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protocols::noesy_assign::Resonance Class Referenceabstract

#include <Resonance.hh>

Inheritance diagram for protocols::noesy_assign::Resonance:
Inheritance graph
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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

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 
)
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
void protocols::noesy_assign::Resonance::_write_to_stream ( std::ostream &  os) const
private
core::chemical::AA protocols::noesy_assign::Resonance::aa ( ) const
inline

References aa_.

void protocols::noesy_assign::Resonance::add_connected_resonance ( ResonanceAP  ptr)
virtual core::Size protocols::noesy_assign::Resonance::ambiguity ( ) const
inlinevirtual
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 ( )
virtual ResonanceOP protocols::noesy_assign::Resonance::clone ( )
pure virtual
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
Resonance::ResonanceAPs const & protocols::noesy_assign::Resonance::connected_resonances ( ) const
core::Real protocols::noesy_assign::Resonance::error ( ) const
inline

References error_.

Resonance const & protocols::noesy_assign::Resonance::first_connected_resonance ( ) const
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
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
core::Size protocols::noesy_assign::Resonance::label ( ) const
inline
bool protocols::noesy_assign::Resonance::match ( core::Real  freq,
core::Real  error,
FoldResonance const &  folder 
) const
inline
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
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
void protocols::noesy_assign::Resonance::write_to_stream ( std::ostream &  os,
core::chemical::AA  aa 
) const
virtual

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
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
ResonanceAPs protocols::noesy_assign::Resonance::connected_resonance_ptrs_
private
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

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