#include <ResonanceList.hh>

Public Types
typedef utility::vector1 < ResonanceOP >	Resonances

typedef ResonanceIDs::const_iterator	const_iterator
	iterators More...

Public Member Functions
	ResonanceList (std::string const &sequence)
	Constructor. More...

virtual	~ResonanceList ()

void	read_from_stream (std::istream &)
	read chemical shift assignments More...

void	write_to_stream (std::ostream &) const
	write chemical shift assignments More...

void	write_talos_format (std::ostream &, bool backbone_only) const
	write in talos format More...

Resonance const &	operator[] (core::Size key) const
	retrieve a Resonance by ResonanceID — throws EXCN_UnknonwResonance if atom not found More...

Resonance const &	operator[] (core::id::NamedAtomID const &) const
	retrive a Resonance by atom — throws EXCN_UnknonwResonance if atom not found More...

Resonances const &	resonances_at_residue (core::Size resid) const
	all resonances of a certain residue — requires that update_residue_map() has been called (which is done by read_from_stream() ) More...

const_iterator	begin () const

const_iterator	end () const

bool	has_residue (core::Size resi) const
	have at least one resonance for residue "resi" More...

core::chemical::AA	aa_from_resid (core::Size resi) const
	retrieve aminoacid of residue "resi" More...

std::string const &	sequence () const
	retrieve the protein sequence More...

core::Size	size () const
	number of Resonances More...

core::Size	start_key () const
	first ResonanceID (given by input file) More...

core::Size	last_key () const
	last ResonanceID ( given by input file ) More...

Protected Member Functions
Resonance const &	operator[] (core::Size key)
	retrieve a Resonance by ResonanceID — no error checking More...

void	update_residue_map ()
	sort Resonances by residue number and store in by_resid_ More...

Private Types
typedef std::map< core::Size, Resonances >	ResidueMap

typedef std::map< core::Size, ResonanceOP >	ResonanceIDs

Private Member Functions
	ResonanceList (ResonanceList const &a)

ResonanceList &	operator= (ResonanceList const &)

Private Attributes
ResonanceIDs	map_
	master map... More...

ResidueMap	by_resid_
	slave map... created by update_residue_map() More...

std::string	sequence_
	sequence of the proteion More...

Detailed Description

: the ResonanceList provides a map of chemical shifts. each atom-chemical shift tupel has a "resonanceID" as a key. (integer)

used classes:

Resonance is an atom with chemical shift information ResonanceIDs (typedef) is a map from ID to Resonance ResidueMap (typedef) is a map from residue number to a vector of Resonances.

Member Typedef Documentation

typedef ResonanceIDs::const_iterator protocols::noesy_assign::ResonanceList::const_iterator

iterators

typedef std::map< core::Size, Resonances > protocols::noesy_assign::ResonanceList::ResidueMap

private

typedef std::map< core::Size, ResonanceOP > protocols::noesy_assign::ResonanceList::ResonanceIDs

private

typedef utility::vector1< ResonanceOP > protocols::noesy_assign::ResonanceList::Resonances

Constructor & Destructor Documentation

protocols::noesy_assign::ResonanceList::ResonanceList ( ResonanceList const & a )

inlineprivate

protocols::noesy_assign::ResonanceList::ResonanceList ( std::string const & sequence )

Constructor.

protocols::noesy_assign::ResonanceList::~ResonanceList ( )

virtual

Member Function Documentation

core::chemical::AA protocols::noesy_assign::ResonanceList::aa_from_resid ( core::Size resi ) const

retrieve aminoacid of residue "resi"

translate sequence information into AA

References core::chemical::aa_from_oneletter_code(), runtime_assert, and sequence_.

Referenced by protocols::noesy_assign::CrossPeak3D::assign_labelled_spin(), read_from_stream(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), protocols::noesy_assign::PeakFileFormat_xpk::write_assignment(), write_talos_format(), and write_to_stream().

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

inline

References map_.

Referenced by protocols::noesy_assign::PeakAssignmentResidueMap::add_all_atoms(), and protocols::noesy_assign::CrossPeak3D::assign_labelled_spin().

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

inline

References map_.

Referenced by protocols::noesy_assign::PeakAssignmentResidueMap::add_all_atoms(), protocols::noesy_assign::CrossPeak3D::assign_labelled_spin(), and protocols::noesy_assign::CrossPeak::assign_spin().

bool protocols::noesy_assign::ResonanceList::has_residue ( core::Size resi ) const

have at least one resonance for residue "resi"

References by_resid_.

core::Size protocols::noesy_assign::ResonanceList::last_key ( ) const

inline

last ResonanceID ( given by input file )

References map_.

ResonanceList& protocols::noesy_assign::ResonanceList::operator= ( ResonanceList const & )

inlineprivate

Resonance const & protocols::noesy_assign::ResonanceList::operator[] ( core::Size key ) const

retrieve a Resonance by ResonanceID — throws EXCN_UnknonwResonance if atom not found

retrieve Resonance — throws EXCN_UnknonwResonance if atom not found

References map_.

Resonance const & protocols::noesy_assign::ResonanceList::operator[] ( core::id::NamedAtomID const & atom ) const

retrive a Resonance by atom — throws EXCN_UnknonwResonance if atom not found

retrieve Resonance — throws EXCN_UnknonwResonance if atom not found

References by_resid_, map_, and core::id::NamedAtomID::rsd().

Resonance const& protocols::noesy_assign::ResonanceList::operator[] ( core::Size key )

inlineprotected

retrieve a Resonance by ResonanceID — no error checking

References map_.

void protocols::noesy_assign::ResonanceList::read_from_stream ( std::istream & is )

ResonanceList::Resonances const & protocols::noesy_assign::ResonanceList::resonances_at_residue ( core::Size resid ) const

all resonances of a certain residue — requires that update_residue_map() has been called (which is done by read_from_stream() )

retrieve list of Resonance at certain residue — throws EXCN_UnknonwResonance if residue number not found

References by_resid_.

std::string const& protocols::noesy_assign::ResonanceList::sequence ( ) const

inline

retrieve the protein sequence

References sequence_.

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

inline

number of Resonances

References map_.

core::Size protocols::noesy_assign::ResonanceList::start_key ( ) const

inline

first ResonanceID (given by input file)

References map_.

void protocols::noesy_assign::ResonanceList::update_residue_map ( )

protected

sort Resonances by residue number and store in by_resid_

create map with all resonances sorted by residue number

References by_resid_, map_, and runtime_assert.

Referenced by read_from_stream().

void protocols::noesy_assign::ResonanceList::write_talos_format	(	std::ostream &	os,
		bool	backbone_only
	)		const

write in talos format

write ResonanceList in TALOS format

References aa_from_resid(), map_, oneletter_code_from_aa(), runtime_assert, sequence_, protocols::noesy_assign::tr, and utility_exit_with_message.

void protocols::noesy_assign::ResonanceList::write_to_stream ( std::ostream & os ) const

write chemical shift assignments

write ResonanceList to stream

References aa_from_resid(), map_, runtime_assert, and sequence_.

Member Data Documentation

ResidueMap protocols::noesy_assign::ResonanceList::by_resid_

private

slave map... created by update_residue_map()

Referenced by has_residue(), operator[](), resonances_at_residue(), and update_residue_map().

ResonanceIDs protocols::noesy_assign::ResonanceList::map_

private

master map...

Referenced by begin(), end(), last_key(), operator[](), read_from_stream(), size(), start_key(), update_residue_map(), write_talos_format(), and write_to_stream().

std::string protocols::noesy_assign::ResonanceList::sequence_

private

sequence of the proteion

Referenced by aa_from_resid(), read_from_stream(), sequence(), write_talos_format(), and write_to_stream().

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

symlinks/rosetta/src/protocols/noesy_assign/ResonanceList.hh
symlinks/rosetta/src/protocols/noesy_assign/ResonanceList.cc

Public Types

Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation