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protocols::noesy_assign::ResonanceList Class Reference

#include <ResonanceList.hh>

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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.

Definition at line 64 of file ResonanceList.hh.

Member Typedef Documentation

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

iterators

Definition at line 103 of file ResonanceList.hh.

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

Definition at line 70 of file ResonanceList.hh.

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

Definition at line 71 of file ResonanceList.hh.

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

Definition at line 67 of file ResonanceList.hh.

Constructor & Destructor Documentation

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

Definition at line 73 of file ResonanceList.hh.

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

Constructor.

Definition at line 69 of file ResonanceList.cc.

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

Definition at line 72 of file ResonanceList.cc.

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

Definition at line 75 of file ResonanceList.cc.

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

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

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

Definition at line 105 of file ResonanceList.hh.

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

Definition at line 106 of file ResonanceList.hh.

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"

Definition at line 410 of file ResonanceList.cc.

References by_resid_.

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

last ResonanceID ( given by input file )

Definition at line 124 of file ResonanceList.hh.

References map_.

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

Definition at line 76 of file ResonanceList.hh.

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

Definition at line 382 of file ResonanceList.cc.

References core::id::BOGUS_NAMED_ATOM_ID, and 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

Definition at line 369 of file ResonanceList.cc.

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

Definition at line 128 of file ResonanceList.hh.

References map_.

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

read chemical shift assignments

Definition at line 143 of file ResonanceList.cc.

References core::chemical::aa_ala, core::chemical::aa_from_name(), core::chemical::aa_from_oneletter_code(), aa_from_resid(), core::chemical::aa_gly, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_thr, core::chemical::aa_val, protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::noesy_assign::PeakAssignmentParameters::ignore_resonancefile_intensities_, protocols::noesy_assign::PeakAssignmentParameters::ignore_resonancefile_tolerances_, map_, core::chemical::name_from_aa(), core::chemical::oneletter_code_from_aa(), core::scoring::constraints::parse_NMR_name(), protocols::noesy_assign::process_last_resonances(), sequence_, tr(), and update_residue_map().

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

Definition at line 400 of file ResonanceList.cc.

References core::id::BOGUS_NAMED_ATOM_ID, and by_resid_.

Referenced by protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis2().

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

retrieve the protein sequence

Definition at line 115 of file ResonanceList.hh.

References sequence_.

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

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

number of Resonances

Definition at line 118 of file ResonanceList.hh.

References map_.

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

first ResonanceID (given by input file)

Definition at line 121 of file ResonanceList.hh.

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

Definition at line 391 of file ResonanceList.cc.

References by_resid_, and map_.

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

Definition at line 314 of file ResonanceList.cc.

References aa_from_resid(), map_, core::chemical::oneletter_code_from_aa(), sequence_, and tr().

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

write chemical shift assignments

write ResonanceList to stream

Definition at line 299 of file ResonanceList.cc.

References aa_from_resid(), map_, and sequence_.

Member Data Documentation

ResidueMap protocols::noesy_assign::ResonanceList::by_resid_
private

slave map... created by update_residue_map()

Definition at line 138 of file ResonanceList.hh.

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

ResonanceIDs protocols::noesy_assign::ResonanceList::map_
private

master map...

Definition at line 135 of file ResonanceList.hh.

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

Definition at line 141 of file ResonanceList.hh.

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:
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