Rosetta 3.4
Public Member Functions
protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData Class Reference

#include <NestedEnergyTermOptEData.hh>

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List of all members.

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.
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.
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).
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.
virtual void write_to_file (std::ofstream &outfile) const
 Add a special for loop to print out the unfolded state energy EnergyMap values.
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.
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.
void set_unfolded_energy_emap_vector (utility::vector1< EnergyMap > emap_vector)
utility::vector1< EnergyMap > & unfolded_energy_emap_vector ()
virtual Size memory_use () const

Constructor & Destructor Documentation

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

Member Function Documentation

Real protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::get_score ( 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 [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()

Reimplemented from protocols::optimize_weights::PNatAAOptEPositionData.

References core::TR().

Size protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::memory_use ( ) const [virtual]
void protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::print_score ( std::ostream &  ostr,
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 [virtual]

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

NestedEnergyTermPNatAAOptEPositionData::print_score()

Reimplemented from protocols::optimize_weights::PNatAAOptEPositionData.

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

NestedEnergyTermPNatAAOptEPositionData::process_score()

References core::scoring::hbond_lr_bb, core::scoring::name_from_score_type(), core::chemical::num_canonical_aas, core::scoring::omega, core::pack::tt(), and core::scoring::rna::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]

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