protocols::noesy_assign::PeakCalibrator Class Reference

#include <PeakCalibrator.hh>

Inheritance diagram for protocols::noesy_assign::PeakCalibrator:

Collaboration diagram for protocols::noesy_assign::PeakCalibrator:

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_

Detailed Description

Definition at line 55 of file PeakCalibrator.hh.

Member Typedef Documentation

typedef std::list< core::Real > protocols::noesy_assign::PeakCalibrator::TargetValues

private

Definition at line 99 of file PeakCalibrator.hh.

typedef std::bitset< MAX_TYPE > protocols::noesy_assign::PeakCalibrator::TypeCumulator

Definition at line 60 of file PeakCalibrator.hh.

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 58 of file PeakCalibrator.cc.

protocols::noesy_assign::PeakCalibrator::PeakCalibrator

(

int

target_sign)

Definition at line 100 of file PeakCalibrator.cc.

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_, and max_type_direct_.

Member Function Documentation

void protocols::noesy_assign::PeakCalibrator::add_peak

(

CrossPeakOP

peak)

Definition at line 241 of file PeakCalibrator.cc.

References peaks_.

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

static

Definition at line 258 of file PeakCalibrator.cc.

References core::chemical::aa_ala, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_met, core::chemical::aa_thr, core::chemical::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, 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

Definition at line 74 of file PeakCalibrator.hh.

References calibration_constant_.

Referenced by operator()().

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

Definition at line 176 of file PeakCalibrator.cc.

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

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

(

)

Definition at line 202 of file PeakCalibrator.cc.

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

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

inlinevirtual

Reimplemented in protocols::noesy_assign::StructureDependentPeakCalibrator.

Definition at line 91 of file PeakCalibrator.hh.

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.

Definition at line 71 of file PeakCalibrator.hh.

bool protocols::noesy_assign::PeakCalibrator::interpolate_on_statistics

(

)

Definition at line 128 of file PeakCalibrator.cc.

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_, protocols::noesy_assign::METHYL, protocols::noesy_assign::SIDECHAIN, target_, target_sign_, target_values_, and tolerance_.

Referenced by do_calibration().

void protocols::noesy_assign::PeakCalibrator::interpolate_too_big

(

core::Size

type)

Definition at line 171 of file PeakCalibrator.cc.

References calibration_constant_, calibration_constant_highs_, and calibration_constant_lows_.

Referenced by interpolate_on_statistics().

void protocols::noesy_assign::PeakCalibrator::interpolate_too_small

(

core::Size

type)

Definition at line 166 of file PeakCalibrator.cc.

References calibration_constant_, calibration_constant_highs_, and calibration_constant_lows_.

Referenced by interpolate_on_statistics().

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

inline

Definition at line 73 of file PeakCalibrator.hh.

References calibration_constant().

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

inlineprotected

Definition at line 94 of file PeakCalibrator.hh.

References peaks_.

void protocols::noesy_assign::PeakCalibrator::reset_calibration_constants

(

)

Definition at line 194 of file PeakCalibrator.cc.

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

Referenced by do_calibration().

void protocols::noesy_assign::PeakCalibrator::reset_statistics

(

)

Definition at line 119 of file PeakCalibrator.cc.

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

Referenced by do_calibration().

void protocols::noesy_assign::PeakCalibrator::set_new_upper_bounds

(

)

Definition at line 245 of file PeakCalibrator.cc.

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
	)

Definition at line 114 of file PeakCalibrator.cc.

References target_, and tolerance_.

Member Data Documentation

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

private

Definition at line 101 of file PeakCalibrator.hh.

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

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

private

Definition at line 98 of file PeakCalibrator.hh.

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

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

private

Definition at line 103 of file PeakCalibrator.hh.

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

Definition at line 105 of file PeakCalibrator.hh.

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

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

private

Definition at line 104 of file PeakCalibrator.hh.

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

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

private

Definition at line 106 of file PeakCalibrator.hh.

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

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

private

Definition at line 97 of file PeakCalibrator.hh.

Referenced by interpolate_on_statistics(), and PeakCalibrator().

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

private

Definition at line 111 of file PeakCalibrator.hh.

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

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

private

Definition at line 114 of file PeakCalibrator.hh.

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

int protocols::noesy_assign::PeakCalibrator::target_sign_

private

Definition at line 115 of file PeakCalibrator.hh.

Referenced by interpolate_on_statistics().

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

private

Definition at line 100 of file PeakCalibrator.hh.

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

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

private

Definition at line 113 of file PeakCalibrator.hh.

Referenced by interpolate_on_statistics(), and set_target_and_tolerance().

---

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

• src/protocols/noesy_assign/PeakCalibrator.hh
• src/protocols/noesy_assign/PeakCalibrator.cc