fast access to assignments that are stored in CrossPeak – similar to FragID WARNING WARNING WARNING THREAD UNSAFE. THIS CLASS USES THE FUNCTION covalent_compliance WHICH RELIES ON THREAD-UNSAFE SINGLETON CovalentCompliance More...

#include <PeakAssignment.hh>

Inheritance diagram for protocols::noesy_assign::PeakAssignment:

[legend]

Public Types
typedef core::scoring::constraints::AmbiguousNMRDistanceConstraintOP	NmrConstraintOP

typedef core::scoring::constraints::AmbiguousNMRDistanceConstraint	NmrConstraint

Public Member Functions
	~PeakAssignment () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

	PeakAssignment (CrossPeak *, core::Size assign_spin1, core::Size assign_spin2)

core::Size	spin_id (core::Size select) const

core::Size	resonance_id (core::Size select) const
	return resonance_id, i.e., pointer into Resonance list that will resolve in assigned atom More...

bool	has_label (core::Size select) const

bool	has_proton (core::Size select) const

core::Size	float_ambiguity () const

core::Size	label_resonance_id (core::Size select) const
	return resonance_id, i.e., pointer into Resonance list that will resolve in assigned atom More...

core::id::NamedAtomID const &	atom (core::Size iatom) const
	returns atom 1 or 2 of the assigned cross-peak. — might throw Exception if atom not found in ResonanceList More...

core::id::NamedAtomID const &	label_atom (core::Size iatom) const

Resonance const &	resonance (core::Size iatom) const

Resonance const &	label_resonance (core::Size iatom) const

CALIBRATION_ATOM_TYPE	calibration_atom_type (core::Size iatom) const

core::scoring::constraints::ConstraintOP	create_constraint (core::pose::Pose const &pose, core::scoring::func::FuncOP=nullptr) const

NmrConstraintOP	create_constraint (core::pose::Pose const &pose, core::Size ifloat, core::scoring::func::FuncOP=nullptr) const

core::Size	resid (core::Size iatom) const
	returns residue number of a1 or a2 of the assigned cross-peak, — might throw Exception if atom not found More...

bool	operator== (PeakAssignment const &other) const

bool	is_symmetric_partner_of (PeakAssignment const &other) const

ResonanceList const &	resonances () const

CrossPeak &	crosspeak ()

CrossPeak const &	crosspeak () const

void	set_symmetry (core::Real setting=0)

core::Real	symmetry_compliance () const

core::Real	chemshift_compliance () const

void	set_network_anchoring (core::Real setting)

void	set_network_anchoring_per_residue (core::Real reswise_setting)

core::Real	network_anchoring () const

core::Real	network_anchoring_per_residue () const

core::Real	decoy_compatibility () const

void	set_decoy_compatibility (core::Real setting)

void	update_chemshiftscore_from_peak ()

void	update_upperdistance_score ()

core::Real	peak_volume () const
	this is not normalized More...

core::Real	normalized_peak_volume () const
	only correct if peak_volumes have been update in CrossPeaks. More...

void	show (std::ostream &os) const

void	dump_weights (std::ostream &os) const

void	set_native_distance_viol (core::Real setting)

core::Real	native_distance_viol ()

Private Member Functions
void	update_resonances_from_peak ()

core::scoring::constraints::AmbiguousNMRConstraintOP	create_float_constraint (core::pose::Pose const &pose, core::scoring::func::FuncOP=nullptr) const

Detailed Description

fast access to assignments that are stored in CrossPeak – similar to FragID WARNING WARNING WARNING THREAD UNSAFE. THIS CLASS USES THE FUNCTION covalent_compliance WHICH RELIES ON THREAD-UNSAFE SINGLETON CovalentCompliance

Member Typedef Documentation

◆ NmrConstraint

typedef core::scoring::constraints::AmbiguousNMRDistanceConstraint protocols::noesy_assign::PeakAssignment::NmrConstraint

◆ NmrConstraintOP

typedef core::scoring::constraints::AmbiguousNMRDistanceConstraintOP protocols::noesy_assign::PeakAssignment::NmrConstraintOP

Constructor & Destructor Documentation

◆ ~PeakAssignment()

protocols::noesy_assign::PeakAssignment::~PeakAssignment ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

◆ PeakAssignment()

protocols::noesy_assign::PeakAssignment::PeakAssignment	(	CrossPeak *	cp,
		core::Size	assign_spin1,
		core::Size	assign_spin2
	)

References update_resonances_from_peak().

