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protocols::optimize_weights::PNatStructureOptEData Class Reference

#include <OptEData.hh>

Inheritance diagram for protocols::optimize_weights::PNatStructureOptEData:
Inheritance graph
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Public Member Functions

 PNatStructureOptEData ()
 
 ~PNatStructureOptEData () override
 
Real get_score (Multivec const &component_weights, Multivec const &vars, Multivec &dE_dvars, core::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 override
 
void print_score (std::ostream &ostr, Multivec const &component_weights, Multivec const &vars, Multivec &dE_dvars, core::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 override
 
Real process_score (std::ostream &ostr, bool print, Multivec const &component_weights, Multivec const &vars, Multivec &dE_dvars, core::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
 
void range (ScoreTypes const &free_score_list, ScoreTypes const &fixed_score_list, EnergyMap &lower_bound, EnergyMap &upper_bound) const override
 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...
 
core::Size size () const override
 
OptEPositionDataType type () const override
 
void write_to_file (std::ofstream &outfile) const override
 
void read_from_file (std::ifstream &infile) override
 
void write_to_binary_file (std::ofstream &outfile) const override
 
void read_from_binary_file (std::ifstream &infile) override
 
core::Size memory_use () const override
 
void set_total_residue (core::Size total_residue)
 
void add_native (SingleStructureDataOP native)
 
void add_decoy (SingleStructureDataOP decoy)
 
void n_top_natives_to_score (core::Size n_top)
 
core::Size n_top_natives_to_score () const
 
void set_normalize_decoy_stddev (bool setting)
 
void set_initial_decoy_stddev (Real setting)
 
Real nativeness (Real rms) const
 
- Public Member Functions inherited from protocols::optimize_weights::OptEPositionData
 OptEPositionData ()
 
 ~OptEPositionData () override
 
void tag (std::string const &tag_in)
 
std::string const & tag () const
 

Static Public Member Functions

static void set_nativeness_low (Real nativeness_rms_low)
 
static void set_nativeness_high (Real nativeness_rms_low)
 
static Real nativeness_low ()
 
static Real nativeness_high ()
 

Protected Attributes

core::Size total_residue_
 
SingleStructureDataOPs natives_
 
SingleStructureDataOPs decoys_
 
core::Size n_top_natives_to_score_
 
core::Size n_high_entropy_decoys_
 
bool normalize_decoy_stddev_
 
Real initial_decoy_stddev_
 
Real nativeness_sum_
 

Static Protected Attributes

static Real nativeness_rms_low_
 
static Real nativeness_rms_high_
 
static Real const high_entropy_rms_cutoff_
 

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::PNatStructureOptEData::PNatStructureOptEData ( )

Referenced by memory_use().

protocols::optimize_weights::PNatStructureOptEData::~PNatStructureOptEData ( )
overridedefault

Member Function Documentation

void protocols::optimize_weights::PNatStructureOptEData::add_decoy ( SingleStructureDataOP  decoy)
void protocols::optimize_weights::PNatStructureOptEData::add_native ( SingleStructureDataOP  native)
Real protocols::optimize_weights::PNatStructureOptEData::get_score ( optimization::Multivec const &  component_weights,
optimization::Multivec const &  vars,
optimization::Multivec dE_dvars,
core::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
overridevirtual
Parameters
num_energy_dofsBasically, turn over all the private data from OptEMultiFunc

Implements protocols::optimize_weights::OptEPositionData.

Reimplemented in protocols::optimize_weights::PNatLigPoseOptEData.

