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Rosetta
2021.07
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#include <OptEData.hh>
Public Member Functions | |
PNatRotOptEPositionData () | |
~PNatRotOptEPositionData () 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, int const, EnergyMap const &fixed_terms, ScoreTypes const &, 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_native_rotamer_index (utility::vector1< core::Size > const &native_rotamer_index) |
void | set_native_rotamer_chi (utility::vector1< Real > const &native_chi) |
void | set_native_chi_periodicity (utility::vector1< Real > const &native_chi_periodicity) |
bool | count_rotamer_as_native (PNatRotOptERotamerDataOP rotamer) const |
void | set_rotamer_well_counts (utility::vector1< core::Size > const &rotamer_well_counts) |
void | add_rotamer_line_data (PNatRotOptERotamerDataOP rot_in) |
PNatRotOptERotamerDataOPs & | data () |
PNatRotOptERotamerDataOPs const & | data () const |
PNatRotOptERotamerDataOPs::const_iterator | rotamer_data_begin () const |
PNatRotOptERotamerDataOPs::const_iterator | rotamer_data_end () const |
core::chemical::AA | aa () const |
core::chemical::AA & | aa () |
Real | phi () const |
Real | psi () const |
Real & | phi () |
Real & | psi () |
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OptEPositionData () | |
~OptEPositionData () override | |
void | tag (std::string const &tag_in) |
std::string const & | tag () const |
Private Member Functions | |
core::Size | rotamer_index_2_well_id (utility::vector1< core::Size > const &rotamer_index) const |
core::Size | rotamer_index_2_well_id (utility::LexicographicalIterator const &lexiter) const |
bool | is_native_rotamer_well (utility::vector1< core::Size > const &rotamer_index) const |
bool | is_native_rotamer_well (utility::LexicographicalIterator const &lexiter) const |
Private Attributes | |
utility::vector1< core::Size > | native_rotamer_index_ |
utility::vector1< core::Size > | rotamer_well_counts_ |
int | n_wells_ |
core::chemical::AA | aa_ |
Real | phi_ |
Real | psi_ |
PNatRotOptERotamerDataOPs | data_ |
utility::vector1< Real > | native_chi_ |
utility::vector1< Real > | native_chi_periodicity_ |
Additional Inherited Members | |
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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 |
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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::PNatRotOptEPositionData::PNatRotOptEPositionData | ( | ) |
Referenced by memory_use().
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overridedefault |
core::chemical::AA protocols::optimize_weights::PNatRotOptEPositionData::aa | ( | ) | const |
References aa_.
core::chemical::AA & protocols::optimize_weights::PNatRotOptEPositionData::aa | ( | ) |
References aa_.
void protocols::optimize_weights::PNatRotOptEPositionData::add_rotamer_line_data | ( | PNatRotOptERotamerDataOP | rot_in | ) |
References data_.
bool protocols::optimize_weights::PNatRotOptEPositionData::count_rotamer_as_native | ( | PNatRotOptERotamerDataOP | rotamer | ) | const |
References native_chi_, native_chi_periodicity_, rotamer_well_counts_, and protocols::environment::TOLERANCE.
Referenced by process_score().
PNatRotOptERotamerDataOPs & protocols::optimize_weights::PNatRotOptEPositionData::data | ( | ) |
References data_.
PNatRotOptERotamerDataOPs const & protocols::optimize_weights::PNatRotOptEPositionData::data | ( | ) | const |
References data_.
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overridevirtual |
num_energy_dofs | Basically, turn over all the private data from OptEMultiFunc |
Implements protocols::optimize_weights::OptEPositionData.
References process_score(), and protocols::optimize_weights::TR().
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References native_rotamer_index_.
Referenced by process_score().
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References native_rotamer_index_.
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overridevirtual |
Implements protocols::optimize_weights::OptEPositionData.
References data_, native_rotamer_index_, PNatRotOptEPositionData(), rotamer_well_counts_, and protocols::analysis::total.
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overridevirtual |
num_energy_dofs | Basically, turn over all the private data from OptEMultiFunc |
Implements protocols::optimize_weights::OptEPositionData.
References process_score().
Real protocols::optimize_weights::PNatRotOptEPositionData::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 | , | ||
int const | , | ||
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 aa_, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_his, core::chemical::aa_phe, core::chemical::aa_tyr, count_rotamer_as_native(), is_native_rotamer_well(), n_wells_, native_chi_, native_rotamer_index_, phi_, protocols::optimize_weights::prob_native_rotamer, psi_, rotamer_data_begin(), rotamer_data_end(), rotamer_index_2_well_id(), rotamer_well_counts_, and protocols::optimize_weights::OptEPositionData::tag().
Referenced by get_score(), and print_score().
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overridevirtual |
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 rotamer_data_begin(), and rotamer_data_end().
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overridevirtual |
Implements protocols::optimize_weights::OptEPositionData.
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overridevirtual |
Implements protocols::optimize_weights::OptEPositionData.
PNatRotOptERotamerDataOPs::const_iterator protocols::optimize_weights::PNatRotOptEPositionData::rotamer_data_begin | ( | ) | const |
References data_.
Referenced by process_score(), and range().
PNatRotOptERotamerDataOPs::const_iterator protocols::optimize_weights::PNatRotOptEPositionData::rotamer_data_end | ( | ) | const |
References data_.
Referenced by process_score(), and range().
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References rotamer_well_counts_.
Referenced by process_score().
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References rotamer_well_counts_.
void protocols::optimize_weights::PNatRotOptEPositionData::set_native_chi_periodicity | ( | utility::vector1< Real > const & | native_chi_periodicity | ) |
References native_chi_periodicity_.
void protocols::optimize_weights::PNatRotOptEPositionData::set_native_rotamer_chi | ( | utility::vector1< Real > const & | native_chi | ) |
References native_chi_.
void protocols::optimize_weights::PNatRotOptEPositionData::set_native_rotamer_index | ( | utility::vector1< core::Size > const & | native_rotamer_index | ) |
References native_rotamer_index_, and rotamer_well_counts_.
void protocols::optimize_weights::PNatRotOptEPositionData::set_rotamer_well_counts | ( | utility::vector1< core::Size > const & | rotamer_well_counts | ) |
References n_wells_, and rotamer_well_counts_.
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overridevirtual |
Implements protocols::optimize_weights::OptEPositionData.
References data_.
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overridevirtual |
Implements protocols::optimize_weights::OptEPositionData.
References protocols::optimize_weights::prob_native_rotamer.
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overridevirtual |
Implements protocols::optimize_weights::OptEPositionData.
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overridevirtual |
Implements protocols::optimize_weights::OptEPositionData.
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Referenced by aa(), and process_score().
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Referenced by add_rotamer_line_data(), data(), memory_use(), rotamer_data_begin(), rotamer_data_end(), and size().
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Referenced by process_score(), and set_rotamer_well_counts().
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Referenced by count_rotamer_as_native(), process_score(), and set_native_rotamer_chi().
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Referenced by count_rotamer_as_native(), and set_native_chi_periodicity().
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Referenced by is_native_rotamer_well(), memory_use(), process_score(), and set_native_rotamer_index().
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Referenced by phi(), and process_score().
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Referenced by process_score(), and psi().
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