protocols::noesy_assign::Resonance Class Reference

#include <Resonance.hh>

Inheritance diagram for protocols::noesy_assign::Resonance:

Public Types
typedef utility::vector1 < core::Size >	ResonanceIDs
typedef std::pair< core::Size, core::Size >	ResonancePair
typedef utility::vector1 < ResonancePair >	ResonancePairs
typedef utility::vector1 < ResonanceAP >	ResonanceAPs

Public Member Functions
	Resonance ()
	Resonance (core::Size label, core::Real freq, core::Real error, core::id::NamedAtomID const &id, core::chemical::AA, core::Real intensity=1.0)
	~Resonance () override
virtual ResonanceOP	clone ()=0
virtual void	write_to_stream (std::ostream &) const
	output More...
virtual void	write_to_stream (std::ostream &, core::chemical::AA aa) const
virtual core::Size	ambiguity () const
core::Size	label () const
	ResonanceID. More...
virtual core::Size	float_label (core::Size) const
core::id::NamedAtomID const &	atom () const
	Atom. More...
core::Size	resid () const
std::string const &	name () const
bool	is_proton () const
core::Real	freq () const
	resonance frequency (chemical shift) More...
core::Real	error () const
core::Real	tolerance () const
bool	match (core::Real freq, core::Real error, FoldResonance const &folder) const
	Resonance matches the given cross-peaks frequency. More...
virtual bool	match2D (core::Real proton_freq, core::Real proton_error, FoldResonance const &proton_folder, core::Real label_freq, core::Real label_error, FoldResonance const &label_folder, ResonancePairs &matches) const =0
	match the proton and corresponding label atom at same time More...
void	add_connected_resonance (ResonanceAP ptr)
void	clear_connected_resonances ()
bool	has_connected_resonances () const
Resonance const &	first_connected_resonance () const
ResonanceIDs const &	connected_resonance_ids () const
ResonanceAPs const &	connected_resonances () const
virtual core::Real	pmatch (core::Real freq, core::Real error, FoldResonance const &folder) const
void	combine (std::deque< ResonanceOP > &last_resonances, bool drain)
core::chemical::AA	aa () const
core::Real	intensity () const
	in ILV-labelled proteins, the both LV methyls are labelled randomly with 50% probability, whereas I delta methyls are labelled 100% More...
void	set_intensity (core::Real setting)
CALIBRATION_ATOM_TYPE	calibration_atom_type () const
	classification for calibration... e.g., Backbone, sidechain, etc.. More...
core::Real	_pmatch (core::Real freq, core::Real error, FoldResonance const &folder) const

Private Member Functions
void	_write_to_stream (std::ostream &) const

Private Attributes
core::Size	label_
core::Real	freq_
core::Real	error_
bool	is_proton_
core::id::NamedAtomID	atom_
core::chemical::AA	aa_
core::Real	intensity_
CALIBRATION_ATOM_TYPE	calibration_atom_type_
ResonanceIDs	connected_resonance_ids_
ResonanceAPs	connected_resonance_ptrs_

Detailed Description

Resonance combines resonanceID (label), chemical shift (freq), tolerance (error), and the assigned atom (atom, name, resid) (provided accessor methods of "Resonance": label, atom, resid, name, freq, error, tolerance, calibration_atom_type )

Member Typedef Documentation

typedef utility::vector1< ResonanceAP > protocols::noesy_assign::Resonance::ResonanceAPs

typedef utility::vector1< core::Size > protocols::noesy_assign::Resonance::ResonanceIDs

typedef std::pair< core::Size, core::Size > protocols::noesy_assign::Resonance::ResonancePair

typedef utility::vector1< ResonancePair > protocols::noesy_assign::Resonance::ResonancePairs

Constructor & Destructor Documentation

protocols::noesy_assign::Resonance::Resonance ( )

default

protocols::noesy_assign::Resonance::Resonance	(	core::Size	label,
		core::Real	freq,
		core::Real	error,
		core::id::NamedAtomID const &	id,
		core::chemical::AA	aa,
		core::Real	intensity = 1.0
	)

References aa_, protocols::noesy_assign::PeakCalibrator::atom_type(), calibration_atom_type_, and is_proton_.

protocols::noesy_assign::Resonance::~Resonance ( )

overridedefault

Member Function Documentation

core::Real protocols::noesy_assign::Resonance::_pmatch	(	core::Real	freq,
		core::Real	error,
		FoldResonance const &	folder
	)		const

References freq(), protocols::mean_field::max(), and tolerance().