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

Size protocols::optimize_weights::PNatStructureOptEData::memory_use ( ) const
overridevirtual
void protocols::optimize_weights::PNatStructureOptEData::n_top_natives_to_score ( core::Size  n_top)
Size protocols::optimize_weights::PNatStructureOptEData::n_top_natives_to_score ( ) const
Real protocols::optimize_weights::PNatStructureOptEData::nativeness ( Real  rms) const
Real protocols::optimize_weights::PNatStructureOptEData::nativeness_high ( )
static
Real protocols::optimize_weights::PNatStructureOptEData::nativeness_low ( )
static

References nativeness_rms_low_.

void protocols::optimize_weights::PNatStructureOptEData::print_score ( std::ostream &  ostr,
optimization::Multivec const &  component_weights,
optimization::Multivec const &  vars,
optimization::Multivec dE_dvars,
core::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
overridevirtual
Parameters
num_energy_dofsBasically, turn over all the private data from OptEMultiFunc

Implements protocols::optimize_weights::OptEPositionData.

Reimplemented in protocols::optimize_weights::PNatLigPoseOptEData.

References process_score().

Real protocols::optimize_weights::PNatStructureOptEData::process_score ( std::ostream &  ostr,
bool  print,
optimization::Multivec const &  component_weights,
optimization::Multivec const &  vars,
optimization::Multivec dE_dvars,
core::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
void protocols::optimize_weights::PNatStructureOptEData::range ( ScoreTypes const &  free_score_list,
ScoreTypes const &  fixed_score_list,
EnergyMap lower_bound,
EnergyMap upper_bound 
) const
overridevirtual

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 decoys_, natives_, and protocols::optimize_weights::OptEPositionData::update_range().

void protocols::optimize_weights::PNatStructureOptEData::read_from_binary_file ( std::ifstream &  infile)
overridevirtual
void protocols::optimize_weights::PNatStructureOptEData::read_from_file ( std::ifstream &  infile)
overridevirtual
void protocols::optimize_weights::PNatStructureOptEData::set_initial_decoy_stddev ( Real  setting)

References initial_decoy_stddev_.

void protocols::optimize_weights::PNatStructureOptEData::set_nativeness_high ( Real  nativeness_rms_low)
static
void protocols::optimize_weights::PNatStructureOptEData::set_nativeness_low ( Real  nativeness_rms_low)
static
void protocols::optimize_weights::PNatStructureOptEData::set_normalize_decoy_stddev ( bool  setting)
void protocols::optimize_weights::PNatStructureOptEData::set_total_residue ( core::Size  total_residue)

References total_residue_.

Size protocols::optimize_weights::PNatStructureOptEData::size ( ) const
overridevirtual
OptEPositionDataType protocols::optimize_weights::PNatStructureOptEData::type ( ) const
overridevirtual
void protocols::optimize_weights::PNatStructureOptEData::write_to_binary_file ( std::ofstream &  outfile) const
overridevirtual
void protocols::optimize_weights::PNatStructureOptEData::write_to_file ( std::ofstream &  outfile) const
overridevirtual

Member Data Documentation

SingleStructureDataOPs protocols::optimize_weights::PNatStructureOptEData::decoys_
protected
Real const protocols::optimize_weights::PNatStructureOptEData::high_entropy_rms_cutoff_
staticprotected

Referenced by add_decoy(), and process_score().

Real protocols::optimize_weights::PNatStructureOptEData::initial_decoy_stddev_
protected
core::Size protocols::optimize_weights::PNatStructureOptEData::n_high_entropy_decoys_
protected

Referenced by add_decoy(), and process_score().

core::Size protocols::optimize_weights::PNatStructureOptEData::n_top_natives_to_score_
protected
Real protocols::optimize_weights::PNatStructureOptEData::nativeness_rms_high_
staticprotected
Real protocols::optimize_weights::PNatStructureOptEData::nativeness_rms_low_
staticprotected
Real protocols::optimize_weights::PNatStructureOptEData::nativeness_sum_
protected

Referenced by add_native(), and process_score().

SingleStructureDataOPs protocols::optimize_weights::PNatStructureOptEData::natives_
protected
bool protocols::optimize_weights::PNatStructureOptEData::normalize_decoy_stddev_
protected
core::Size protocols::optimize_weights::PNatStructureOptEData::total_residue_
protected

Referenced by process_score(), and set_total_residue().


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