Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData Class Reference

#include <NestedEnergyTermOptEData.hh>

Public Member Functions

 NestedEnergyTermPNatAAOptEPositionData ()
 
virtual ~NestedEnergyTermPNatAAOptEPositionData ()
 
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
 Does actual work for OptE minimization Special implementation of get_score that includes logic to handle unfolded state energy calculation. See header file and OptEData.hh for more information. More...
 
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
 Special implementation of print_score that includes logic to handle unfolded state energy calculation. More...
 
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). More...
 
virtual OptEPositionDataType type () const
 To be sure we create the right types when writing/reading from files, need to add a special OptEPositionData type that gets returned here. More...
 
virtual void write_to_file (std::ofstream &outfile) const
 Add a special for loop to print out the unfolded state energy EnergyMap values. More...
 
virtual void read_from_file (std::ifstream &infile)
 
virtual void write_to_binary_file (std::ofstream &outfile) const
 Leaving this unimplemented since I don't feel like figuring out how to output an EnergyMap in binary and also because reading/writing binary files is not being used in the optE protocol currently. More...
 
virtual void read_from_binary_file (std::ifstream &infile)
 Leaving this unimplemented since I don't feel like figuring out how to output an EnergyMap in binary and also because reading/writing binary files is not being used in the optE protocol currently. More...
 
void set_unfolded_energy_emap_vector (utility::vector1< EnergyMap > emap_vector)
 
utility::vector1< EnergyMap > & unfolded_energy_emap_vector ()
 
virtual Size memory_use () const
 
- Public Member Functions inherited from protocols::optimize_weights::PNatAAOptEPositionData
 PNatAAOptEPositionData ()
 
virtual ~PNatAAOptEPositionData ()
 
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
 
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
 
void set_position (Size pos_in)
 
Size position () const
 
void set_native_aa (AA nat_in)
 
AA native_aa () const
 
void set_neighbor_count (Size nb_in)
 
Size neighbor_count () const
 
void add_rotamer_line_data (PNatAAOptERotamerDataOP rot_in)
 
PNatAAOptERotamerDataOPsdata ()
 
PNatAAOptERotamerDataOPs const & data () const
 
PNatAAOptERotamerDataOPs::const_iterator rotamer_data_begin () const
 
PNatAAOptERotamerDataOPs::const_iterator rotamer_data_end () const
 
- Public Member Functions inherited from protocols::optimize_weights::OptEPositionData
 OptEPositionData ()
 
virtual ~OptEPositionData ()
 
void tag (std::string const &tag_in)
 
std::string const & tag () const
 

Private Attributes

utility::vector1< EnergyMapunfolded_energy_emap_vector_
 used by derived class as well – finds the energies for the best rotamer for each amino acid More...
 

Additional Inherited Members

- Public Types inherited from protocols::optimize_weights::PNatAAOptEPositionData
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::PNatAAOptEPositionData
void process_rotamers (Multivec const &vars, Size const num_energy_dofs, EnergyMap const &fixed_terms, ScoreTypes const &score_list, ScoreTypes const &fixed_score_list, Size const aa_range, utility::vector1< Real > const &dummy_set, utility::vector1< Real > &best_energy_by_aa, utility::vector1< utility::vector1< Real > > &unweighted_E_dof, Multivec &ref_deriv_weight) const
 used by derived class as well – finds the energies for the best rotamer for each amino acid More...
 
- 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...
 

Constructor & Destructor Documentation

protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::NestedEnergyTermPNatAAOptEPositionData ( )
protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::~NestedEnergyTermPNatAAOptEPositionData ( )
virtual

Member Function Documentation

Real protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::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

Does actual work for OptE minimization Special implementation of get_score that includes logic to handle unfolded state energy calculation. See header file and OptEData.hh for more information.

NestedEnergyTermPNatAAOptEPositionData::get_score()

References core::scoring::TR.

Size protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::memory_use ( ) const
virtual
void protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::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
virtual

Special implementation of print_score that includes logic to handle unfolded state energy calculation.

NestedEnergyTermPNatAAOptEPositionData::print_score()

Real protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::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).

NestedEnergyTermPNatAAOptEPositionData::process_score()

References cutoff, F, core::scoring::hbond_lr_bb, I, optE::inv_kT_nataa, core::scoring::name_from_score_type(), protocols::sic_dock::neighbor_count(), core::chemical::num_canonical_aas, core::scoring::omega, option, tag, protocols::loops::tt, type, and protocols::comparative_modeling::features::X.

void protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_binary_file ( std::ifstream &  infile)
virtual

Leaving this unimplemented since I don't feel like figuring out how to output an EnergyMap in binary and also because reading/writing binary files is not being used in the optE protocol currently.

NestedEnergyTermPNatAAOptEPositionData::read_from_binary_file()

Reimplemented from protocols::optimize_weights::PNatAAOptEPositionData.

void protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file ( std::ifstream &  infile)
virtual
void protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::set_unfolded_energy_emap_vector ( utility::vector1< EnergyMap emap_vector)
inline
OptEPositionDataType protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::type ( ) const
virtual

To be sure we create the right types when writing/reading from files, need to add a special OptEPositionData type that gets returned here.

NestedEnergyTermPNatAAOptEPositionData::type()

Reimplemented from protocols::optimize_weights::PNatAAOptEPositionData.

References protocols::optimize_weights::prob_native_amino_acid_with_unfolded_energy.

utility::vector1< EnergyMap >& protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::unfolded_energy_emap_vector ( )
inline
void protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::write_to_binary_file ( std::ofstream &  outfile) const
virtual

Leaving this unimplemented since I don't feel like figuring out how to output an EnergyMap in binary and also because reading/writing binary files is not being used in the optE protocol currently.

NestedEnergyTermPNatAAOptEPositionData::write_to_binary_file()

Reimplemented from protocols::optimize_weights::PNatAAOptEPositionData.

void protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::write_to_file ( std::ofstream &  outfile) const
virtual

Member Data Documentation

utility::vector1< EnergyMap > protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::unfolded_energy_emap_vector_
private

used by derived class as well – finds the energies for the best rotamer for each amino acid

Referenced by set_unfolded_energy_emap_vector(), and unfolded_energy_emap_vector().


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