Member Function Documentation

◆ atom()

core::id::NamedAtomID const& protocols::noesy_assign::PeakAssignment::atom ( core::Size iatom ) const

inline

returns atom 1 or 2 of the assigned cross-peak. — might throw Exception if atom not found in ResonanceList

References resonance_id(), and resonances().

Referenced by protocols::noesy_assign::PeakAssignmentResidueMap::compute_Nk(), create_constraint(), show(), update_upperdistance_score(), protocols::noesy_assign::PeakFileFormat::write_assignment(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), and protocols::noesy_assign::PeakFileFormat_xpk::write_assignment().

◆ calibration_atom_type()

CALIBRATION_ATOM_TYPE protocols::noesy_assign::PeakAssignment::calibration_atom_type ( core::Size iatom ) const

inline

References resonance_id(), and resonances().

◆ chemshift_compliance()

core::Real protocols::noesy_assign::PeakAssignment::chemshift_compliance ( ) const

inline

References chemshift_overlap_.

◆ create_constraint() [1/2]

core::scoring::constraints::ConstraintOP protocols::noesy_assign::PeakAssignment::create_constraint	(	core::pose::Pose const &	pose,
		core::scoring::func::FuncOP	func = `nullptr`
	)		const

References create_float_constraint(), and float_ambiguity().

Referenced by create_float_constraint().

◆ create_constraint() [2/2]

PeakAssignment::NmrConstraintOP protocols::noesy_assign::PeakAssignment::create_constraint	(	core::pose::Pose const &	pose,
		core::Size	ifloat,
		core::scoring::func::FuncOP	func = `nullptr`
	)		const

References atom(), normalized_peak_volume(), resonance(), resonance_id(), resonances(), and protocols::noesy_assign::tr().

◆ create_float_constraint()

core::scoring::constraints::AmbiguousNMRConstraintOP protocols::noesy_assign::PeakAssignment::create_float_constraint	(	core::pose::Pose const &	pose,
		core::scoring::func::FuncOP	func = `nullptr`
	)		const

private

References create_constraint(), and float_ambiguity().

Referenced by create_constraint().

◆ crosspeak() [1/2]

CrossPeak& protocols::noesy_assign::PeakAssignment::crosspeak ( )

inline

References crosspeak_.

Referenced by is_symmetric_partner_of().

◆ crosspeak() [2/2]

CrossPeak const& protocols::noesy_assign::PeakAssignment::crosspeak ( ) const

inline

References crosspeak_.

◆ decoy_compatibility()

core::Real protocols::noesy_assign::PeakAssignment::decoy_compatibility ( ) const

inline

References decoy_compatibility_.

◆ dump_weights()

void protocols::noesy_assign::PeakAssignment::dump_weights ( std::ostream & os ) const

References chemshift_overlap_, covalent_compliance_, protocols::noesy_assign::PeakAssignmentParameters::covalent_compliance_weight_, decoy_compatibility_, core::chemical::element::F, protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::mean_field::max(), native_distance_viol_, network_anchoring_, network_anchoring_per_residue_, symmetry_compliance_, and protocols::noesy_assign::PeakAssignmentParameters::symmetry_compliance_weight_.

Referenced by protocols::noesy_assign::PeakFileFormat::write_assignment_stats().

◆ float_ambiguity()

core::Size protocols::noesy_assign::PeakAssignment::float_ambiguity ( ) const

References protocols::noesy_assign::Resonance::ambiguity(), has_proton(), and resonance().

Referenced by create_constraint(), and create_float_constraint().

◆ has_label()

bool protocols::noesy_assign::PeakAssignment::has_label ( core::Size select ) const

inline

References crosspeak_, and protocols::noesy_assign::CrossPeak::has_label().

Referenced by is_symmetric_partner_of(), and show().

◆ has_proton()

bool protocols::noesy_assign::PeakAssignment::has_proton ( core::Size select ) const

inline

References crosspeak_, and protocols::noesy_assign::CrossPeak::has_proton().

Referenced by float_ambiguity(), and show().

