#include <PeakFileFormat.hh>

Inheritance diagram for protocols::noesy_assign::PeakFileFormat:

Public Member Functions
	PeakFileFormat ()

	~PeakFileFormat () override

void	write_peak (std::ostream &, core::Size ct, CrossPeak const &) const override

void	write_resonances (std::ostream &, CrossPeak const &) const override

void	write_strength (std::ostream &, CrossPeak const &) const override

void	write_assignments (std::ostream &, CrossPeak const &, std::string const &first_line_end) const override

virtual void	write_assignment (std::ostream &, PeakAssignment const &) const

virtual void	write_assignment_indent (std::ostream &, CrossPeak const &) const

virtual void	write_assignment_stats (std::ostream &os, PeakAssignment &pa) const

virtual void	write_nil_assignment (std::ostream &) const

void	read_resonances (std::istream &, CrossPeak &) const override

void	read_assignments (std::istream &is, std::istream &rest_line, CrossPeak &, std::string &next_line) const override

void	read_strength (std::istream &, CrossPeak &) const override

CrossPeakOP	read_peak (std::istream &, std::string &next_line) const override

void	read_header (std::istream &, std::string &next_line) override

void	output_diagnosis (std::ostream &) const override

void	set_format_from_peak (CrossPeak const &) override

void	write_header (std::ostream &) override

bool	compatible_with_current_format (CrossPeak const &) const override

void	set_write_atom_names (bool setting=true)

bool	write_atom_names () const

core::Size	ncol () const

Public Member Functions inherited from protocols::noesy_assign::PeakFileFormat_Base
	PeakFileFormat_Base ()

	~PeakFileFormat_Base () override

void	set_filename (std::string str)

std::string const &	filename () const

bool	ignore_assignments () const

void	set_ignore_assignments (bool setting=true)

bool	write_only_highest_VC () const

void	set_write_only_highest_VC (bool setting=true)

core::Real	min_VC_to_write () const

void	set_min_VC_to_write (core::Real setting)

bool	ignore_negative_intensity () const

void	set_ignore_negative_intensity (bool setting=true)

void	set_minimum_peak_intensity (core::Real setting)

core::Real	minimum_peak_intensity () const

Static Public Member Functions
static void	register_options ()

Protected Attributes
utility::vector1< std::string >	column_labels_

utility::vector1< core::Size >	col2proton_

utility::vector1< bool >	col2islabel_

Protected Attributes inherited from protocols::noesy_assign::PeakFileFormat_Base
CrossPeakInfoOP	info1_

CrossPeakInfoOP	info2_

std::string	filename_

Private Attributes
bool	write_atom_names_

Static Private Attributes
static bool	options_registered_

Constructor & Destructor Documentation

protocols::noesy_assign::PeakFileFormat::PeakFileFormat ( )

References protocols::evaluation::options_registered_.

protocols::noesy_assign::PeakFileFormat::~PeakFileFormat ( )

overridedefault

Member Function Documentation

bool protocols::noesy_assign::PeakFileFormat::compatible_with_current_format ( CrossPeak const & cp ) const

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

References protocols::noesy_assign::CrossPeak::info().

core::Size protocols::noesy_assign::PeakFileFormat::ncol ( ) const

inline

References col2proton_.

void protocols::noesy_assign::PeakFileFormat::output_diagnosis ( std::ostream & os ) const

overridevirtual

Reimplemented from protocols::noesy_assign::PeakFileFormat_Base.

Referenced by protocols::noesy_assign::CrossPeakList::read_from_stream().

void protocols::noesy_assign::PeakFileFormat::read_assignments	(	std::istream &	is,
		std::istream &	rest_line,
		CrossPeak &	cp,
		std::string &	next_line
	)		const

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

References protocols::noesy_assign::CrossPeak::add_full_assignment(), protocols::noesy_assign::CrossPeak::has_label(), tr(), and protocols::hybridization::val.

void protocols::noesy_assign::PeakFileFormat::read_header	(	std::istream &	is,
		std::string &	next_line
	)

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

References protocols::noesy_assign::PeakAssignmentParameters::calibration_max_noe_dist_, core::sequence::end, protocols::abinitio::filename(), protocols::loops::start, core::id::to_string(), protocols::noesy_assign::TOL_H_DIRECT(), protocols::noesy_assign::TOL_H_INDIRECT(), protocols::noesy_assign::TOL_LABEL(), tr(), and protocols::hybridization::val.

Referenced by protocols::noesy_assign::CrossPeakList::read_from_stream().

CrossPeakOP protocols::noesy_assign::PeakFileFormat::read_peak	(	std::istream &	is,
		std::string &	next_line
	)		const

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

References tr().

Referenced by protocols::noesy_assign::CrossPeakList::read_from_stream().

void protocols::noesy_assign::PeakFileFormat::read_resonances	(	std::istream &	is,
		CrossPeak &	cp
	)		const

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

References protocols::noesy_assign::CrossPeak::has_label(), protocols::noesy_assign::CrossPeak::label(), protocols::noesy_assign::CrossPeak::proton(), protocols::noesy_assign::CrossPeak::Spin::set_freq(), and protocols::hybridization::val.

void protocols::noesy_assign::PeakFileFormat::read_strength	(	std::istream &	is,
		CrossPeak &	cp
	)		const

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

References protocols::noesy_assign::CrossPeak::set_volume(), and protocols::hybridization::val.

void protocols::noesy_assign::PeakFileFormat::register_options ( )

static

References protocols::evaluation::options_registered_.

void protocols::noesy_assign::PeakFileFormat::set_format_from_peak ( CrossPeak const & cp )

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

Reimplemented in protocols::noesy_assign::PeakFileFormat_Sparky, and protocols::noesy_assign::PeakFileFormat_xpk.

References protocols::noesy_assign::CrossPeak::info().

Referenced by protocols::noesy_assign::CrossPeakList::write_peak_files(), and protocols::noesy_assign::CrossPeakList::write_to_stream().

void protocols::noesy_assign::PeakFileFormat::set_write_atom_names ( bool setting = true )

inline

References write_atom_names_.

void protocols::noesy_assign::PeakFileFormat::write_assignment	(	std::ostream &	os,
		PeakAssignment const &	pa
	)		const

virtual

Reimplemented in protocols::noesy_assign::PeakFileFormat_Sparky, and protocols::noesy_assign::PeakFileFormat_xpk.

References protocols::noesy_assign::PeakAssignment::atom(), protocols::noesy_assign::PeakAssignment::label_atom(), protocols::noesy_assign::PeakAssignment::label_resonance_id(), protocols::noesy_assign::PeakAssignment::resonance_id(), and protocols::hybridization::val.

void protocols::noesy_assign::PeakFileFormat::write_assignment_indent	(	std::ostream &	os,
		CrossPeak const &	cp
	)		const

virtual

Reimplemented in protocols::noesy_assign::PeakFileFormat_Sparky, and protocols::noesy_assign::PeakFileFormat_xpk.

References protocols::noesy_assign::CrossPeak::has_label().

void protocols::noesy_assign::PeakFileFormat::write_assignment_stats	(	std::ostream &	os,
		PeakAssignment &	pa
	)		const

virtual

Reimplemented in protocols::noesy_assign::PeakFileFormat_Sparky, and protocols::noesy_assign::PeakFileFormat_xpk.

References protocols::noesy_assign::PeakAssignment::dump_weights(), core::chemical::element::F, protocols::noesy_assign::PeakAssignment::normalized_peak_volume(), and protocols::hybridization::val.

void protocols::noesy_assign::PeakFileFormat::write_assignments	(	std::ostream &	os,
		CrossPeak const &	cp,
		std::string const &	first_line_end
	)		const

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

References protocols::noesy_assign::CrossPeak::assignments(), and protocols::hybridization::val.

bool protocols::noesy_assign::PeakFileFormat::write_atom_names ( ) const

inline

References write_atom_names_.

void protocols::noesy_assign::PeakFileFormat::write_header ( std::ostream & os )

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

Reimplemented in protocols::noesy_assign::PeakFileFormat_Sparky, and protocols::noesy_assign::PeakFileFormat_xpk.

References protocols::abinitio::filename(), and core::id::to_string().

Referenced by protocols::noesy_assign::CrossPeakList::write_peak_files(), and protocols::noesy_assign::CrossPeakList::write_to_stream().

virtual void protocols::noesy_assign::PeakFileFormat::write_nil_assignment ( std::ostream & ) const

inlinevirtual

Reimplemented in protocols::noesy_assign::PeakFileFormat_Sparky, and protocols::noesy_assign::PeakFileFormat_xpk.

void protocols::noesy_assign::PeakFileFormat::write_peak	(	std::ostream &	os,
		core::Size	ct,
		CrossPeak const &	cp
	)		const

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

Reimplemented in protocols::noesy_assign::PeakFileFormat_Sparky, and protocols::noesy_assign::PeakFileFormat_xpk.

References protocols::comparative_modeling::features::A, protocols::noesy_assign::CrossPeak::cumulative_peak_volume(), protocols::noesy_assign::CrossPeak::distance_bound(), protocols::noesy_assign::CrossPeak::eliminated(), protocols::noesy_assign::CrossPeak::elimination_reason(), core::chemical::element::F, core::chemical::element::I, protocols::noesy_assign::CrossPeak::probability(), protocols::noesy_assign::CrossPeak::quality_class(), protocols::noesy_assign::CrossPeak::quality_class_str(), and protocols::noesy_assign::CrossPeak::smallest_native_violation().

Referenced by protocols::noesy_assign::CrossPeakList::read_from_stream(), protocols::noesy_assign::CrossPeakList::write_peak_files(), and protocols::noesy_assign::CrossPeakList::write_to_stream().

void protocols::noesy_assign::PeakFileFormat::write_resonances	(	std::ostream &	os,
		CrossPeak const &	cp
	)		const

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

References core::chemical::element::F, protocols::noesy_assign::CrossPeak::Spin::freq(), protocols::noesy_assign::CrossPeak::has_label(), protocols::noesy_assign::CrossPeak::label(), protocols::noesy_assign::CrossPeak::proton(), and protocols::hybridization::val.

void protocols::noesy_assign::PeakFileFormat::write_strength	(	std::ostream &	os,
		CrossPeak const &	cp
	)		const

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

References protocols::comparative_modeling::features::E, and protocols::noesy_assign::CrossPeak::volume().

Member Data Documentation

utility::vector1< bool > protocols::noesy_assign::PeakFileFormat::col2islabel_

protected

utility::vector1< core::Size > protocols::noesy_assign::PeakFileFormat::col2proton_

protected

Referenced by ncol().

utility::vector1< std::string > protocols::noesy_assign::PeakFileFormat::column_labels_

protected

bool protocols::noesy_assign::PeakFileFormat::options_registered_

staticprivate

bool protocols::noesy_assign::PeakFileFormat::write_atom_names_

private

Referenced by set_write_atom_names(), and write_atom_names().

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

src/protocols/noesy_assign/PeakFileFormat.hh
src/protocols/noesy_assign/PeakFileFormat.cc

Public Member Functions

Static Public Member Functions

Protected Attributes

Private Attributes

Static Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation