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protocols::optimize_weights::DDGBindOptEData Class Reference

#include <DDGBindOptEData.hh>

Inheritance diagram for protocols::optimize_weights::DDGBindOptEData:
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Public Types

enum  DDG_Bind_File_Index { WT_COMPLEXES_LIST_FILE = 1, MUT_COMPLEXES_LIST_FILE, WT_UNBOUNDS_LIST_FILE, MUT_UNBOUNDS_LIST_FILE }
 
typedef core::chemical::AA AA
 
- 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
 

Public Member Functions

 DDGBindOptEData ()
 Initialize all of the member variables to 0. More...
 
 ~DDGBindOptEData () 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
 One method to do the score processing which takes a boolean dictating whether to print to an ostream or not. With this function, changes to how scoring works only need to be made in one place as opposed to two (when get_score() and print_score() both had scoring logic in them). Avoiding code duplication is good. More...
 
OptEPositionDataType type () const override
 
void range (ScoreTypes const &free_score_list, ScoreTypes const &fixed_score_list, EnergyMap &lower_bound, EnergyMap &upper_bound) const override
 
core::Size size () const override
 
core::Size memory_use () const override
 
void write_to_file (std::ofstream &) const override
 
void read_from_file (std::ifstream &) override
 
void write_to_binary_file (std::ofstream &) const override
 
void read_from_binary_file (std::ifstream &) override
 
void set_experimental_ddg_bind (Real exp_ddg_bind)
 
void add_mutation (std::pair< core::Size, std::pair< AA, AA > > mutation)
 
void add_wt_complex (SingleStructureDataOP wt)
 
void add_mutant_complex (SingleStructureDataOP mut)
 
void add_wt_unbounds (SingleStructureDataOP wt)
 
void add_mutant_unbounds (SingleStructureDataOP mut)
 
- 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 experimental_ddG_bind_
 
utility::vector1< std::pair
< core::Size, std::pair< AA,
AA > > > 
mutations_
 
SingleStructureDataOPs wt_complexes_
 
SingleStructureDataOPs mutant_complexes_
 
SingleStructureDataOPs wt_unbounds_
 
SingleStructureDataOPs mutant_unbounds_
 

Additional Inherited Members

- 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...
 

Member Typedef Documentation

Member Enumeration Documentation

Enumerator
WT_COMPLEXES_LIST_FILE 
MUT_COMPLEXES_LIST_FILE 
WT_UNBOUNDS_LIST_FILE 
MUT_UNBOUNDS_LIST_FILE 

Constructor & Destructor Documentation

protocols::optimize_weights::DDGBindOptEData::DDGBindOptEData ( )

Initialize all of the member variables to 0.

Referenced by memory_use().

protocols::optimize_weights::DDGBindOptEData::~DDGBindOptEData ( )
overridedefault

Member Function Documentation

void protocols::optimize_weights::DDGBindOptEData::add_mutant_complex ( SingleStructureDataOP  mut)

References mutant_complexes_.

void protocols::optimize_weights::DDGBindOptEData::add_mutant_unbounds ( SingleStructureDataOP  mut)

References mutant_unbounds_.

void protocols::optimize_weights::DDGBindOptEData::add_mutation ( std::pair< core::Size, std::pair< AA, AA > >  mutation)

References mutations_.

void protocols::optimize_weights::DDGBindOptEData::add_wt_complex ( SingleStructureDataOP  wt)

References wt_complexes_.

void protocols::optimize_weights::DDGBindOptEData::add_wt_unbounds ( SingleStructureDataOP  wt)

References wt_unbounds_.

Real protocols::optimize_weights::DDGBindOptEData::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
core::Size protocols::optimize_weights::DDGBindOptEData::memory_use ( ) const
overridevirtual

Only used for user feedback. Nothing in the code uses the result from this to allocate memory.

Implements protocols::optimize_weights::OptEPositionData.

References DDGBindOptEData(), mutant_complexes_, mutant_unbounds_, protocols::analysis::total, wt_complexes_, and wt_unbounds_.

void protocols::optimize_weights::DDGBindOptEData::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
Real protocols::optimize_weights::DDGBindOptEData::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

One method to do the score processing which takes a boolean dictating whether to print to an ostream or not. With this function, changes to how scoring works only need to be made in one place as opposed to two (when get_score() and print_score() both had scoring logic in them). Avoiding code duplication is good.

Parameters
num_energy_dofsBasically, turn over all the private data from OptEMultiFunc

References protocols::comparative_modeling::features::A, protocols::mean_field::arg_min(), protocols::optimize_weights::ddG_bind_correlation, experimental_ddG_bind_, core::chemical::element::F, mutant_complexes_, mutant_unbounds_, mutations_, protocols::optimize_weights::OptEPositionData::tag(), wt_complexes_, wt_unbounds_, and protocols::comparative_modeling::features::X.

Referenced by get_score(), and print_score().

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

Determine the upper and lower bounds on the unweighted component energy terms at this "position" and deposit them in the passed-in EnergyMap objects. Called by the IterativeOptE driver class to print extra information to the minimization data file.

Implements protocols::optimize_weights::OptEPositionData.

References mutant_complexes_, mutant_unbounds_, protocols::optimize_weights::OptEPositionData::update_range(), wt_complexes_, and wt_unbounds_.

void protocols::optimize_weights::DDGBindOptEData::read_from_binary_file ( std::ifstream &  )
inlineoverridevirtual
void protocols::optimize_weights::DDGBindOptEData::read_from_file ( std::ifstream &  )
inlineoverridevirtual
void protocols::optimize_weights::DDGBindOptEData::set_experimental_ddg_bind ( Real  exp_ddg_bind)
core::Size protocols::optimize_weights::DDGBindOptEData::size ( ) const
overridevirtual
OptEPositionDataType protocols::optimize_weights::DDGBindOptEData::type ( ) const
overridevirtual
void protocols::optimize_weights::DDGBindOptEData::write_to_binary_file ( std::ofstream &  ) const
inlineoverridevirtual
void protocols::optimize_weights::DDGBindOptEData::write_to_file ( std::ofstream &  ) const
inlineoverridevirtual

Member Data Documentation

Real protocols::optimize_weights::DDGBindOptEData::experimental_ddG_bind_
private
SingleStructureDataOPs protocols::optimize_weights::DDGBindOptEData::mutant_complexes_
private
SingleStructureDataOPs protocols::optimize_weights::DDGBindOptEData::mutant_unbounds_
private
utility::vector1< std::pair< core::Size, std::pair < AA, AA > > > protocols::optimize_weights::DDGBindOptEData::mutations_
private

Referenced by add_mutation(), and process_score().

SingleStructureDataOPs protocols::optimize_weights::DDGBindOptEData::wt_complexes_
private
SingleStructureDataOPs protocols::optimize_weights::DDGBindOptEData::wt_unbounds_
private

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