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protocols::noesy_assign Namespace Reference

Classes

class  CovalentCompliance
 WARNING WARNING WARNING THIS SINGLETON CLASS HOLDS NON-CONST JOB-SPECIFIC DATA AND MAKES EVERYTHING THAT RELIES ON IT THREAD-UNSAFE. THIS IS NOT HOW SINGLETONS SHOULD BE USED. More...
 
class  CrossPeak
 
class  CrossPeak3D
 
class  CrossPeak4D
 
class  CrossPeakInfo
 shared information about CrossPeak (one for each proton dimension) More...
 
class  CrossPeakList
 
class  DistanceScoreMover
 maintains a list of constraints_ (each PeakAssignment yields one) and peak_constraints_ ( each cross peak with multiple assignments creates one AmbiguousNMRConstraint ). the DistanceMover (prepare scoring and apply directly interacts with the Dk term in CrossPeak (set_decoy_compatibility) More...
 
class  EXCN_NoesyAssign
 
class  EXCN_UnknownAtomname
 
class  EXCN_UnknownResonance
 
class  EXCN_AssignmentNotFound
 
class  EXCN_FileFormat
 
class  FloatingResonance
 
class  FoldResonance
 
class  FragsToAtomDist
 
class  LabelResonance
 
class  MethylNames
 
class  MethylNameLibrary
 
class  NoesyModule
 WARNING WARNING WARNING THREAD UNSAFE FOR USING THE COVALENTCOMPLIANCE CLASS IN A NON-CONST WAY. More...
 
class  PeakAssignment
 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...
 
class  PeakAssignmentParameters
 
class  PeakAssignmentResidueMap
 fast access to assignments by residue number More...
 
class  PeakCalibrator
 
class  PeakCalibratorMap
 
class  PeakFileFormat_Base
 
class  PeakFileFormat
 
class  PeakFileFormat_xeasy
 
class  PeakFileFormat_Sparky
 
class  PeakFileFormat_xpk
 
class  ProtonResonance
 
class  Resonance
 
class  ResonanceList
 
class  StructureDependentPeakCalibrator
 
class  StructureIndependentPeakCalibrator
 

Typedefs

typedef utility::pointer::shared_ptr< CrossPeakCrossPeakOP
 
typedef utility::pointer::shared_ptr< CrossPeak const > CrossPeakCOP
 
typedef utility::pointer::weak_ptr< CrossPeakCrossPeakAP
 
typedef utility::pointer::weak_ptr< CrossPeak const > CrossPeakCAP
 
typedef utility::pointer::shared_ptr< CrossPeakInfoCrossPeakInfoOP
 
typedef utility::pointer::shared_ptr< CrossPeakInfo const > CrossPeakInfoCOP
 
typedef utility::pointer::weak_ptr< CrossPeakInfoCrossPeakInfoAP
 
typedef utility::pointer::weak_ptr< CrossPeakInfo const > CrossPeakInfoCAP
 
typedef utility::pointer::shared_ptr< CrossPeakListCrossPeakListOP
 
typedef utility::pointer::shared_ptr< CrossPeakList const > CrossPeakListCOP
 
typedef utility::pointer::weak_ptr< CrossPeakListCrossPeakListAP
 
typedef utility::pointer::weak_ptr< CrossPeakList const > CrossPeakListCAP
 
typedef utility::pointer::shared_ptr< DistanceScoreMoverDistanceScoreMoverOP
 
typedef utility::pointer::shared_ptr< DistanceScoreMover const > DistanceScoreMoverCOP
 
typedef utility::pointer::weak_ptr< DistanceScoreMoverDistanceScoreMoverAP
 
typedef utility::pointer::weak_ptr< DistanceScoreMover const > DistanceScoreMoverCAP
 
typedef utility::pointer::shared_ptr< FloatingResonanceFloatingResonanceOP
 
typedef utility::pointer::shared_ptr< FloatingResonance const > FloatingResonanceCOP
 
typedef utility::pointer::weak_ptr< FloatingResonanceFloatingResonanceAP
 
typedef utility::pointer::weak_ptr< FloatingResonance const > FloatingResonanceCAP
 
