicity)
void protocols::optimize_weights::PNatRotOptEPositionData::set_native_rotamer_chi ( utility::vector1< Real > const &  native_chi)

References native_chi_.

void protocols::optimize_weights::PNatRotOptEPositionData::set_native_rotamer_index ( utility::vector1< Size > const &  native_rotamer_index)
void protocols::optimize_weights::PNatRotOptEPositionData::set_rotamer_well_counts ( utility::vector1< Size > const &  rotamer_well_counts)
Size protocols::optimize_weights::PNatRotOptEPositionData::size ( ) const
virtual
OptEPositionDataType protocols::optimize_weights::PNatRotOptEPositionData::type ( ) const
virtual
void protocols::optimize_weights::PNatRotOptEPositionData::write_to_binary_file ( std::ofstream &  outfile) const
virtual
void protocols::optimize_weights::PNatRotOptEPositionData::write_to_file ( std::ofstream &  outfile) const
virtual

Member Data Documentation

core::chemical::AA protocols::optimize_weights::PNatRotOptEPositionData::aa_
private

Referenced by aa(), and process_score().

PNatRotOptERotamerDataOPs protocols::optimize_weights::PNatRotOptEPositionData::data_
private
int protocols::optimize_weights::PNatRotOptEPositionData::n_wells_
private
utility::vector1< Real > protocols::optimize_weights::PNatRotOptEPositionData::native_chi_
private
utility::vector1< Real > protocols::optimize_weights::PNatRotOptEPositionData::native_chi_periodicity_
private
utility::vector1< Size > protocols::optimize_weights::PNatRotOptEPositionData::native_rotamer_index_
private
Real protocols::optimize_weights::PNatRotOptEPositionData::phi_
private

Referenced by phi(), and process_score().

Real protocols::optimize_weights::PNatRotOptEPositionData::psi_
private

Referenced by process_score(), and psi().

utility::vector1< Size > protocols::optimize_weights::PNatRotOptEPositionData::rotamer_well_counts_
private

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