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protocols::noesy_assign::PeakAssignmentResidueMap Class Reference

fast access to assignments by residue number More...

#include <PeakAssignmentResidueMap.hh>

Inheritance diagram for protocols::noesy_assign::PeakAssignmentResidueMap:
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Public Types

typedef std::list
< PeakAssignmentOP
PeakAssignments
 
typedef std::map< core::Size,
PeakAssignments
PeakAssignmentMap
 
typedef utility::vector1
< PeakAssignmentMap
ResidueList
 

Public Member Functions

 PeakAssignmentResidueMap ()
 
 ~PeakAssignmentResidueMap () override
 
void add (CrossPeakList const &)
 add all PeakAssignments in all Crosspeaks of list More...
 
void add (PeakAssignmentOP const &)
 add individual PeakAssignment More...
 
void add_all_atoms (ResonanceList const &)
 add all resonances for backward compatibility in covalent-part of network-analysis More...
 
void remove (PeakAssignment const &)
 remove individual PeakAssignment More...
 
void check_for_symmetric_peaks (CrossPeakList &, bool accumulate_symmetry)
 invalidate non symmetric peaks More...
 
void network_analysis (core::Size n_total_assignments)
 remove all ambiguous assignments to i,i+1 CrossPeaks. More...
 
void network_analysis2 ()
 
PeakAssignments const & assignments (core::Size resi, core::Size resj) const
 get list of PeakAssignments for pair of residues — throws Exception More...
 
PeakAssignmentsassignments (core::Size resi, core::Size resj)
 
void assignments (core::Size resi, core::Size resj, PeakAssignments &collector) const
 add assignments found between resi and resj to collector More...
 
bool has (core::Size resi, core::Size resj)
 has some (valid or invalid) assignments between residue pair More...
 
core::Size total_residue () const
 

Private Types

typedef std::set
< core::id::NamedAtomID
AtomList
 
typedef utility::vector1
< AtomList
AtomByResList
 

Private Member Functions

PeakAssignments const & _assignments (core::Size resi, core::Size resj) const
 same as "assignments()" but returns BOGUS_ASSIGNMENTS if not found More...
 
PeakAssignments_assignments (core::Size resi, core::Size resj)
 
core::Real compute_Nk (PeakAssignment const &alpha_beta, core::id::NamedAtomID const &gamma_atom, bool connect_in_i, bool connect_in_j, bool sequential, PeakAssignments const &close_to_i_assignments, PeakAssignments const &close_to_j_assignments, core::Real longrange_peak_volume) const
 subroutine to compute Nk for alpha->gamma->beta path. More...
 
void fill_covalent_gammas (core::Size, std::map< core::id::NamedAtomID, bool > &collector) const
 subroutine to collect putative gammas that need to be queried due to covalent structure More...
 

Private Attributes

ResidueList residues_
 
PeakAssignments BOGUS_ASSIGNMENTS
 
AtomByResList atoms_
 

Detailed Description

fast access to assignments by residue number

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::noesy_assign::PeakAssignmentResidueMap::PeakAssignmentResidueMap ( )
protocols::noesy_assign::PeakAssignmentResidueMap::~PeakAssignmentResidueMap ( )
overridedefault

Member Function Documentation

PeakAssignments const& protocols::noesy_assign::PeakAssignmentResidueMap::_assignments ( core::Size  resi,
core::Size  resj 
) const
private

same as "assignments()" but returns BOGUS_ASSIGNMENTS if not found

Referenced by check_for_symmetric_peaks(), has(), and network_analysis2().

PeakAssignmentResidueMap::PeakAssignments & protocols::noesy_assign::PeakAssignmentResidueMap::_assignments ( core::Size  resi,
core::Size  resj 
)
private
void protocols::noesy_assign::PeakAssignmentResidueMap::add ( CrossPeakList const &  cpl)

add all PeakAssignments in all Crosspeaks of list

References protocols::noesy_assign::CrossPeakList::peaks().

void protocols::noesy_assign::PeakAssignmentResidueMap::add ( PeakAssignmentOP const &  assignment)

add individual PeakAssignment

References atoms_, and residues_.

void protocols::noesy_assign::PeakAssignmentResidueMap::add_all_atoms ( ResonanceList const &  rslist)

add all resonances for backward compatibility in covalent-part of network-analysis

References atoms_.

PeakAssignmentResidueMap::PeakAssignments const & protocols::noesy_assign::PeakAssignmentResidueMap::assignments ( core::Size  resi,
core::Size  resj 
) const

get list of PeakAssignments for pair of residues — throws Exception

References protocols::noesy_assign::BOGUS_ASSIGNMENT, core::sequence::end, and residues_.

Referenced by check_for_symmetric_peaks(), network_analysis(), and remove().

PeakAssignmentResidueMap::PeakAssignments & protocols::noesy_assign::PeakAssignmentResidueMap::assignments ( core::Size  resi,
core::Size  resj 
)
void protocols::noesy_assign::PeakAssignmentResidueMap::assignments ( core::Size  resi,
core::Size  resj,
PeakAssignments collector 
) const

add assignments found between resi and resj to collector

References core::sequence::end, and residues_.

void protocols::noesy_assign::PeakAssignmentResidueMap::check_for_symmetric_peaks ( CrossPeakList cpl,
bool  accumulate_symmetry 
)
Real protocols::noesy_assign::PeakAssignmentResidueMap::compute_Nk ( PeakAssignment const &  alpha_beta,
core::id::NamedAtomID const &  gamma_atom,
bool  connect_in_i,
bool  connect_in_j,
bool  sequential,
PeakAssignments const &  close_to_i_assignments,
PeakAssignments const &  close_to_j_assignments,
core::Real  longrange_peak_volume 
) const
private
void protocols::noesy_assign::PeakAssignmentResidueMap::fill_covalent_gammas ( core::Size  alpha_resid,
std::map< core::id::NamedAtomID, bool > &  collector 
) const
private

subroutine to collect putative gammas that need to be queried due to covalent structure

References atoms_.

Referenced by network_analysis().

bool protocols::noesy_assign::PeakAssignmentResidueMap::has ( core::Size  resi,
core::Size  resj 
)

has some (valid or invalid) assignments between residue pair

References _assignments().

void protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis ( core::Size  n_total_assignments)

remove all ambiguous assignments to i,i+1 CrossPeaks.

References assignments(), compute_Nk(), fill_covalent_gammas(), residues_, core::id::NamedAtomID::rsd(), and protocols::noesy_assign::tr().

void protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis2 ( )
void protocols::noesy_assign::PeakAssignmentResidueMap::remove ( PeakAssignment const &  assignment)

remove individual PeakAssignment

remove assignment...

References assignments(), and protocols::noesy_assign::PeakAssignment::resid().

core::Size protocols::noesy_assign::PeakAssignmentResidueMap::total_residue ( ) const
inline

References residues_.

Member Data Documentation

AtomByResList protocols::noesy_assign::PeakAssignmentResidueMap::atoms_
private
PeakAssignments protocols::noesy_assign::PeakAssignmentResidueMap::BOGUS_ASSIGNMENTS
private

Referenced by _assignments().

ResidueList protocols::noesy_assign::PeakAssignmentResidueMap::residues_
private

map with resid of atom(2) as search key. per residue - a PeakAssignmentMap — all residues that are connected by an initial assignment

Referenced by _assignments(), add(), assignments(), network_analysis(), network_analysis2(), and total_residue().


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