using SizeList = utility::vector1< core::Size >
 
typedef utility::vector1< std::pair< std::string, SizeList > > AtomGrps
 
using GroupList = utility::vector1< AtomGrps >
 
typedef std::map< core::id::AtomID, FragsToAtomDist::DistanceRecordInnerMap
 
typedef std::map< core::id::AtomID, InnerMapDistanceMap
 
typedef utility::pointer::shared_ptr< FragsToAtomDistFragsToAtomDistOP
 
typedef utility::pointer::shared_ptr< FragsToAtomDist const > FragsToAtomDistCOP
 
typedef utility::pointer::weak_ptr< FragsToAtomDistFragsToAtomDistAP
 
typedef utility::pointer::weak_ptr< FragsToAtomDist const > FragsToAtomDistCAP
 
typedef utility::pointer::shared_ptr< LabelResonanceLabelResonanceOP
 
typedef utility::pointer::shared_ptr< LabelResonance const > LabelResonanceCOP
 
typedef utility::pointer::weak_ptr< LabelResonanceLabelResonanceAP
 
typedef utility::pointer::weak_ptr< LabelResonance const > LabelResonanceCAP
 
typedef utility::pointer::shared_ptr< NoesyModuleNoesyModuleOP
 
typedef utility::pointer::shared_ptr< NoesyModule const > NoesyModuleCOP
 
typedef utility::pointer::weak_ptr< NoesyModuleNoesyModuleAP
 
typedef utility::pointer::weak_ptr< NoesyModule const > NoesyModuleCAP
 
typedef utility::pointer::shared_ptr< PeakAssignmentPeakAssignmentOP
 
typedef utility::pointer::shared_ptr< PeakAssignment const > PeakAssignmentCOP
 
typedef utility::pointer::weak_ptr< PeakAssignmentPeakAssignmentAP
 
typedef utility::pointer::weak_ptr< PeakAssignment const > PeakAssignmentCAP
 
using PeakAssignments = PeakAssignmentResidueMap::PeakAssignments
 
typedef utility::pointer::shared_ptr< PeakAssignmentResidueMapPeakAssignmentResidueMapOP
 
typedef utility::pointer::shared_ptr< PeakAssignmentResidueMap const > PeakAssignmentResidueMapCOP
 
typedef utility::pointer::weak_ptr< PeakAssignmentResidueMapPeakAssignmentResidueMapAP
 
typedef utility::pointer::weak_ptr< PeakAssignmentResidueMap const > PeakAssignmentResidueMapCAP
 
typedef std::bitset< MAX_TYPECalibrationTypeCumulator
 
typedef utility::pointer::shared_ptr< PeakCalibratorPeakCalibratorOP
 
typedef utility::pointer::shared_ptr< PeakCalibrator const > PeakCalibratorCOP
 
typedef utility::pointer::weak_ptr< PeakCalibratorPeakCalibratorAP
 
typedef utility::pointer::weak_ptr< PeakCalibrator const > PeakCalibratorCAP
 
typedef utility::pointer::shared_ptr< PeakFileFormatPeakFileFormatOP
 
typedef utility::pointer::shared_ptr< PeakFileFormat const > PeakFileFormatCOP
 
typedef utility::pointer::shared_ptr< ProtonResonanceProtonResonanceOP
 
typedef utility::pointer::shared_ptr< ProtonResonance const > ProtonResonanceCOP
 
typedef utility::pointer::weak_ptr< ProtonResonanceProtonResonanceAP
 
typedef utility::pointer::weak_ptr< ProtonResonance const > ProtonResonanceCAP
 
typedef utility::pointer::shared_ptr< ResonanceResonanceOP
 
typedef utility::pointer::shared_ptr< Resonance const > ResonanceCOP
 
typedef utility::pointer::weak_ptr< ResonanceResonanceAP
 
typedef utility::pointer::weak_ptr< Resonance const > ResonanceCAP
 
typedef utility::pointer::shared_ptr< ResonanceListResonanceListOP
 
typedef utility::pointer::shared_ptr< ResonanceList const > ResonanceListCOP
 
typedef utility::pointer::weak_ptr< ResonanceListResonanceListAP
 
typedef utility::pointer::weak_ptr< ResonanceList const > ResonanceListCAP
 

Enumerations

enum  CALIBRATION_ATOM_TYPE {
  BACKBONE = 1 , BETA_NON_METHYL , METHYL , SIDECHAIN ,
  MAX_TYPE
}
 

Functions

bool fall_back (core::id::NamedAtomID const &_atom1, core::id::NamedAtomID const &_atom2)
 
core::Real round (core::Real d, core::Size digits)
 
Real sigmoid (Real x, Real tau, Real m, int sign=1)
 
std::ostream & operator<< (std::ostream &os, CrossPeak const &peak)
 
std::ostream & operator<< (std::ostream &os, CrossPeakInfo const &cpi)
 
void open_stream (utility::io::ozstream &os, std::string const &prefix, std::string const &peak_filename)
 
std::ostream & operator<< (std::ostream &os, FragsToAtomDist::DistanceRecord const &dr)
 
std::istream & operator>> (std::istream &is, FragsToAtomDist::DistanceRecord &dr)
 
void initialize_group_list (GroupList &grp_list, core::pose::Pose const &pose)
 
void store_distmap_with_namedatoms (FragsToAtomDist::NamedDistanceMap &named_distmap, DistanceMap const &distmap, GroupList const &proton_groups)
 
void store_distance_snapshot (DistanceMap &distmap, core::pose::Pose const &short_pose, core::Size start, core::Size short_size, GroupList const &grps)
 
std::istream & operator>> (std::istream &, FragsToAtomDist::DistanceRecord const &)
 
std::ostream & operator<< (std::ostream &os, PeakAssignment const &pa)
 
static basic::Tracer tr ("protocols.noesy_assign.parameters")
 
void retrieve_assignment (PeakAssignments const &list, core::Size resonance_id1, core::Size resonance_id2, PeakAssignments &intra_res_NOEs)
 
Real sum_IntraNOE (PeakAssignments const &list, id::NamedAtomID const &atom1, id::NamedAtomID const &atom2)
 
Real sum_peak_volumes (PeakAssignments const &list, core::Size i, core::Size j)
 
Size const TOL_H_INDIRECT (1)
 
Size const TOL_H_DIRECT (2)
 
Size const TOL_LABEL (3)
 
void process_last_resonances (std::deque< ResonanceOP > &last_resonances, bool drain=false)
 
std::string label_atom_name (std::string const &proton_name, core::chemical::AA aa)
 
bool covalent_compliance (core::id::NamedAtomID const &atom1, core::id::NamedAtomID const &atom2)
 WARNING WARNING WARNING THE COVALENTCOMPLIANCE CLASS IS THREAD UNSAFE. More...
 

Variables

PeakAssignment const BOGUS_ASSIGNMENT (nullptr, 0, 0)
 

Typedef Documentation

◆ AtomGrps

typedef utility::vector1< std::pair< std::string, SizeList> > protocols::noesy_assign::AtomGrps

◆ CalibrationTypeCumulator

◆ CrossPeakAP

typedef utility::pointer::weak_ptr< CrossPeak > protocols::noesy_assign::CrossPeakAP

◆ CrossPeakCAP

typedef utility::pointer::weak_ptr< CrossPeak const > protocols::noesy_assign::CrossPeakCAP

◆ CrossPeakCOP

typedef utility::pointer::shared_ptr< CrossPeak const > protocols::noesy_assign::CrossPeakCOP

◆ CrossPeakInfoAP

typedef utility::pointer::weak_ptr< CrossPeakInfo > protocols::noesy_assign::CrossPeakInfoAP

◆ CrossPeakInfoCAP

typedef utility::pointer::weak_ptr< CrossPeakInfo const > protocols::noesy_assign::CrossPeakInfoCAP

◆ CrossPeakInfoCOP

typedef utility::pointer::shared_ptr< CrossPeakInfo const > protocols::noesy_assign::CrossPeakInfoCOP

◆ CrossPeakInfoOP

typedef utility::pointer::shared_ptr< CrossPeakInfo > protocols::noesy_assign::CrossPeakInfoOP