◆ is_symmetric_partner_of()

bool protocols::noesy_assign::PeakAssignment::is_symmetric_partner_of ( PeakAssignment const & other ) const

References crosspeak(), crosspeak_, protocols::noesy_assign::CrossPeak::exp_hash(), has_label(), label_resonance_id(), resonance_id(), and protocols::noesy_assign::CrossPeak::same_peak().

◆ label_atom()

core::id::NamedAtomID const& protocols::noesy_assign::PeakAssignment::label_atom ( core::Size iatom ) const

inline

References label_resonance_id(), and resonances().

Referenced by show(), protocols::noesy_assign::PeakFileFormat::write_assignment(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), and protocols::noesy_assign::PeakFileFormat_xpk::write_assignment().

◆ label_resonance()

Resonance const& protocols::noesy_assign::PeakAssignment::label_resonance ( core::Size iatom ) const

inline

References label_resonance_id(), and resonances().

◆ label_resonance_id()

core::Size protocols::noesy_assign::PeakAssignment::label_resonance_id ( core::Size select ) const

return resonance_id, i.e., pointer into Resonance list that will resolve in assigned atom

References protocols::noesy_assign::CrossPeak::Spin::assignment(), crosspeak_, protocols::noesy_assign::CrossPeak::has_label(), protocols::noesy_assign::CrossPeak::label(), and spin_id().

Referenced by is_symmetric_partner_of(), label_atom(), label_resonance(), protocols::noesy_assign::PeakFileFormat::write_assignment(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), and protocols::noesy_assign::PeakFileFormat_xpk::write_assignment().

◆ native_distance_viol()

core::Real protocols::noesy_assign::PeakAssignment::native_distance_viol ( )

inline

References native_distance_viol_.

◆ network_anchoring()

core::Real protocols::noesy_assign::PeakAssignment::network_anchoring ( ) const

inline

References network_anchoring_.

◆ network_anchoring_per_residue()

core::Real protocols::noesy_assign::PeakAssignment::network_anchoring_per_residue ( ) const

inline

References network_anchoring_per_residue_.

◆ normalized_peak_volume()

Real protocols::noesy_assign::PeakAssignment::normalized_peak_volume ( ) const

only correct if peak_volumes have been update in CrossPeaks.

References crosspeak_, protocols::noesy_assign::CrossPeak::cumulative_peak_volume(), and peak_volume().

Referenced by create_constraint(), and protocols::noesy_assign::PeakFileFormat::write_assignment_stats().

◆ operator==()

bool protocols::noesy_assign::PeakAssignment::operator== ( PeakAssignment const & other ) const

inline

References crosspeak_, and spin_id().

◆ peak_volume()

Real protocols::noesy_assign::PeakAssignment::peak_volume ( ) const

this is not normalized

References chemshift_overlap_, covalent_compliance_, protocols::noesy_assign::PeakAssignmentParameters::covalent_compliance_weight_, decoy_compatibility_, protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::mean_field::max(), protocols::mean_field::min(), network_anchoring_, protocols::noesy_assign::PeakAssignmentParameters::smax_, symmetry_compliance_, and protocols::noesy_assign::PeakAssignmentParameters::symmetry_compliance_weight_.

Referenced by normalized_peak_volume().

◆ resid()

core::Size protocols::noesy_assign::PeakAssignment::resid ( core::Size iatom ) const

inline

returns residue number of a1 or a2 of the assigned cross-peak, — might throw Exception if atom not found

References resonance_id(), and resonances().

Referenced by protocols::noesy_assign::PeakAssignmentResidueMap::check_for_symmetric_peaks(), protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis(), protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis2(), and protocols::noesy_assign::PeakAssignmentResidueMap::remove().

◆ resonance()

Resonance const& protocols::noesy_assign::PeakAssignment::resonance ( core::Size iatom ) const

inline

References resonance_id(), and resonances().

Referenced by create_constraint(), and float_ambiguity().

◆ resonance_id()

core::Size protocols::noesy_assign::PeakAssignment::resonance_id ( core::Size select ) const

inline

return resonance_id, i.e., pointer into Resonance list that will resolve in assigned atom

References resonance1_, and resonance2_.

