protocols::noesy_assign::PeakFileFormat Class Reference

#include <PeakFileFormat.hh>

Inheritance diagram for protocols::noesy_assign::PeakFileFormat:

Collaboration diagram for protocols::noesy_assign::PeakFileFormat:

Public Member Functions
	PeakFileFormat ()
	PeakFileFormat (ResonanceListOP const &)
virtual	~PeakFileFormat ()
virtual void	write_peak (std::ostream &, core::Size ct, CrossPeak const &) const
virtual void	write_resonances (std::ostream &, CrossPeak const &) const
virtual void	write_strength (std::ostream &, CrossPeak const &) const
virtual void	write_assignments (std::ostream &, CrossPeak const &, std::string const &first_line_end) const
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
virtual void	read_resonances (std::istream &, CrossPeak &) const
virtual void	read_assignments (std::istream &is, std::istream &rest_line, CrossPeak &, std::string &next_line) const
virtual void	read_strength (std::istream &, CrossPeak &) const
virtual CrossPeakOP	read_peak (std::istream &, std::string &next_line) const
virtual void	read_header (std::istream &, std::string &next_line)
virtual void	output_diagnosis (std::ostream &) const
virtual void	set_format_from_peak (CrossPeak const &)
virtual void	write_header (std::ostream &)
virtual bool	compatible_with_current_format (CrossPeak const &) const
void	set_write_atom_names (bool setting=true)
bool	write_atom_names () const
core::Size	ncol () const
ResonanceList const &	resonances () const
Public Member Functions inherited from protocols::noesy_assign::PeakFileFormat_Base
	PeakFileFormat_Base ()
virtual	~PeakFileFormat_Base ()
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)

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
ResonanceListOP	resonances_
bool	write_atom_names_

Static Private Attributes
static bool	options_registered_

Detailed Description

Definition at line 133 of file PeakFileFormat.hh.

Constructor & Destructor Documentation

protocols::noesy_assign::PeakFileFormat::PeakFileFormat

(

)

Definition at line 76 of file PeakFileFormat.cc.

References options_registered_.

protocols::noesy_assign::PeakFileFormat::PeakFileFormat

(

ResonanceListOP const &

res)

Definition at line 82 of file PeakFileFormat.cc.

References options_registered_.

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

virtual

Definition at line 88 of file PeakFileFormat.cc.

Member Function Documentation

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

virtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

Definition at line 174 of file PeakFileFormat.cc.

References protocols::noesy_assign::CrossPeak::info(), protocols::noesy_assign::PeakFileFormat_Base::info1_, and protocols::noesy_assign::PeakFileFormat_Base::info2_.

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

inline

Definition at line 168 of file PeakFileFormat.hh.

References col2proton_.

Referenced by read_assignments(), read_peak(), read_resonances(), protocols::noesy_assign::PeakFileFormat_xpk::write_assignment(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), write_assignment(), and write_resonances().

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

virtual

Reimplemented from protocols::noesy_assign::PeakFileFormat_Base.

Definition at line 686 of file PeakFileFormat.cc.

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().

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

virtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

Definition at line 515 of file PeakFileFormat.cc.

References protocols::noesy_assign::CrossPeak::add_full_assignment(), col2islabel_, col2proton_, protocols::noesy_assign::CrossPeak::has_label(), protocols::noesy_assign::PeakFileFormat_Base::ignore_assignments(), ncol(), and tr().

Referenced by read_peak().

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

virtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

Definition at line 208 of file PeakFileFormat.cc.

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::loops::start, protocols::noesy_assign::TOL_H_DIRECT(), protocols::noesy_assign::TOL_H_INDIRECT(), protocols::noesy_assign::TOL_LABEL(), and tr().

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

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

virtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

Definition at line 419 of file PeakFileFormat.cc.

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

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

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

virtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

Definition at line 465 of file PeakFileFormat.cc.

References col2islabel_, col2proton_, protocols::noesy_assign::CrossPeak::has_label(), protocols::noesy_assign::CrossPeak::label(), ncol(), protocols::noesy_assign::CrossPeak::proton(), and protocols::noesy_assign::CrossPeak::Spin::set_freq().

Referenced by read_peak().

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

virtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

Definition at line 502 of file PeakFileFormat.cc.

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

Referenced by read_peak().

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

static

Definition at line 61 of file PeakFileFormat.cc.

References protocols::evaluation::options_registered_.

ResonanceList const& protocols::noesy_assign::PeakFileFormat::resonances ( ) const

inline

Definition at line 169 of file PeakFileFormat.hh.

References resonances_.

Referenced by protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), and protocols::noesy_assign::PeakFileFormat_xpk::write_assignment().

