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 ()

virtual	~PeakAssignmentResidueMap ()

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 (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 (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 ( )

virtual

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_, protocols::cyclic_peptide::insert, 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_, protocols::noesy_assign::ResonanceList::begin(), and protocols::noesy_assign::ResonanceList::end().

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::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	(	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 ( 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(), 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().

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

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

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation