protocols::noesy_assign::PeakFileFormat Class Reference

#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

PeakFileFormat()

protocols::noesy_assign::PeakFileFormat::PeakFileFormat

(

)

References options_registered_.

~PeakFileFormat()

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

overridedefault

Member Function Documentation

compatible_with_current_format()

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

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

References protocols::noesy_assign::PeakFileFormat_Base::info1_, and protocols::noesy_assign::PeakFileFormat_Base::info2_.

ncol()

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

inline

References col2proton_.

Referenced by read_assignments(), read_peak(), read_resonances(), write_assignment(), and write_resonances().

output_diagnosis()

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

overridevirtual

Reimplemented from protocols::noesy_assign::PeakFileFormat_Base.

References col2islabel_, col2proton_, protocols::noesy_assign::PeakFileFormat_Base::info1_, and protocols::noesy_assign::PeakFileFormat_Base::info2_.

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

read_assignments()

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 col2islabel_, col2proton_, protocols::noesy_assign::PeakFileFormat_Base::ignore_assignments(), ncol(), protocols::noesy_assign::tr(), and protocols::hybridization::val.

Referenced by read_peak().

read_header()

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_, col2islabel_, col2proton_, column_labels_, core::sequence::end, protocols::noesy_assign::PeakFileFormat_Base::filename(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::noesy_assign::PeakFileFormat_Base::info1_, protocols::noesy_assign::PeakFileFormat_Base::info2_, output_diagnosis(), protocols::noesy_assign::PeakFileFormat_Base::set_filename(), protocols::noesy_assign::PeakFileFormat_Base::set_ignore_negative_intensity(), protocols::noesy_assign::PeakFileFormat_Base::set_minimum_peak_intensity(), protocols::loops::start, core::id::to_string(), protocols::noesy_assign::TOL_H_DIRECT(), protocols::noesy_assign::TOL_H_INDIRECT(), protocols::noesy_assign::TOL_LABEL(), protocols::noesy_assign::tr(), and protocols::hybridization::val.

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

read_peak()

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

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

References col2proton_, protocols::noesy_assign::PeakFileFormat_Base::info1_, protocols::noesy_assign::PeakFileFormat_Base::info2_, ncol(), read_assignments(), read_resonances(), read_strength(), and protocols::noesy_assign::tr().

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

read_resonances()

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

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

References col2islabel_, col2proton_, ncol(), and protocols::hybridization::val.

Referenced by read_peak().

read_strength()

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

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

References protocols::hybridization::val.

Referenced by read_peak().

register_options()

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

static

References options_registered_.

Referenced by protocols::noesy_assign::NoesyModule::register_options().

set_format_from_peak()

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_xpk, and protocols::noesy_assign::PeakFileFormat_Sparky.

References col2islabel_, col2proton_, protocols::noesy_assign::PeakFileFormat_Base::info1_, protocols::noesy_assign::PeakFileFormat_Base::info2_, and protocols::noesy_assign::PeakFileFormat_Base::set_filename().

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

set_write_atom_names()

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

inline

References write_atom_names_.

write_assignment()

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

virtual

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

References protocols::noesy_assign::PeakAssignment::atom(), col2islabel_, col2proton_, protocols::noesy_assign::PeakAssignment::label_atom(), protocols::noesy_assign::PeakAssignment::label_resonance_id(), ncol(), protocols::noesy_assign::PeakAssignment::resonance_id(), protocols::hybridization::val, and write_atom_names_.

Referenced by write_assignments().

write_assignment_indent()

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

virtual

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

Referenced by write_assignments().

write_assignment_stats()

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

virtual

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

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

Referenced by write_assignments().

write_assignments()

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::PeakFileFormat_Base::min_VC_to_write(), protocols::hybridization::val, write_assignment(), write_assignment_indent(), write_assignment_stats(), write_nil_assignment(), and protocols::noesy_assign::PeakFileFormat_Base::write_only_highest_VC().

Referenced by write_peak().

write_atom_names()

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

inline

References write_atom_names_.

write_header()

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

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

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

References col2proton_, protocols::noesy_assign::PeakFileFormat_Base::filename(), protocols::noesy_assign::PeakFileFormat_Base::info1_, protocols::noesy_assign::PeakFileFormat_Base::info2_, and core::id::to_string().

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

write_nil_assignment()

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

inlinevirtual

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

Referenced by write_assignments().

write_peak()

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_xpk, and protocols::noesy_assign::PeakFileFormat_Sparky.

References protocols::comparative_modeling::features::A, core::chemical::element::F, core::chemical::element::I, write_assignments(), write_resonances(), and write_strength().

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

write_resonances()

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

overridevirtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

References col2islabel_, col2proton_, core::chemical::element::F, ncol(), and protocols::hybridization::val.

Referenced by write_peak().

write_strength()

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.

Referenced by write_peak().

Member Data Documentation

col2islabel_

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

protected

Referenced by output_diagnosis(), read_assignments(), read_header(), read_resonances(), set_format_from_peak(), write_assignment(), and write_resonances().

col2proton_

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

protected

Referenced by ncol(), output_diagnosis(), read_assignments(), read_header(), read_peak(), read_resonances(), set_format_from_peak(), write_assignment(), write_header(), and write_resonances().

column_labels_

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

protected

Referenced by read_header().

options_registered_

bool protocols::noesy_assign::PeakFileFormat::options_registered_

staticprivate

Referenced by PeakFileFormat(), and register_options().

write_atom_names_

bool protocols::noesy_assign::PeakFileFormat::write_atom_names_

private

Referenced by set_write_atom_names(), write_assignment(), and write_atom_names().

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

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