protocols::noesy_assign::CrossPeakList Class Reference

#include <CrossPeakList.hh>

Inheritance diagram for protocols::noesy_assign::CrossPeakList:

Public Types
typedef std::list< CrossPeakOP >	CrossPeaks
typedef CrossPeaks::const_iterator	const_iterator
typedef CrossPeaks::iterator	iterator

Public Member Functions
	CrossPeakList ()
	~CrossPeakList () override
void	read_from_stream (std::istream &, PeakFileFormat &input_adaptor, ResonanceListOP resonances)
void	write_to_stream (std::ostream &, PeakFileFormat &output_adaptor) const
void	write_peak_files (std::string const &prefix, PeakFileFormat &output_adaptor) const
void	find_assignments ()
void	update_chemshiftscore ()
void	update_symmetry_score ()
void	update_upperdistance_score ()
template<class DecoyIterator >
void	update_decoy_compatibility_score (DecoyIterator const &begin, DecoyIterator const &end)
void	eliminate_spurious_peaks ()
template<class DecoyIterator >
void	calibrate (DecoyIterator const &begin, DecoyIterator const &end)
void	generate_fa_and_cen_constraints (core::scoring::constraints::ConstraintSetOP fa_set, core::scoring::constraints::ConstraintSetOP cen_set, core::pose::Pose const &pose, core::pose::Pose const &centroid_pose, core::Size min_seq_separation, core::Size min_quali, core::Size max_quali, core::Real padding=0.0, bool ignore_elimination_candidates=true, bool elimination_candidates=false) const
PeakAssignmentResidueMap const &	assignments () const
PeakAssignmentResidueMap &	assignments ()
core::Size	count_assignments () const
void	delete_diagonal_peaks ()
void	update_peak_volumina ()
void	network_analysis ()
void	set_trivial_decoy_compatibility_score ()
CrossPeaks const &	peaks () const
const_iterator	begin () const
const_iterator	end () const
iterator	begin ()
iterator	end ()
core::Size	size () const

Private Member Functions
void	update_assignment_list ()
core::Real	calibrate (PeakCalibrator const &calibrator)
	return average upper distance bound More...

Private Attributes
CrossPeaks	peaks_
PeakAssignmentResidueMapOP	assignments_

Member Typedef Documentation

const_iterator

typedef CrossPeaks::const_iterator protocols::noesy_assign::CrossPeakList::const_iterator

CrossPeaks

typedef std::list< CrossPeakOP > protocols::noesy_assign::CrossPeakList::CrossPeaks

iterator

typedef CrossPeaks::iterator protocols::noesy_assign::CrossPeakList::iterator

Constructor & Destructor Documentation

CrossPeakList()

protocols::noesy_assign::CrossPeakList::CrossPeakList

(

)

~CrossPeakList()

protocols::noesy_assign::CrossPeakList::~CrossPeakList ( )

overridedefault

Member Function Documentation

assignments() [1/2]

PeakAssignmentResidueMap& protocols::noesy_assign::CrossPeakList::assignments ( )

inline

References assignments_.

assignments() [2/2]

PeakAssignmentResidueMap const& protocols::noesy_assign::CrossPeakList::assignments ( ) const

inline

References assignments_.

Referenced by update_symmetry_score().

begin() [1/2]

iterator protocols::noesy_assign::CrossPeakList::begin ( )

inline

References peaks_.

begin() [2/2]

const_iterator protocols::noesy_assign::CrossPeakList::begin ( ) const

inline

References peaks_.

Referenced by protocols::noesy_assign::DistanceScoreMover::apply(), calibrate(), delete_diagonal_peaks(), protocols::noesy_assign::DistanceScoreMover::DistanceScoreMover(), eliminate_spurious_peaks(), protocols::noesy_assign::DistanceScoreMover::finalize_scoring(), protocols::noesy_assign::PeakCalibratorMap::PeakCalibratorMap(), protocols::noesy_assign::DistanceScoreMover::prepare_scoring(), set_trivial_decoy_compatibility_score(), update_assignment_list(), update_chemshiftscore(), update_peak_volumina(), and update_upperdistance_score().

calibrate() [1/2]

template<class DecoyIterator >

void protocols::noesy_assign::CrossPeakList::calibrate	(	DecoyIterator const &	begin,
		DecoyIterator const &	end
	)

References begin(), protocols::noesy_assign::PeakAssignmentParameters::calibration_cycles_, protocols::noesy_assign::PeakAssignmentParameters::calibration_eliminate_, protocols::noesy_assign::PeakAssignmentParameters::calibration_target_, protocols::noesy_assign::PeakAssignmentParameters::dcalibrate_, protocols::noesy_assign::PeakCalibratorMap::do_calibration(), protocols::noesy_assign::PeakCalibratorMap::eliminate_violated_constraints(), end(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::jumping::JumpSample::remove_chainbreaks(), protocols::noesy_assign::PeakCalibratorMap::set_target_and_tolerance(), and protocols::noesy_assign::tr().

calibrate() [2/2]

Real protocols::noesy_assign::CrossPeakList::calibrate ( PeakCalibrator const &  calibrator )

private

return average upper distance bound

References begin(), and end().

count_assignments()

Size protocols::noesy_assign::CrossPeakList::count_assignments

(

)

const

Referenced by network_analysis().

delete_diagonal_peaks()

void protocols::noesy_assign::CrossPeakList::delete_diagonal_peaks

(

)

References assignments_, begin(), end(), peaks_, and protocols::noesy_assign::tr().

eliminate_spurious_peaks()

void protocols::noesy_assign::CrossPeakList::eliminate_spurious_peaks

(

)

References begin(), and end().

end() [1/2]

iterator protocols::noesy_assign::CrossPeakList::end ( )

inline

References peaks_.

end() [2/2]

const_iterator protocols::noesy_assign::CrossPeakList::end ( ) const

inline

References peaks_.

Referenced by protocols::noesy_assign::DistanceScoreMover::apply(), calibrate(), delete_diagonal_peaks(), protocols::noesy_assign::DistanceScoreMover::DistanceScoreMover(), eliminate_spurious_peaks(), protocols::noesy_assign::DistanceScoreMover::finalize_scoring(), protocols::noesy_assign::PeakCalibratorMap::PeakCalibratorMap(), protocols::noesy_assign::DistanceScoreMover::prepare_scoring(), set_trivial_decoy_compatibility_score(), update_assignment_list(), update_chemshiftscore(), update_peak_volumina(), and update_upperdistance_score().

find_assignments()

void protocols::noesy_assign::CrossPeakList::find_assignments

(

)

References assignments_, peaks_, and protocols::noesy_assign::tr().

generate_fa_and_cen_constraints()

void protocols::noesy_assign::CrossPeakList::generate_fa_and_cen_constraints	(	core::scoring::constraints::ConstraintSetOP	fa_set,
		core::scoring::constraints::ConstraintSetOP	cen_set,
		core::pose::Pose const &	pose,
		core::pose::Pose const &	centroid_pose,
		core::Size	min_seq_separation,
		core::Size	min_quali,
		core::Size	max_quali,
		core::Real	padding = 0.0,
		bool	ignore_elimination_candidates = true,
		bool	elimination_candidates = false
	)		const

References core::id::EXCN_AtomNotFound::atom(), protocols::noesy_assign::CrossPeak::MAX_CLASS, core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue_type(), core::id::NamedAtomID::rsd(), core::chemical::ResidueType::show_all_atom_names(), and protocols::noesy_assign::tr().

network_analysis()

void protocols::noesy_assign::CrossPeakList::network_analysis

(

)

References assignments_, count_assignments(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::noesy_assign::PeakAssignmentParameters::network_mode_, protocols::noesy_assign::tr(), and update_assignment_list().

peaks()

CrossPeaks const& protocols::noesy_assign::CrossPeakList::peaks ( ) const

inline

References peaks_.

Referenced by protocols::noesy_assign::PeakAssignmentResidueMap::add(), protocols::noesy_assign::PeakAssignmentResidueMap::check_for_symmetric_peaks(), and update_assignment_list().

read_from_stream()

void protocols::noesy_assign::CrossPeakList::read_from_stream	(	std::istream &	is,
		PeakFileFormat &	input_adaptor,
		ResonanceListOP	resonances
	)

References protocols::noesy_assign::PeakFileFormat_Base::ignore_negative_intensity(), protocols::noesy_assign::PeakFileFormat_Base::minimum_peak_intensity(), protocols::noesy_assign::PeakFileFormat::output_diagnosis(), peaks_, protocols::noesy_assign::PeakFileFormat::read_header(), protocols::noesy_assign::PeakFileFormat::read_peak(), protocols::noesy_assign::tr(), and protocols::noesy_assign::PeakFileFormat::write_peak().

set_trivial_decoy_compatibility_score()

void protocols::noesy_assign::CrossPeakList::set_trivial_decoy_compatibility_score

(

)

References begin(), end(), and protocols::noesy_assign::tr().

size()

core::Size protocols::noesy_assign::CrossPeakList::size ( ) const

inline

References peaks_.

update_assignment_list()

void protocols::noesy_assign::CrossPeakList::update_assignment_list ( )

private

References assignments_, begin(), end(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::noesy_assign::PeakAssignmentParameters::network_use_all_covalent_atoms_, and peaks().

Referenced by network_analysis(), and update_symmetry_score().

update_chemshiftscore()

void protocols::noesy_assign::CrossPeakList::update_chemshiftscore

(

)

References begin(), end(), and protocols::noesy_assign::tr().

update_decoy_compatibility_score()

template<class DecoyIterator >

void protocols::noesy_assign::CrossPeakList::update_decoy_compatibility_score	(	DecoyIterator const &	begin,
		DecoyIterator const &	end
	)

References protocols::noesy_assign::PeakAssignmentParameters::dcut_, core::pose::Pose::fold_tree(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::jumping::JumpSample::remove_chainbreaks(), and protocols::noesy_assign::tr().

update_peak_volumina()

void protocols::noesy_assign::CrossPeakList::update_peak_volumina

(

)

References begin(), end(), and protocols::noesy_assign::tr().

update_symmetry_score()

void protocols::noesy_assign::CrossPeakList::update_symmetry_score

(

)

References assignments(), assignments_, protocols::noesy_assign::PeakAssignmentResidueMap::check_for_symmetric_peaks(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::noesy_assign::PeakAssignmentParameters::min_contribution_symmetric_peaks_, protocols::noesy_assign::tr(), and update_assignment_list().

update_upperdistance_score()

void protocols::noesy_assign::CrossPeakList::update_upperdistance_score

(

)

References begin(), end(), and protocols::noesy_assign::tr().

write_peak_files()

void protocols::noesy_assign::CrossPeakList::write_peak_files	(	std::string const &	prefix,
		PeakFileFormat &	output_adaptor
	)		const

References protocols::abinitio::filename(), protocols::noesy_assign::open_stream(), peaks_, protocols::noesy_assign::PeakFileFormat::set_format_from_peak(), protocols::noesy_assign::PeakFileFormat::write_header(), and protocols::noesy_assign::PeakFileFormat::write_peak().

write_to_stream()

void protocols::noesy_assign::CrossPeakList::write_to_stream	(	std::ostream &	os,
		PeakFileFormat &	output_adaptor
	)		const

References peaks_, protocols::noesy_assign::PeakFileFormat::set_format_from_peak(), protocols::noesy_assign::PeakFileFormat::write_header(), and protocols::noesy_assign::PeakFileFormat::write_peak().

Member Data Documentation

assignments_

PeakAssignmentResidueMapOP protocols::noesy_assign::CrossPeakList::assignments_

private

Referenced by assignments(), delete_diagonal_peaks(), find_assignments(), network_analysis(), update_assignment_list(), and update_symmetry_score().

peaks_

CrossPeaks protocols::noesy_assign::CrossPeakList::peaks_

private

Referenced by begin(), delete_diagonal_peaks(), end(), find_assignments(), peaks(), read_from_stream(), size(), write_peak_files(), and write_to_stream().

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

• src/protocols/noesy_assign/CrossPeakList.hh
• src/protocols/noesy_assign/CrossPeakList.cc
• src/protocols/noesy_assign/CrossPeakList.impl.hh