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

virtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

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

Definition at line 178 of file PeakFileFormat.cc.

References col2islabel_, col2proton_, protocols::noesy_assign::CrossPeakInfo::has_label(), protocols::noesy_assign::CrossPeak::info(), 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().

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

inline

Definition at line 161 of file PeakFileFormat.hh.

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.

Definition at line 627 of file PeakFileFormat.cc.

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(), and write_atom_names_.

Referenced by write_assignments().

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.

Definition at line 622 of file PeakFileFormat.cc.

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

Referenced by write_assignments().

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.

Definition at line 645 of file PeakFileFormat.cc.

References protocols::noesy_assign::PeakAssignment::dump_weights(), and protocols::noesy_assign::PeakAssignment::normalized_peak_volume().

Referenced by write_assignments().

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

virtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

Definition at line 652 of file PeakFileFormat.cc.

References protocols::noesy_assign::CrossPeak::assignments(), protocols::noesy_assign::PeakFileFormat_Base::min_VC_to_write(), write_assignment(), write_assignment_indent(), write_assignment_stats(), write_nil_assignment(), and protocols::noesy_assign::PeakFileFormat_Base::write_only_highest_VC().

Referenced by protocols::noesy_assign::PeakFileFormat_Sparky::write_peak(), protocols::noesy_assign::PeakFileFormat_xpk::write_peak(), and write_peak().

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

inline

Definition at line 164 of file PeakFileFormat.hh.

References write_atom_names_.

Referenced by protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), and protocols::noesy_assign::PeakFileFormat_xpk::write_assignment().

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

virtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

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

Definition at line 116 of file PeakFileFormat.cc.

References col2proton_, protocols::noesy_assign::PeakFileFormat_Base::filename(), protocols::noesy_assign::PeakFileFormat_Base::info1_, protocols::noesy_assign::PeakFileFormat_Base::info2_, and core::io::serialization::size().

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.

Definition at line 145 of file PeakFileFormat.hh.

Referenced by write_assignments().

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

virtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

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

Definition at line 94 of file PeakFileFormat.cc.

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(), protocols::noesy_assign::CrossPeak::probability(), protocols::noesy_assign::CrossPeak::quality_class(), protocols::noesy_assign::CrossPeak::quality_class_str(), protocols::noesy_assign::CrossPeak::smallest_native_violation(), 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().

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

virtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

Definition at line 484 of file PeakFileFormat.cc.

References col2islabel_, col2proton_, protocols::noesy_assign::CrossPeak::Spin::freq(), protocols::noesy_assign::CrossPeak::has_label(), protocols::noesy_assign::CrossPeak::label(), ncol(), and protocols::noesy_assign::CrossPeak::proton().

Referenced by protocols::noesy_assign::PeakFileFormat_Sparky::write_peak(), protocols::noesy_assign::PeakFileFormat_xpk::write_peak(), and write_peak().

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

virtual

Implements protocols::noesy_assign::PeakFileFormat_Base.

Definition at line 510 of file PeakFileFormat.cc.

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

Referenced by write_peak().

Member Data Documentation

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

protected

Definition at line 173 of file PeakFileFormat.hh.

Referenced by output_diagnosis(), read_assignments(), read_header(), read_resonances(), protocols::noesy_assign::PeakFileFormat_Sparky::set_format_from_peak(), protocols::noesy_assign::PeakFileFormat_xpk::set_format_from_peak(), set_format_from_peak(), protocols::noesy_assign::PeakFileFormat_xpk::write_assignment(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), write_assignment(), and write_resonances().

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

protected

Definition at line 172 of file PeakFileFormat.hh.

Referenced by ncol(), output_diagnosis(), read_assignments(), read_header(), read_peak(), read_resonances(), protocols::noesy_assign::PeakFileFormat_Sparky::set_format_from_peak(), protocols::noesy_assign::PeakFileFormat_xpk::set_format_from_peak(), set_format_from_peak(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), protocols::noesy_assign::PeakFileFormat_xpk::write_assignment(), write_assignment(), write_header(), and write_resonances().

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

protected

Definition at line 171 of file PeakFileFormat.hh.

Referenced by read_header().

bool protocols::noesy_assign::PeakFileFormat::options_registered_

staticprivate

Definition at line 176 of file PeakFileFormat.hh.

Referenced by PeakFileFormat().

ResonanceListOP protocols::noesy_assign::PeakFileFormat::resonances_

private

Definition at line 177 of file PeakFileFormat.hh.

Referenced by resonances().

bool protocols::noesy_assign::PeakFileFormat::write_atom_names_

private

Definition at line 178 of file PeakFileFormat.hh.

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