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Rosetta Protocols
2014.35
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#include <DDGBindOptEData.hh>
Public Member Functions | |
DDGBindOptEData () | |
Initialize all of the member variables to 0. More... | |
virtual | ~DDGBindOptEData () |
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 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... | |
virtual OptEPositionDataType | type () const |
virtual void | range (ScoreTypes const &free_score_list, ScoreTypes const &fixed_score_list, EnergyMap &lower_bound, EnergyMap &upper_bound) const |
virtual Size | size () const |
virtual Size | memory_use () const |
virtual void | write_to_file (std::ofstream &) const |
virtual void | read_from_file (std::ifstream &) |
virtual void | write_to_binary_file (std::ofstream &) const |
virtual void | read_from_binary_file (std::ifstream &) |
void | set_experimental_ddg_bind (Real exp_ddg_bind) |
void | add_mutation (std::pair< 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) |
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OptEPositionData () | |
virtual | ~OptEPositionData () |
void | tag (std::string const &tag_in) |
std::string const & | tag () const |
Additional Inherited Members | |
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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... | |
protocols::optimize_weights::DDGBindOptEData::DDGBindOptEData | ( | ) |
Initialize all of the member variables to 0.
DDGBindOptEData::DDGBindOptEData()
Referenced by memory_use().
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void protocols::optimize_weights::DDGBindOptEData::add_mutant_complex | ( | SingleStructureDataOP | mut | ) |
void protocols::optimize_weights::DDGBindOptEData::add_mutant_unbounds | ( | SingleStructureDataOP | mut | ) |
void protocols::optimize_weights::DDGBindOptEData::add_mutation | ( | std::pair< Size, std::pair< AA, AA > > | mutation | ) |
DDGBindOptEData::add_mutation()
References mutations_.
void protocols::optimize_weights::DDGBindOptEData::add_wt_complex | ( | SingleStructureDataOP | wt | ) |
DDGBindOptEData::add_wt_complex()
References wt_complexes_.
void protocols::optimize_weights::DDGBindOptEData::add_wt_unbounds | ( | SingleStructureDataOP | wt | ) |
DDGBindOptEData::add_wt_unbounds()
References wt_unbounds_.
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Implements protocols::optimize_weights::OptEPositionData.
References process_score().
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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_.
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DDGBindOptEData::print_score()
Implements protocols::optimize_weights::OptEPositionData.
References process_score().
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, | ||
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.
DDGBindOptEData::process_score()
num_energy_dofs | Basically, turn over all the private data from OptEMultiFunc |
References arg_min(), protocols::optimize_weights::ddG_bind_correlation, experimental_ddG_bind_, 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().
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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_.
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Implements protocols::optimize_weights::OptEPositionData.
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Implements protocols::optimize_weights::OptEPositionData.
void protocols::optimize_weights::DDGBindOptEData::set_experimental_ddg_bind | ( | Real | exp_ddg_bind | ) |
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Implements protocols::optimize_weights::OptEPositionData.
References mutant_complexes_, mutant_unbounds_, wt_complexes_, and wt_unbounds_.
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inlinevirtual |
Implements protocols::optimize_weights::OptEPositionData.
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inlinevirtual |
Implements protocols::optimize_weights::OptEPositionData.
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private |
Referenced by process_score(), and set_experimental_ddg_bind().
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Referenced by add_mutant_complex(), memory_use(), process_score(), range(), and size().
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Referenced by add_mutant_unbounds(), memory_use(), process_score(), range(), and size().
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Referenced by add_mutation(), and process_score().
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Referenced by add_wt_complex(), memory_use(), process_score(), range(), and size().
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Referenced by add_wt_unbounds(), memory_use(), process_score(), range(), and size().