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protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData Class Reference

#include <NestedEnergyTermOptEData.hh>

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

 NestedEnergyTermDDGMutationOptEData ()
 
 ~NestedEnergyTermDDGMutationOptEData () 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). More...
 
OptEPositionDataType type () const override
 
core::Size memory_use () const override
 
void set_wt_unfolded_energies_emap (EnergyMap e)
 
void set_mut_unfolded_energies_emap (EnergyMap e)
 
- Public Member Functions inherited from protocols::optimize_weights::DDGMutationOptEData
 DDGMutationOptEData ()
 
 ~DDGMutationOptEData () 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_wt_aa (AA wt_aa)
 
void set_mut_aa (AA mut_aa)
 
void set_experimental_ddg (Real ddg)
 
void add_wt (SingleStructureDataOP wt)
 
void add_mutant (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

EnergyMap wt_unfolded_energies_emap_
 
EnergyMap mut_unfolded_energies_emap_
 

Additional Inherited Members

- Public Types inherited from protocols::optimize_weights::DDGMutationOptEData
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
 
- 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::DDGMutationOptEData
Real experimental_ddG_
 
AA wt_aa_
 
AA mut_aa_
 
SingleStructureDataOPs wts_
 
SingleStructureDataOPs muts_
 

Constructor & Destructor Documentation

protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::NestedEnergyTermDDGMutationOptEData ( )
default
protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::~NestedEnergyTermDDGMutationOptEData ( )
overridedefault

Member Function Documentation

Real protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::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 &  free_score_list,
ScoreTypes const &  fixed_score_list 
) const
overridevirtual

This get_score() method needs to contain some extra logic for the unfolded state energy term. Right now, the value under unfolded energy is 0.0, because that's what the EnergyMethod is coded to return. But, as in the NatAA class above, we need use the unweighted, unfolded energies and the current weight set to come up with a unfolded energy.

Parameters
num_energy_dofsBasically, turn over all the private data from OptEMultiFunc

Implements protocols::optimize_weights::OptEPositionData.

References core::scoring::TR().

Size protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::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 protocols::analysis::total.

void protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::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.

Real protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::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).

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_mutation_correlation, protocols::optimize_weights::ddG_mutation_correlation_with_unfolded_energy, core::chemical::element::F, core::scoring::fa_rep, core::scoring::name_from_score_type(), core::scoring::TR(), core::scoring::unfolded, and protocols::comparative_modeling::features::X.

void protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::set_mut_unfolded_energies_emap ( EnergyMap  e)
inline
void protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::set_wt_unfolded_energies_emap ( EnergyMap  e)
inline
OptEPositionDataType protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::type ( ) const
overridevirtual

Member Data Documentation

EnergyMap protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::mut_unfolded_energies_emap_
private
EnergyMap protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::wt_unfolded_energies_emap_
private

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