protocols::noesy_assign::PeakAssignmentResidueMap Class Reference

fast access to assignments by residue number More...

#include <PeakAssignmentResidueMap.hh>

Inheritance diagram for protocols::noesy_assign::PeakAssignmentResidueMap:

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...
PeakAssignments &	assignments (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

typedef utility::vector1< AtomList > protocols::noesy_assign::PeakAssignmentResidueMap::AtomByResList

private

typedef std::set< core::id::NamedAtomID > protocols::noesy_assign::PeakAssignmentResidueMap::AtomList

private

typedef std::map< core::Size, PeakAssignments > protocols::noesy_assign::PeakAssignmentResidueMap::PeakAssignmentMap

typedef std::list< PeakAssignmentOP > protocols::noesy_assign::PeakAssignmentResidueMap::PeakAssignments

typedef utility::vector1< PeakAssignmentMap > protocols::noesy_assign::PeakAssignmentResidueMap::ResidueList

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

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

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
	)

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

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
	)

invalidate non symmetric peaks

References _assignments(), assignments(), protocols::noesy_assign::CrossPeakList::peaks(), protocols::noesy_assign::PeakAssignment::resid(), and protocols::noesy_assign::PeakAssignment::set_symmetry().

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

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

subroutine to compute Nk for alpha->gamma->beta path.

References protocols::noesy_assign::PeakAssignment::atom(), protocols::noesy_assign::covalent_compliance(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::mean_field::max(), protocols::noesy_assign::sum_IntraNOE(), protocols::noesy_assign::PeakAssignmentParameters::vmax_, and protocols::noesy_assign::PeakAssignmentParameters::vmin_.

Referenced by network_analysis().

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

(

)

References _assignments(), atoms_, protocols::noesy_assign::covalent_compliance(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::mean_field::max(), residues_, protocols::noesy_assign::PeakAssignment::set_network_anchoring_per_residue(), protocols::noesy_assign::sum_peak_volumes(), protocols::noesy_assign::tr(), protocols::noesy_assign::PeakAssignmentParameters::vmax_, and protocols::noesy_assign::PeakAssignmentParameters::vmin_.

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

Referenced by add(), add_all_atoms(), fill_covalent_gammas(), and network_analysis2().

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().

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

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