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protocols::optimize_weights::PNatLigPoseOptEData Class Reference

#include <PNatLigPoseOptEData.hh>

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

 PNatLigPoseOptEData ()
 
 ~PNatLigPoseOptEData () override
 
virtual Real do_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, bool const print) const
 
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
 
OptEPositionDataType type () const override
 
- Public Member Functions inherited from protocols::optimize_weights::PNatStructureOptEData
 PNatStructureOptEData ()
 
 ~PNatStructureOptEData () 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
 
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
 

Private Attributes

Real kT_
 
Real multiplier_
 

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
 
- Static Public Member Functions inherited from protocols::optimize_weights::PNatStructureOptEData
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 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...
 
- Protected Attributes inherited from protocols::optimize_weights::PNatStructureOptEData
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 inherited from protocols::optimize_weights::PNatStructureOptEData
static Real nativeness_rms_low_
 
static Real nativeness_rms_high_
 
static Real const high_entropy_rms_cutoff_
 

Constructor & Destructor Documentation

protocols::optimize_weights::PNatLigPoseOptEData::PNatLigPoseOptEData ( )
protocols::optimize_weights::PNatLigPoseOptEData::~PNatLigPoseOptEData ( )
overridedefault

Member Function Documentation

Real protocols::optimize_weights::PNatLigPoseOptEData::do_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,
bool const  print 
) const
virtual
Real protocols::optimize_weights::PNatLigPoseOptEData::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
overridevirtual
Parameters
num_energy_dofsBasically, turn over all the private data from OptEMultiFunc

Reimplemented from protocols::optimize_weights::PNatStructureOptEData.

References do_score().

void protocols::optimize_weights::PNatLigPoseOptEData::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
inlineoverridevirtual
Parameters
num_energy_dofsBasically, turn over all the private data from OptEMultiFunc

Reimplemented from protocols::optimize_weights::PNatStructureOptEData.

References do_score().

OptEPositionDataType protocols::optimize_weights::PNatLigPoseOptEData::type ( ) const
overridevirtual

Member Data Documentation

Real protocols::optimize_weights::PNatLigPoseOptEData::kT_
private

Referenced by do_score().

Real protocols::optimize_weights::PNatLigPoseOptEData::multiplier_
private

Referenced by do_score().


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