Referenced by atom(), calibration_atom_type(), create_constraint(), is_symmetric_partner_of(), resid(), resonance(), protocols::noesy_assign::PeakFileFormat::write_assignment(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), and protocols::noesy_assign::PeakFileFormat_xpk::write_assignment().

◆ resonances()

ResonanceList const & protocols::noesy_assign::PeakAssignment::resonances ( ) const

References crosspeak_, and protocols::noesy_assign::CrossPeak::resonances().

Referenced by atom(), calibration_atom_type(), create_constraint(), label_atom(), label_resonance(), protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis2(), resid(), resonance(), update_chemshiftscore_from_peak(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), and protocols::noesy_assign::PeakFileFormat_xpk::write_assignment().

◆ set_decoy_compatibility()

void protocols::noesy_assign::PeakAssignment::set_decoy_compatibility ( core::Real setting )

inline

References decoy_compatibility_.

◆ set_native_distance_viol()

void protocols::noesy_assign::PeakAssignment::set_native_distance_viol ( core::Real setting )

inline

References native_distance_viol_.

◆ set_network_anchoring()

void protocols::noesy_assign::PeakAssignment::set_network_anchoring ( core::Real setting )

inline

References network_anchoring_.

◆ set_network_anchoring_per_residue()

void protocols::noesy_assign::PeakAssignment::set_network_anchoring_per_residue ( core::Real reswise_setting )

inline

References network_anchoring_per_residue_.

◆ set_symmetry()

void protocols::noesy_assign::PeakAssignment::set_symmetry ( core::Real setting = 0 )

inline

References symmetry_compliance_.

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

◆ show()

void protocols::noesy_assign::PeakAssignment::show ( std::ostream & os ) const

References atom(), has_label(), has_proton(), and label_atom().

Referenced by protocols::noesy_assign::operator<<().

◆ spin_id()

core::Size protocols::noesy_assign::PeakAssignment::spin_id ( core::Size select ) const

inline

References spin_assign_index1_, and spin_assign_index2_.

Referenced by label_resonance_id(), operator==(), update_chemshiftscore_from_peak(), and update_resonances_from_peak().

◆ symmetry_compliance()

core::Real protocols::noesy_assign::PeakAssignment::symmetry_compliance ( ) const

inline

References symmetry_compliance_.

◆ update_chemshiftscore_from_peak()

void protocols::noesy_assign::PeakAssignment::update_chemshiftscore_from_peak ( )

References protocols::noesy_assign::CrossPeak::Spin::assignment(), chemshift_overlap_, protocols::noesy_assign::PeakAssignmentParameters::chemshift_overlap_weight_, crosspeak_, protocols::noesy_assign::CrossPeak::dimension(), protocols::noesy_assign::CrossPeak::folder(), protocols::noesy_assign::CrossPeak::Spin::freq(), protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::noesy_assign::Resonance::pmatch(), resonances(), protocols::noesy_assign::CrossPeak::spin(), spin_id(), core::simple_metrics::metrics::sum, and protocols::noesy_assign::CrossPeak::tolerance().

◆ update_resonances_from_peak()

void protocols::noesy_assign::PeakAssignment::update_resonances_from_peak ( )

private

References protocols::noesy_assign::CrossPeak::Spin::assignment(), crosspeak_, protocols::noesy_assign::CrossPeak::proton(), resonance1_, resonance2_, and spin_id().

Referenced by PeakAssignment().

◆ update_upperdistance_score()

void protocols::noesy_assign::PeakAssignment::update_upperdistance_score ( )

WARNING WARNING WARNING THREAD UNSAFE covalent_compliance RELIES ON THREAD-UNSAFE SINGLETON CovalentCompliance

References atom(), protocols::noesy_assign::covalent_compliance(), and covalent_compliance_.

Member Data Documentation

◆ chemshift_overlap_

core::Real protocols::noesy_assign::PeakAssignment::chemshift_overlap_

private

Referenced by chemshift_compliance(), dump_weights(), peak_volume(), and update_chemshiftscore_from_peak().

◆ covalent_compliance_

bool protocols::noesy_assign::PeakAssignment::covalent_compliance_

private

Referenced by dump_weights(), peak_volume(), and update_upperdistance_score().