Referenced by protocols::noesy_assign::FloatingResonance::match2D(), and pmatch().

void protocols::noesy_assign::Resonance::_write_to_stream ( std::ostream &  os ) const

private

References core::id::NamedAtomID::atom(), atom_, error_, core::chemical::element::F, freq_, label_, and core::id::NamedAtomID::rsd().

Referenced by write_to_stream().

core::chemical::AA protocols::noesy_assign::Resonance::aa ( ) const

inline

References aa_.

void protocols::noesy_assign::Resonance::add_connected_resonance

(

ResonanceAP

ptr

)

References connected_resonance_ids_, and connected_resonance_ptrs_.

virtual core::Size protocols::noesy_assign::Resonance::ambiguity ( ) const

inlinevirtual

Reimplemented in protocols::noesy_assign::FloatingResonance.

Referenced by protocols::noesy_assign::PeakAssignment::float_ambiguity().

core::id::NamedAtomID const& protocols::noesy_assign::Resonance::atom ( ) const

inline

Atom.

References atom_.

CALIBRATION_ATOM_TYPE protocols::noesy_assign::Resonance::calibration_atom_type ( ) const

inline

classification for calibration... e.g., Backbone, sidechain, etc..

References calibration_atom_type_.

void protocols::noesy_assign::Resonance::clear_connected_resonances

(

)

References connected_resonance_ids_, and connected_resonance_ptrs_.

virtual ResonanceOP protocols::noesy_assign::Resonance::clone ( )

pure virtual

Implemented in protocols::noesy_assign::LabelResonance, protocols::noesy_assign::ProtonResonance, and protocols::noesy_assign::FloatingResonance.

void protocols::noesy_assign::Resonance::combine	(	std::deque< ResonanceOP > &	last_resonances,
		bool	drain = false
	)

References atom_, intensity(), intensity_, name(), and resid().

ResonanceIDs const& protocols::noesy_assign::Resonance::connected_resonance_ids ( ) const

inline

References connected_resonance_ids_.

Resonance::ResonanceAPs const & protocols::noesy_assign::Resonance::connected_resonances

(

)

const

References connected_resonance_ptrs_.

Referenced by protocols::noesy_assign::LabelResonance::match2D(), and protocols::noesy_assign::FloatingResonance::match2D().

core::Real protocols::noesy_assign::Resonance::error ( ) const

inline

References error_.

Resonance const & protocols::noesy_assign::Resonance::first_connected_resonance

(

)

const

References connected_resonance_ptrs_.

Referenced by protocols::noesy_assign::ProtonResonance::match2D(), and protocols::noesy_assign::FloatingResonance::match2D().

virtual core::Size protocols::noesy_assign::Resonance::float_label ( core::Size  ) const

inlinevirtual

Reimplemented in protocols::noesy_assign::FloatingResonance.

References label_.

core::Real protocols::noesy_assign::Resonance::freq ( ) const

inline

resonance frequency (chemical shift)

References freq_.

Referenced by _pmatch().

bool protocols::noesy_assign::Resonance::has_connected_resonances ( ) const

inline

References connected_resonance_ids_.

Referenced by protocols::noesy_assign::ProtonResonance::match2D(), protocols::noesy_assign::LabelResonance::match2D(), and protocols::noesy_assign::FloatingResonance::match2D().

core::Real protocols::noesy_assign::Resonance::intensity ( ) const

inline

in ILV-labelled proteins, the both LV methyls are labelled randomly with 50% probability, whereas I delta methyls are labelled 100%

References intensity_.

Referenced by combine().

bool protocols::noesy_assign::Resonance::is_proton ( ) const

inline

References is_proton_.

Referenced by protocols::noesy_assign::FloatingResonance::match2D().

core::Size protocols::noesy_assign::Resonance::label ( ) const

inline

ResonanceID.

References label_.

Referenced by protocols::noesy_assign::FloatingResonance::FloatingResonance(), protocols::noesy_assign::ProtonResonance::match2D(), protocols::noesy_assign::LabelResonance::match2D(), protocols::noesy_assign::FloatingResonance::match2D(), and protocols::noesy_assign::ResonanceList::update_bond_connections().

bool protocols::noesy_assign::Resonance::match ( core::Real  freq, core::Real  error, FoldResonance const &  folder  ) const

inline

Resonance matches the given cross-peaks frequency.

References pmatch().

Referenced by protocols::noesy_assign::ProtonResonance::match2D(), and protocols::noesy_assign::LabelResonance::match2D().

virtual bool protocols::noesy_assign::Resonance::match2D ( core::Real  proton_freq, core::Real  proton_error, FoldResonance const &  proton_folder, core::Real  label_freq, core::Real  label_error, FoldResonance const &  label_folder, ResonancePairs &  matches  ) const

pure virtual

match the proton and corresponding label atom at same time

Implemented in protocols::noesy_assign::FloatingResonance, protocols::noesy_assign::LabelResonance, and protocols::noesy_assign::ProtonResonance.

std::string const& protocols::noesy_assign::Resonance::name ( ) const

inline

References core::id::NamedAtomID::atom(), and atom_.

Referenced by combine().

core::Real protocols::noesy_assign::Resonance::pmatch ( core::Real  freq, core::Real  error, FoldResonance const &  folder  ) const

virtual

Reimplemented in protocols::noesy_assign::FloatingResonance.

References _pmatch().

Referenced by match(), and protocols::noesy_assign::PeakAssignment::update_chemshiftscore_from_peak().

core::Size protocols::noesy_assign::Resonance::resid ( ) const

inline

References atom_, and core::id::NamedAtomID::rsd().

Referenced by combine().

void protocols::noesy_assign::Resonance::set_intensity ( core::Real  setting )

inline

References intensity_.

core::Real protocols::noesy_assign::Resonance::tolerance ( ) const

inline

References error_.

Referenced by _pmatch().

void protocols::noesy_assign::Resonance::write_to_stream ( std::ostream &  os ) const

virtual

output

Reimplemented in protocols::noesy_assign::FloatingResonance.

References _write_to_stream().

Referenced by protocols::noesy_assign::FloatingResonance::write_to_stream().

void protocols::noesy_assign::Resonance::write_to_stream ( std::ostream &  os, core::chemical::AA  aa  ) const

virtual

Reimplemented in protocols::noesy_assign::FloatingResonance.

References _write_to_stream(), core::chemical::name_from_aa(), and core::chemical::oneletter_code_from_aa().

Member Data Documentation

core::chemical::AA protocols::noesy_assign::Resonance::aa_

private

Referenced by aa(), and Resonance().

core::id::NamedAtomID protocols::noesy_assign::Resonance::atom_

private

Referenced by _write_to_stream(), atom(), combine(), name(), and resid().

CALIBRATION_ATOM_TYPE protocols::noesy_assign::Resonance::calibration_atom_type_

private

Referenced by calibration_atom_type(), and Resonance().

ResonanceIDs protocols::noesy_assign::Resonance::connected_resonance_ids_

private

Referenced by add_connected_resonance(), clear_connected_resonances(), connected_resonance_ids(), and has_connected_resonances().

ResonanceAPs protocols::noesy_assign::Resonance::connected_resonance_ptrs_

private

Referenced by add_connected_resonance(), clear_connected_resonances(), connected_resonances(), and first_connected_resonance().

core::Real protocols::noesy_assign::Resonance::error_

private

Referenced by _write_to_stream(), error(), and tolerance().

core::Real protocols::noesy_assign::Resonance::freq_

private

Referenced by _write_to_stream(), and freq().

core::Real protocols::noesy_assign::Resonance::intensity_

private

Referenced by combine(), intensity(), and set_intensity().

bool protocols::noesy_assign::Resonance::is_proton_

private

Referenced by is_proton(), and Resonance().

core::Size protocols::noesy_assign::Resonance::label_

private

Referenced by _write_to_stream(), float_label(), and label().

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

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