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protocols::noesy_assign::PeakAssignment Class Reference

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:
Inheritance graph
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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
 
CrossPeakcrosspeak ()
 
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
 

Private Attributes

CrossPeakcrosspeak_
 
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_
 

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

Constructor & Destructor Documentation

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

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

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

Member Function Documentation

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

References resonance_id(), and resonances().

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

References chemshift_overlap_.

core::scoring::constraints::ConstraintOP protocols::noesy_assign::PeakAssignment::create_constraint ( core::pose::Pose const &  pose,
core::scoring::func::FuncOP  func = nullptr 
) const
PeakAssignment::NmrConstraintOP protocols::noesy_assign::PeakAssignment::create_constraint ( core::pose::Pose const &  pose,
core::Size  ifloat,
core::scoring::func::FuncOP  func = nullptr 
) const
core::scoring::constraints::AmbiguousNMRConstraintOP protocols::noesy_assign::PeakAssignment::create_float_constraint ( core::pose::Pose const &  pose,
core::scoring::func::FuncOP  func = nullptr 
) const
private
CrossPeak& protocols::noesy_assign::PeakAssignment::crosspeak ( )
inline

References crosspeak_.

Referenced by is_symmetric_partner_of().

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

References crosspeak_.

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

References decoy_compatibility_.

void protocols::noesy_assign::PeakAssignment::dump_weights ( std::ostream &  os) const
core::Size protocols::noesy_assign::PeakAssignment::float_ambiguity ( ) const
bool protocols::noesy_assign::PeakAssignment::has_label ( core::Size  select) const
inline
bool protocols::noesy_assign::PeakAssignment::has_proton ( core::Size  select) const
inline
bool protocols::noesy_assign::PeakAssignment::is_symmetric_partner_of ( PeakAssignment const &  other) const
core::id::NamedAtomID const& protocols::noesy_assign::PeakAssignment::label_atom ( core::Size  iatom) const
inline
Resonance const& protocols::noesy_assign::PeakAssignment::label_resonance ( core::Size  iatom) const
inline
core::Size protocols::noesy_assign::PeakAssignment::label_resonance_id ( core::Size  select) const
core::Real protocols::noesy_assign::PeakAssignment::native_distance_viol ( )
inline

References native_distance_viol_.

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

References network_anchoring_.

core::Real protocols::noesy_assign::PeakAssignment::network_anchoring_per_residue ( ) const
inline
Real protocols::noesy_assign::PeakAssignment::normalized_peak_volume ( ) const
bool protocols::noesy_assign::PeakAssignment::operator== ( PeakAssignment const &  other) const
inline

References crosspeak_, and spin_id().

Real protocols::noesy_assign::PeakAssignment::peak_volume ( ) const
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(), and protocols::noesy_assign::PeakAssignmentResidueMap::remove().

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

References resonance_id(), and resonances().

Referenced by create_constraint(), and float_ambiguity().

core::Size protocols::noesy_assign::PeakAssignment::resonance_id ( core::Size  select) const
inline
ResonanceList const & protocols::noesy_assign::PeakAssignment::resonances ( ) const
void protocols::noesy_assign::PeakAssignment::set_decoy_compatibility ( core::Real  setting)
inline

References decoy_compatibility_.

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

References native_distance_viol_.

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

References network_anchoring_.

void protocols::noesy_assign::PeakAssignment::set_network_anchoring_per_residue ( core::Real  reswise_setting)
inline
void protocols::noesy_assign::PeakAssignment::set_symmetry ( core::Real  setting = 0)
inline
void protocols::noesy_assign::PeakAssignment::show ( std::ostream &  os) const
core::Size protocols::noesy_assign::PeakAssignment::spin_id ( core::Size  select) const
inline
core::Real protocols::noesy_assign::PeakAssignment::symmetry_compliance ( ) const
inline

References symmetry_compliance_.

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

core::Real protocols::noesy_assign::PeakAssignment::chemshift_overlap_
private
bool protocols::noesy_assign::PeakAssignment::covalent_compliance_
private
CrossPeak* protocols::noesy_assign::PeakAssignment::crosspeak_
private
core::Real protocols::noesy_assign::PeakAssignment::decoy_compatibility_
private
core::Real protocols::noesy_assign::PeakAssignment::native_distance_viol_
private
core::Real protocols::noesy_assign::PeakAssignment::network_anchoring_
private
core::Real protocols::noesy_assign::PeakAssignment::network_anchoring_per_residue_
private
core::Size protocols::noesy_assign::PeakAssignment::resonance1_
private
core::Size protocols::noesy_assign::PeakAssignment::resonance2_
private
core::Size protocols::noesy_assign::PeakAssignment::spin_assign_index1_
private

Referenced by spin_id().

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

Referenced by spin_id().

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

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