◆ CrossPeakListAP

typedef utility::pointer::weak_ptr< CrossPeakList > protocols::noesy_assign::CrossPeakListAP

◆ CrossPeakListCAP

typedef utility::pointer::weak_ptr< CrossPeakList const > protocols::noesy_assign::CrossPeakListCAP

◆ CrossPeakListCOP

typedef utility::pointer::shared_ptr< CrossPeakList const > protocols::noesy_assign::CrossPeakListCOP

◆ CrossPeakListOP

typedef utility::pointer::shared_ptr< CrossPeakList > protocols::noesy_assign::CrossPeakListOP

◆ CrossPeakOP

typedef utility::pointer::shared_ptr< CrossPeak > protocols::noesy_assign::CrossPeakOP

◆ DistanceMap

◆ DistanceScoreMoverAP

◆ DistanceScoreMoverCAP

typedef utility::pointer::weak_ptr< DistanceScoreMover const > protocols::noesy_assign::DistanceScoreMoverCAP

◆ DistanceScoreMoverCOP

typedef utility::pointer::shared_ptr< DistanceScoreMover const > protocols::noesy_assign::DistanceScoreMoverCOP

◆ DistanceScoreMoverOP

typedef utility::pointer::shared_ptr< DistanceScoreMover > protocols::noesy_assign::DistanceScoreMoverOP

◆ FloatingResonanceAP

typedef utility::pointer::weak_ptr< FloatingResonance > protocols::noesy_assign::FloatingResonanceAP

◆ FloatingResonanceCAP

typedef utility::pointer::weak_ptr< FloatingResonance const > protocols::noesy_assign::FloatingResonanceCAP

◆ FloatingResonanceCOP

typedef utility::pointer::shared_ptr< FloatingResonance const > protocols::noesy_assign::FloatingResonanceCOP

◆ FloatingResonanceOP

typedef utility::pointer::shared_ptr< FloatingResonance > protocols::noesy_assign::FloatingResonanceOP

◆ FragsToAtomDistAP

typedef utility::pointer::weak_ptr< FragsToAtomDist > protocols::noesy_assign::FragsToAtomDistAP

◆ FragsToAtomDistCAP

typedef utility::pointer::weak_ptr< FragsToAtomDist const > protocols::noesy_assign::FragsToAtomDistCAP

◆ FragsToAtomDistCOP

typedef utility::pointer::shared_ptr< FragsToAtomDist const > protocols::noesy_assign::FragsToAtomDistCOP

◆ FragsToAtomDistOP

typedef utility::pointer::shared_ptr< FragsToAtomDist > protocols::noesy_assign::FragsToAtomDistOP

◆ GroupList

using protocols::noesy_assign::GroupList = typedef utility::vector1<AtomGrps>

◆ InnerMap

◆ LabelResonanceAP

typedef utility::pointer::weak_ptr< LabelResonance > protocols::noesy_assign::LabelResonanceAP

◆ LabelResonanceCAP

typedef utility::pointer::weak_ptr< LabelResonance const > protocols::noesy_assign::LabelResonanceCAP

◆ LabelResonanceCOP

typedef utility::pointer::shared_ptr< LabelResonance const > protocols::noesy_assign::LabelResonanceCOP

◆ LabelResonanceOP

typedef utility::pointer::shared_ptr< LabelResonance > protocols::noesy_assign::LabelResonanceOP

◆ NoesyModuleAP

typedef utility::pointer::weak_ptr< NoesyModule > protocols::noesy_assign::NoesyModuleAP

◆ NoesyModuleCAP

typedef utility::pointer::weak_ptr< NoesyModule const > protocols::noesy_assign::NoesyModuleCAP

◆ NoesyModuleCOP

typedef utility::pointer::shared_ptr< NoesyModule const > protocols::noesy_assign::NoesyModuleCOP

◆ NoesyModuleOP

typedef utility::pointer::shared_ptr< NoesyModule > protocols::noesy_assign::NoesyModuleOP

◆ PeakAssignmentAP

typedef utility::pointer::weak_ptr< PeakAssignment > protocols::noesy_assign::PeakAssignmentAP

◆ PeakAssignmentCAP

typedef utility::pointer::weak_ptr< PeakAssignment const > protocols::noesy_assign::PeakAssignmentCAP

◆ PeakAssignmentCOP

typedef utility::pointer::shared_ptr< PeakAssignment const > protocols::noesy_assign::PeakAssignmentCOP

◆ PeakAssignmentOP

typedef utility::pointer::shared_ptr< PeakAssignment > protocols::noesy_assign::PeakAssignmentOP

◆ PeakAssignmentResidueMapAP

◆ PeakAssignmentResidueMapCAP

◆ PeakAssignmentResidueMapCOP

◆ PeakAssignmentResidueMapOP

◆ PeakAssignments

◆ PeakCalibratorAP

typedef utility::pointer::weak_ptr< PeakCalibrator > protocols::noesy_assign::PeakCalibratorAP

◆ PeakCalibratorCAP

typedef utility::pointer::weak_ptr< PeakCalibrator const > protocols::noesy_assign::PeakCalibratorCAP

◆ PeakCalibratorCOP

typedef utility::pointer::shared_ptr< PeakCalibrator const > protocols::noesy_assign::PeakCalibratorCOP

◆ PeakCalibratorOP

typedef utility::pointer::shared_ptr< PeakCalibrator > protocols::noesy_assign::PeakCalibratorOP

◆ PeakFileFormatCOP

typedef utility::pointer::shared_ptr< PeakFileFormat const > protocols::noesy_assign::PeakFileFormatCOP

◆ PeakFileFormatOP

typedef utility::pointer::shared_ptr< PeakFileFormat > protocols::noesy_assign::PeakFileFormatOP

◆ ProtonResonanceAP

typedef utility::pointer::weak_ptr< ProtonResonance > protocols::noesy_assign::ProtonResonanceAP

◆ ProtonResonanceCAP

typedef utility::pointer::weak_ptr< ProtonResonance const > protocols::noesy_assign::ProtonResonanceCAP

◆ ProtonResonanceCOP

typedef utility::pointer::shared_ptr< ProtonResonance const > protocols::noesy_assign::ProtonResonanceCOP

◆ ProtonResonanceOP

typedef utility::pointer::shared_ptr< ProtonResonance > protocols::noesy_assign::ProtonResonanceOP

◆ ResonanceAP

typedef utility::pointer::weak_ptr< Resonance > protocols::noesy_assign::ResonanceAP

◆ ResonanceCAP

typedef utility::pointer::weak_ptr< Resonance const > protocols::noesy_assign::ResonanceCAP

◆ ResonanceCOP

typedef utility::pointer::shared_ptr< Resonance const > protocols::noesy_assign::ResonanceCOP

◆ ResonanceListAP

typedef utility::pointer::weak_ptr< ResonanceList > protocols::noesy_assign::ResonanceListAP

◆ ResonanceListCAP

typedef utility::pointer::weak_ptr< ResonanceList const > protocols::noesy_assign::ResonanceListCAP

◆ ResonanceListCOP

typedef utility::pointer::shared_ptr< ResonanceList const > protocols::noesy_assign::ResonanceListCOP

◆ ResonanceListOP

typedef utility::pointer::shared_ptr< ResonanceList > protocols::noesy_assign::ResonanceListOP

◆ ResonanceOP

typedef utility::pointer::shared_ptr< Resonance > protocols::noesy_assign::ResonanceOP

◆ SizeList

using protocols::noesy_assign::SizeList = typedef utility::vector1<core::Size>

Enumeration Type Documentation

◆ CALIBRATION_ATOM_TYPE

Enumerator
BACKBONE 
BETA_NON_METHYL 
METHYL 
SIDECHAIN 
MAX_TYPE 

Function Documentation

◆ covalent_compliance()

bool protocols::noesy_assign::covalent_compliance ( core::id::NamedAtomID const &  atom1,
core::id::NamedAtomID const &  atom2 
)

WARNING WARNING WARNING THE COVALENTCOMPLIANCE CLASS IS THREAD UNSAFE.

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

Referenced by protocols::noesy_assign::PeakAssignmentResidueMap::compute_Nk(), protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis2(), and protocols::noesy_assign::PeakAssignment::update_upperdistance_score().

◆ fall_back()

bool protocols::noesy_assign::fall_back ( core::id::NamedAtomID const &  _atom1,
core::id::NamedAtomID const &  _atom2 
)

◆ initialize_group_list()

void protocols::noesy_assign::initialize_group_list ( GroupList grp_list,
core::pose::Pose const &  pose 
)

◆ label_atom_name()

std::string protocols::noesy_assign::label_atom_name ( std::string const &  proton_name,
core::chemical::AA  aa 
)

◆ open_stream()

void protocols::noesy_assign::open_stream ( utility::io::ozstream &  os,
std::string const &  prefix,
std::string const &  peak_filename 
)

◆ operator<<() [1/4]

std::ostream& protocols::noesy_assign::operator<< ( std::ostream &  os,
CrossPeak const &  peak 
)
inline

◆ operator<<() [2/4]

std::ostream & protocols::noesy_assign::operator<< ( std::ostream &  os,
CrossPeakInfo const &  cpi 
)

◆ operator<<() [3/4]

std::ostream & protocols::noesy_assign::operator<< ( std::ostream &  os,
FragsToAtomDist::DistanceRecord const &  dr 
)

◆ operator<<() [4/4]

std::ostream & protocols::noesy_assign::operator<< ( std::ostream &  os,
PeakAssignment const &  pa 
)

◆ operator>>() [1/2]

std::istream& protocols::noesy_assign::operator>> ( std::istream &  ,
FragsToAtomDist::DistanceRecord const &   
)

◆ operator>>() [2/2]

std::istream& protocols::noesy_assign::operator>> ( std::istream &  is,
FragsToAtomDist::DistanceRecord dr 
)

◆ process_last_resonances()

void protocols::noesy_assign::process_last_resonances ( std::deque< ResonanceOP > &  last_resonances,
bool  drain = false 
)

◆ retrieve_assignment()

void protocols::noesy_assign::retrieve_assignment ( PeakAssignments const &  list,
core::Size  resonance_id1,
core::Size  resonance_id2,
PeakAssignments intra_res_NOEs 
)

◆ round()

core::Real protocols::noesy_assign::round ( core::Real  d,
core::Size  digits 
)

Referenced by protocols::carbohydrates::GlycanSampler::apply(), protocols::carbohydrates::GlycanTreeModeler::apply(), protocols::carbohydrates::SimpleGlycosylateMover::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::task_operations::MutationSetDesignOperation::apply(), core::scoring::fiber_diffraction::bessel_roots(), core::energy_methods::AACompositionEnergy::calculate_energy(), protocols::loophash::MPI_LoopHashRefine_Master::check_library_expiry_dates(), protocols::mpi_refinement::MPI_Refine_Master::check_library_expiry_dates(), core::scoring::epr_deer::metrics::DEERData::convolute(), protocols::noesy_assign::CrossPeak::create_fa_and_cen_constraint(), protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs(), protocols::mpi_refinement::MPI_Refine_Master::create_WUs(), protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints(), protocols::sewing::hashing::Hasher::generate_key(), protocols::sewing::hashing::LigandBindingResPlacer::generate_ligand_key(), protocols::simple_moves::StructProfileMover::generate_profile_score_wo_background(), core::scoring::epr_deer::EPRSpinLabel::histogram(), core::scoring::orbitals::OrbitalsStatistics::increment_histogram_bin(), protocols::simple_moves::DEEROptimizeCoordsMover::init_data(), protocols::loops::loop_mover::loops_set_chainbreak_weight(), protocols::mean_field::ResPred::operator()(), protocols::mean_field::ResHasher::operator()(), core::scoring::epr_deer::DEERIO::parse_dist_lines(), core::chemical::mainchain_potential::MainchainScoreTable::parse_rama_map_file_shapovalov(), core::energy_methods::FaMPAsymEzCBEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCGEnergy::residue_energy(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), protocols::dna::DnaInterfacePacker::reversion_scan(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::run(), protocols::rna::movers::show_accuracy_report(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::symmetrize_library(), protocols::moves::RampingMover::update_weights(), core::chemical::mainchain_potential::MainchainScoreTable::write_mainchain_scoretable_to_stream(), and protocols::features::strand_assembly::WriteToDB_avg_b_factor_CB_at_each_component().

◆ sigmoid()

Real protocols::noesy_assign::sigmoid ( Real  x,
Real  tau,
Real  m,
int  sign = 1 
)

◆ store_distance_snapshot()

void protocols::noesy_assign::store_distance_snapshot ( DistanceMap distmap,
core::pose::Pose const &  short_pose,
core::Size  start,
core::Size  short_size,
GroupList const &  grps 
)

◆ store_distmap_with_namedatoms()

void protocols::noesy_assign::store_distmap_with_namedatoms ( FragsToAtomDist::NamedDistanceMap named_distmap,
DistanceMap const &  distmap,
GroupList const &  proton_groups 
)

◆ sum_IntraNOE()

Real protocols::noesy_assign::sum_IntraNOE ( PeakAssignments const &  list,
id::NamedAtomID const &  atom1,
id::NamedAtomID const &  atom2 
)

◆ sum_peak_volumes()

Real protocols::noesy_assign::sum_peak_volumes ( PeakAssignments const &  list,
core::Size  i,
core::Size  j 
)

◆ TOL_H_DIRECT()

Size const protocols::noesy_assign::TOL_H_DIRECT ( )

◆ TOL_H_INDIRECT()

Size const protocols::noesy_assign::TOL_H_INDIRECT ( )

◆ TOL_LABEL()

Size const protocols::noesy_assign::TOL_LABEL ( )

◆ tr()

static basic::Tracer protocols::noesy_assign::tr ( "protocols.noesy_assign.parameters"  )
static

Referenced by protocols::noesy_assign::MethylNames::add_methyl(), protocols::noesy_assign::MethylNames::add_proton(), protocols::noesy_assign::DistanceScoreMover::apply(), protocols::noesy_assign::CrossPeak3D::assign_labelled_spin(), protocols::noesy_assign::CrossPeak3D::assign_spin(), protocols::noesy_assign::CrossPeakList::calibrate(), protocols::noesy_assign::PeakAssignment::create_constraint(), protocols::noesy_assign::CrossPeakList::delete_diagonal_peaks(), protocols::noesy_assign::DistanceScoreMover::DistanceScoreMover(), protocols::noesy_assign::PeakCalibrator::do_calibration(), protocols::noesy_assign::CrossPeakList::find_assignments(), protocols::noesy_assign::FloatingResonance::float_label(), protocols::noesy_assign::NoesyModule::generate_constraint_files(), protocols::noesy_assign::CrossPeakList::generate_fa_and_cen_constraints(), label_atom_name(), protocols::noesy_assign::MethylNameLibrary::load_database_table(), protocols::noesy_assign::CrossPeakList::network_analysis(), protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis(), protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis2(), protocols::noesy_assign::PeakFileFormat::read_assignments(), protocols::noesy_assign::ResonanceList::read_from_stream(), protocols::noesy_assign::CrossPeakList::read_from_stream(), protocols::noesy_assign::PeakFileFormat::read_header(), protocols::noesy_assign::NoesyModule::read_input_files(), protocols::noesy_assign::PeakFileFormat::read_peak(), protocols::noesy_assign::CrossPeakList::set_trivial_decoy_compatibility_score(), protocols::noesy_assign::PeakAssignmentParameters::show_on_tracer(), protocols::noesy_assign::ResonanceList::update_bond_connections(), protocols::noesy_assign::CrossPeakList::update_chemshiftscore(), protocols::noesy_assign::CrossPeakList::update_decoy_compatibility_score(), protocols::noesy_assign::CrossPeakList::update_peak_volumina(), protocols::noesy_assign::CrossPeakList::update_symmetry_score(), protocols::noesy_assign::CrossPeakList::update_upperdistance_score(), and protocols::noesy_assign::ResonanceList::write_talos_format().

Variable Documentation

◆ BOGUS_ASSIGNMENT

PeakAssignment const protocols::noesy_assign::BOGUS_ASSIGNMENT ( nullptr  ,
,
 
)