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Rosetta
2016.11
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#include <OptEData.hh>
Public Types | |
typedef core::chemical::AA | AA |
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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 | |
DDGMutationOptEData () | |
virtual | ~DDGMutationOptEData () |
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 |
virtual void | range (ScoreTypes const &free_score_list, ScoreTypes const &fixed_score_list, EnergyMap &lower_bound, EnergyMap &upper_bound) const |
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... | |
virtual Size | size () const |
virtual OptEPositionDataType | type () const |
virtual void | write_to_file (std::ofstream &outfile) const |
virtual void | read_from_file (std::ifstream &infile) |
virtual void | write_to_binary_file (std::ofstream &outfile) const |
virtual void | read_from_binary_file (std::ifstream &infile) |
virtual Size | memory_use () const |
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) |
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OptEPositionData () | |
virtual | ~OptEPositionData () |
void | tag (std::string const &tag_in) |
std::string const & | tag () const |
Protected Attributes | |
Real | experimental_ddG_ |
AA | wt_aa_ |
AA | mut_aa_ |
SingleStructureDataOPs | wts_ |
SingleStructureDataOPs | muts_ |
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::DDGMutationOptEData::DDGMutationOptEData | ( | ) |
Referenced by memory_use().
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void protocols::optimize_weights::DDGMutationOptEData::add_mutant | ( | SingleStructureDataOP | mut | ) |
References muts_.
void protocols::optimize_weights::DDGMutationOptEData::add_wt | ( | SingleStructureDataOP | wt | ) |
References wts_.
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virtual |
num_energy_dofs | Basically, turn over all the private data from OptEMultiFunc |
Implements protocols::optimize_weights::OptEPositionData.
Reimplemented in protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData.
References process_score(), and protocols::optimize_weights::TR().
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Implements protocols::optimize_weights::OptEPositionData.
Reimplemented in protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData.
References DDGMutationOptEData(), muts_, protocols::analysis::total, and wts_.
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num_energy_dofs | Basically, turn over all the private data from OptEMultiFunc |
Implements protocols::optimize_weights::OptEPositionData.
Reimplemented in protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData.
References process_score().
Real protocols::optimize_weights::DDGMutationOptEData::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 |
num_energy_dofs | Basically, turn over all the private data from OptEMultiFunc |
References protocols::optimize_weights::ddG_mutation_correlation, experimental_ddG_, core::scoring::fa_rep, mut_aa_, muts_, protocols::optimize_weights::OptEPositionData::tag(), wt_aa_, and wts_.
Referenced by get_score(), and print_score().
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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 muts_, protocols::optimize_weights::OptEPositionData::update_range(), and wts_.
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Implements protocols::optimize_weights::OptEPositionData.
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Implements protocols::optimize_weights::OptEPositionData.
void protocols::optimize_weights::DDGMutationOptEData::set_experimental_ddg | ( | Real | ddg | ) |
References experimental_ddG_.
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Implements protocols::optimize_weights::OptEPositionData.
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Implements protocols::optimize_weights::OptEPositionData.
Reimplemented in protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData.
References protocols::optimize_weights::ddG_mutation_correlation.
Referenced by protocols::optimize_weights::OptEPositionDataFactory::optE_type_name().
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Implements protocols::optimize_weights::OptEPositionData.
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Implements protocols::optimize_weights::OptEPositionData.
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Referenced by process_score(), and set_experimental_ddg().
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Referenced by process_score(), and set_mut_aa().
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Referenced by add_mutant(), memory_use(), process_score(), range(), and size().
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Referenced by process_score(), and set_wt_aa().
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Referenced by add_wt(), memory_use(), process_score(), range(), and size().