◆ crosspeak_

CrossPeak* protocols::noesy_assign::PeakAssignment::crosspeak_

private

Referenced by crosspeak(), has_label(), has_proton(), is_symmetric_partner_of(), label_resonance_id(), normalized_peak_volume(), operator==(), resonances(), update_chemshiftscore_from_peak(), and update_resonances_from_peak().

◆ decoy_compatibility_

core::Real protocols::noesy_assign::PeakAssignment::decoy_compatibility_

private

Referenced by decoy_compatibility(), dump_weights(), peak_volume(), and set_decoy_compatibility().

◆ native_distance_viol_

core::Real protocols::noesy_assign::PeakAssignment::native_distance_viol_

private

Referenced by dump_weights(), native_distance_viol(), and set_native_distance_viol().

◆ network_anchoring_

core::Real protocols::noesy_assign::PeakAssignment::network_anchoring_

private

Referenced by dump_weights(), network_anchoring(), peak_volume(), and set_network_anchoring().

◆ network_anchoring_per_residue_

core::Real protocols::noesy_assign::PeakAssignment::network_anchoring_per_residue_

private

Referenced by dump_weights(), network_anchoring_per_residue(), and set_network_anchoring_per_residue().

◆ resonance1_

core::Size protocols::noesy_assign::PeakAssignment::resonance1_

private

Referenced by resonance_id(), and update_resonances_from_peak().

◆ resonance2_

core::Size protocols::noesy_assign::PeakAssignment::resonance2_

private

Referenced by resonance_id(), and update_resonances_from_peak().

◆ spin_assign_index1_

core::Size protocols::noesy_assign::PeakAssignment::spin_assign_index1_

private

Referenced by spin_id().

◆ spin_assign_index2_

core::Size protocols::noesy_assign::PeakAssignment::spin_assign_index2_

private

Referenced by spin_id().

◆ symmetry_compliance_

core::Real protocols::noesy_assign::PeakAssignment::symmetry_compliance_

private

Referenced by dump_weights(), peak_volume(), set_symmetry(), and symmetry_compliance().

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

src/protocols/noesy_assign/PeakAssignment.hh
src/protocols/noesy_assign/PeakAssignment.cc

Private Attributes
CrossPeak *	crosspeak_

core::Size	spin_assign_index1_

core::Size	spin_assign_index2_

core::Size	resonance1_

core::Size	resonance2_

core::Real	chemshift_overlap_

core::Real	symmetry_compliance_

bool	covalent_compliance_

core::Real	decoy_compatibility_

core::Real	network_anchoring_

core::Real	network_anchoring_per_residue_

core::Real	native_distance_viol_

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ NmrConstraint

◆ NmrConstraintOP

Constructor & Destructor Documentation

◆ ~PeakAssignment()

◆ PeakAssignment()

Member Function Documentation

◆ atom()

◆ calibration_atom_type()

◆ chemshift_compliance()

◆ create_constraint() [1/2]

◆ create_constraint() [2/2]

◆ create_float_constraint()

◆ crosspeak() [1/2]

◆ crosspeak() [2/2]

◆ decoy_compatibility()

◆ dump_weights()

◆ float_ambiguity()

◆ has_label()

◆ has_proton()

◆ is_symmetric_partner_of()

◆ label_atom()

◆ label_resonance()

◆ label_resonance_id()

◆ native_distance_viol()

◆ network_anchoring()

◆ network_anchoring_per_residue()

◆ normalized_peak_volume()

◆ operator==()

◆ peak_volume()

◆ resid()

◆ resonance()

◆ resonance_id()

◆ resonances()

◆ set_decoy_compatibility()

◆ set_native_distance_viol()

◆ set_network_anchoring()

◆ set_network_anchoring_per_residue()

◆ set_symmetry()

◆ show()

◆ spin_id()

◆ symmetry_compliance()

◆ update_chemshiftscore_from_peak()

◆ update_resonances_from_peak()

◆ update_upperdistance_score()

Member Data Documentation

◆ chemshift_overlap_

◆ covalent_compliance_

◆ crosspeak_

◆ decoy_compatibility_

◆ native_distance_viol_

◆ network_anchoring_

◆ network_anchoring_per_residue_

◆ resonance1_

◆ resonance2_

◆ spin_assign_index1_

◆ spin_assign_index2_

◆ symmetry_compliance_