Rosetta Protocols  2014.35
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Types | Private Attributes | List of all members
protocols::noesy_assign::PeakCalibrator Class Referenceabstract

#include <PeakCalibrator.hh>

Public Types

typedef std::bitset< MAX_TYPE > TypeCumulator
 

Public Member Functions

virtual ~PeakCalibrator ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
 
 PeakCalibrator (int target_sign)
 
virtual PeakCalibratorOP fresh_instance ()=0
 
void reset_statistics ()
 
void collect_target_statistics (core::Real, TypeCumulator const &)
 
bool interpolate_on_statistics ()
 
virtual void collect_upperbound_statistics (core::Size, TypeCumulator const &)=0
 
virtual void init_calibrator ()
 
core::Real operator() (CALIBRATION_ATOM_TYPE atom) const
 
core::Real calibration_constant (CALIBRATION_ATOM_TYPE type) const
 
void interpolate_too_small (core::Size type)
 
void interpolate_too_big (core::Size type)
 
void reset_calibration_constants ()
 
void add_peak (CrossPeakOP peak)
 
void set_new_upper_bounds ()
 
void do_calibration ()
 
void set_target_and_tolerance (core::Real target, core::Real tolerance)
 
virtual void eliminate_violated_constraints ()
 

Static Public Member Functions

static CALIBRATION_ATOM_TYPE atom_type (core::id::NamedAtomID const &atom, core::chemical::AA aa)
 

Protected Member Functions

utility::vector1< CrossPeakOP >
const & 		peaks ()
 

Private Types

typedef std::list< core::Real > TargetValues
 

Private Attributes

core::Size max_type_direct_
 
core::Real accumulated_target_ [MAX_TYPE]
 
TargetValues target_values_ [MAX_TYPE]
 
core::Size accumulated_count_ [MAX_TYPE]
 
core::Real calibration_constant_ [MAX_TYPE]
 
core::Real calibration_constant_lows_ [MAX_TYPE]
 
core::Real calibration_constant_highs_ [MAX_TYPE]
 
core::Size max_type_
 
utility::vector1< CrossPeakOP > peaks_
 
core::Real tolerance_
 
core::Real target_
 
int target_sign_
 

Member Typedef Documentation

typedef std::list< core::Real > protocols::noesy_assign::PeakCalibrator::TargetValues
private
typedef std::bitset< MAX_TYPE > protocols::noesy_assign::PeakCalibrator::TypeCumulator

Constructor & Destructor Documentation

protocols::noesy_assign::PeakCalibrator::~PeakCalibrator ( )
virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

protocols::noesy_assign::PeakCalibrator::PeakCalibrator ( int  target_sign)

References protocols::noesy_assign::PeakAssignmentParameters::atom_dependent_calibration_, protocols::noesy_assign::BACKBONE, protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::noesy_assign::MAX_TYPE, max_type_, max_type_direct_, and params.

Member Function Documentation

void protocols::noesy_assign::PeakCalibrator::add_peak ( CrossPeakOP  peak)

References peaks_.

CALIBRATION_ATOM_TYPE protocols::noesy_assign::PeakCalibrator::atom_type ( core::id::NamedAtomID const &  atom,
core::chemical::AA  aa 
)
static

References aa_ala, aa_ile, aa_leu, aa_met, aa_thr, aa_val, core::id::NamedAtomID::atom(), protocols::noesy_assign::PeakAssignmentParameters::atom_dependent_calibration_, protocols::noesy_assign::BACKBONE, protocols::noesy_assign::BETA_NON_METHYL, protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::noesy_assign::METHYL, params, and protocols::noesy_assign::SIDECHAIN.

Referenced by protocols::noesy_assign::Resonance::Resonance().

core::Real protocols::noesy_assign::PeakCalibrator::calibration_constant ( CALIBRATION_ATOM_TYPE  type) const
inline

References calibration_constant_.

Referenced by operator()().

void protocols::noesy_assign::PeakCalibrator::collect_target_statistics ( core::Real  target,
TypeCumulator const &  types 
)

References accumulated_count_, accumulated_target_, protocols::noesy_assign::BACKBONE, max_type_, target_values_, and type.

virtual void protocols::noesy_assign::PeakCalibrator::collect_upperbound_statistics ( core::Size  ,
TypeCumulator const &   
)
pure virtual

Implemented in protocols::noesy_assign::StructureIndependentPeakCalibrator, and protocols::noesy_assign::StructureDependentPeakCalibrator.

Referenced by set_new_upper_bounds().

void protocols::noesy_assign::PeakCalibrator::do_calibration ( )

References accumulated_count_, accumulated_target_, protocols::noesy_assign::BACKBONE, calibration_constant_, CALIBRATOR_TYPE_NAMES, interpolate_on_statistics(), max_cycles, max_type_, peaks_, reset_calibration_constants(), reset_statistics(), set_new_upper_bounds(), target_, protocols::noesy_assign::tr, and type.

virtual void protocols::noesy_assign::PeakCalibrator::eliminate_violated_constraints ( )
inlinevirtual

Reimplemented in protocols::noesy_assign::StructureDependentPeakCalibrator.

virtual PeakCalibratorOP protocols::noesy_assign::PeakCalibrator::fresh_instance ( )
pure virtual

Implemented in protocols::noesy_assign::StructureIndependentPeakCalibrator, and protocols::noesy_assign::StructureDependentPeakCalibrator.

virtual void protocols::noesy_assign::PeakCalibrator::init_calibrator ( )
inlinevirtual

Reimplemented in protocols::noesy_assign::StructureDependentPeakCalibrator.

bool protocols::noesy_assign::PeakCalibrator::interpolate_on_statistics ( )

References accumulated_count_, accumulated_target_, protocols::noesy_assign::BACKBONE, protocols::noesy_assign::BETA_NON_METHYL, calibration_constant_, protocols::noesy_assign::PeakAssignmentParameters::calibration_use_median_, protocols::noesy_assign::PeakAssignmentParameters::get_nonconst_instance(), interpolate_too_big(), interpolate_too_small(), max_type_direct_, median(), protocols::noesy_assign::METHYL, params, protocols::noesy_assign::SIDECHAIN, target_, target_sign_, target_values_, tolerance_, and type.

Referenced by do_calibration().

void protocols::noesy_assign::PeakCalibrator::interpolate_too_big ( core::Size  type)

References calibration_constant_, calibration_constant_highs_, calibration_constant_lows_, and log().

Referenced by interpolate_on_statistics().

void protocols::noesy_assign::PeakCalibrator::interpolate_too_small ( core::Size  type)

References calibration_constant_, calibration_constant_highs_, calibration_constant_lows_, and log().

Referenced by interpolate_on_statistics().

core::Real protocols::noesy_assign::PeakCalibrator::operator() ( CALIBRATION_ATOM_TYPE  atom) const
inline

References calibration_constant().

utility::vector1< CrossPeakOP > const& protocols::noesy_assign::PeakCalibrator::peaks ( )
inlineprotected

References peaks_.

void protocols::noesy_assign::PeakCalibrator::reset_calibration_constants ( )

References protocols::noesy_assign::BACKBONE, calibration_constant_, calibration_constant_highs_, calibration_constant_lows_, max_type_, and type.

Referenced by do_calibration().

void protocols::noesy_assign::PeakCalibrator::reset_statistics ( )

References accumulated_count_, accumulated_target_, protocols::noesy_assign::BACKBONE, max_type_, target_values_, and type.

Referenced by do_calibration().

void protocols::noesy_assign::PeakCalibrator::set_new_upper_bounds ( )

References collect_upperbound_statistics(), and peaks_.

Referenced by do_calibration().

void protocols::noesy_assign::PeakCalibrator::set_target_and_tolerance ( core::Real  target,
core::Real  tolerance 
)

References target_, and tolerance_.

Member Data Documentation

core::Size protocols::noesy_assign::PeakCalibrator::accumulated_count_[MAX_TYPE]
private

Referenced by collect_target_statistics(), do_calibration(), interpolate_on_statistics(), and reset_statistics().

core::Real protocols::noesy_assign::PeakCalibrator::accumulated_target_[MAX_TYPE]
private

Referenced by collect_target_statistics(), do_calibration(), interpolate_on_statistics(), and reset_statistics().

core::Real protocols::noesy_assign::PeakCalibrator::calibration_constant_[MAX_TYPE]
private

Referenced by calibration_constant(), do_calibration(), interpolate_on_statistics(), interpolate_too_big(), interpolate_too_small(), and reset_calibration_constants().

core::Real protocols::noesy_assign::PeakCalibrator::calibration_constant_highs_[MAX_TYPE]
private

Referenced by interpolate_too_big(), interpolate_too_small(), and reset_calibration_constants().

core::Real protocols::noesy_assign::PeakCalibrator::calibration_constant_lows_[MAX_TYPE]
private

Referenced by interpolate_too_big(), interpolate_too_small(), and reset_calibration_constants().

core::Size protocols::noesy_assign::PeakCalibrator::max_type_
private

Referenced by collect_target_statistics(), do_calibration(), PeakCalibrator(), reset_calibration_constants(), and reset_statistics().

core::Size protocols::noesy_assign::PeakCalibrator::max_type_direct_
private

Referenced by interpolate_on_statistics(), and PeakCalibrator().

utility::vector1< CrossPeakOP > protocols::noesy_assign::PeakCalibrator::peaks_
private

Referenced by add_peak(), do_calibration(), peaks(), and set_new_upper_bounds().

core::Real protocols::noesy_assign::PeakCalibrator::target_
private

Referenced by do_calibration(), interpolate_on_statistics(), and set_target_and_tolerance().

int protocols::noesy_assign::PeakCalibrator::target_sign_
private

Referenced by interpolate_on_statistics().

TargetValues protocols::noesy_assign::PeakCalibrator::target_values_[MAX_TYPE]
private

Referenced by collect_target_statistics(), interpolate_on_statistics(), and reset_statistics().

core::Real protocols::noesy_assign::PeakCalibrator::tolerance_
private

Referenced by interpolate_on_statistics(), and set_target_and_tolerance().

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