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< CrossPeak >	CrossPeakOP
typedef utility::pointer::shared_ptr< CrossPeak const >	CrossPeakCOP
typedef utility::pointer::weak_ptr< CrossPeak >	CrossPeakAP
typedef utility::pointer::weak_ptr< CrossPeak const >	CrossPeakCAP
typedef utility::pointer::shared_ptr< CrossPeakInfo >	CrossPeakInfoOP
typedef utility::pointer::shared_ptr< CrossPeakInfo const >	CrossPeakInfoCOP
typedef utility::pointer::weak_ptr< CrossPeakInfo >	CrossPeakInfoAP
typedef utility::pointer::weak_ptr< CrossPeakInfo const >	CrossPeakInfoCAP
typedef utility::pointer::shared_ptr< CrossPeakList >	CrossPeakListOP
typedef utility::pointer::shared_ptr< CrossPeakList const >	CrossPeakListCOP
typedef utility::pointer::weak_ptr< CrossPeakList >	CrossPeakListAP
typedef utility::pointer::weak_ptr< CrossPeakList const >	CrossPeakListCAP
typedef utility::pointer::shared_ptr< DistanceScoreMover >	DistanceScoreMoverOP
typedef utility::pointer::shared_ptr< DistanceScoreMover const >	DistanceScoreMoverCOP
typedef utility::pointer::weak_ptr< DistanceScoreMover >	DistanceScoreMoverAP
typedef utility::pointer::weak_ptr< DistanceScoreMover const >	DistanceScoreMoverCAP
typedef utility::pointer::shared_ptr< FloatingResonance >	FloatingResonanceOP
typedef utility::pointer::shared_ptr< FloatingResonance const >	FloatingResonanceCOP
typedef utility::pointer::weak_ptr< FloatingResonance >	FloatingResonanceAP
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::DistanceRecord >	InnerMap
typedef std::map< core::id::AtomID, InnerMap >	DistanceMap
typedef utility::pointer::shared_ptr< FragsToAtomDist >	FragsToAtomDistOP
typedef utility::pointer::shared_ptr< FragsToAtomDist const >	FragsToAtomDistCOP
typedef utility::pointer::weak_ptr< FragsToAtomDist >	FragsToAtomDistAP
typedef utility::pointer::weak_ptr< FragsToAtomDist const >	FragsToAtomDistCAP
typedef utility::pointer::shared_ptr< LabelResonance >	LabelResonanceOP
typedef utility::pointer::shared_ptr< LabelResonance const >	LabelResonanceCOP
typedef utility::pointer::weak_ptr< LabelResonance >	LabelResonanceAP
typedef utility::pointer::weak_ptr< LabelResonance const >	LabelResonanceCAP
typedef utility::pointer::shared_ptr< NoesyModule >	NoesyModuleOP
typedef utility::pointer::shared_ptr< NoesyModule const >	NoesyModuleCOP
typedef utility::pointer::weak_ptr< NoesyModule >	NoesyModuleAP
typedef utility::pointer::weak_ptr< NoesyModule const >	NoesyModuleCAP
typedef utility::pointer::shared_ptr< PeakAssignment >	PeakAssignmentOP
typedef utility::pointer::shared_ptr< PeakAssignment const >	PeakAssignmentCOP
typedef utility::pointer::weak_ptr< PeakAssignment >	PeakAssignmentAP
typedef utility::pointer::weak_ptr< PeakAssignment const >	PeakAssignmentCAP
using	PeakAssignments = PeakAssignmentResidueMap::PeakAssignments
typedef utility::pointer::shared_ptr< PeakAssignmentResidueMap >	PeakAssignmentResidueMapOP
typedef utility::pointer::shared_ptr< PeakAssignmentResidueMap const >	PeakAssignmentResidueMapCOP
typedef utility::pointer::weak_ptr< PeakAssignmentResidueMap >	PeakAssignmentResidueMapAP
typedef utility::pointer::weak_ptr< PeakAssignmentResidueMap const >	PeakAssignmentResidueMapCAP
typedef std::bitset< MAX_TYPE >	CalibrationTypeCumulator
typedef utility::pointer::shared_ptr< PeakCalibrator >	PeakCalibratorOP
typedef utility::pointer::shared_ptr< PeakCalibrator const >	PeakCalibratorCOP
typedef utility::pointer::weak_ptr< PeakCalibrator >	PeakCalibratorAP
typedef utility::pointer::weak_ptr< PeakCalibrator const >	PeakCalibratorCAP
typedef utility::pointer::shared_ptr< PeakFileFormat >	PeakFileFormatOP
typedef utility::pointer::shared_ptr< PeakFileFormat const >	PeakFileFormatCOP
typedef utility::pointer::shared_ptr< ProtonResonance >	ProtonResonanceOP
typedef utility::pointer::shared_ptr< ProtonResonance const >	ProtonResonanceCOP
typedef utility::pointer::weak_ptr< ProtonResonance >	ProtonResonanceAP
typedef utility::pointer::weak_ptr< ProtonResonance const >	ProtonResonanceCAP
typedef utility::pointer::shared_ptr< Resonance >	ResonanceOP
typedef utility::pointer::shared_ptr< Resonance const >	ResonanceCOP
typedef utility::pointer::weak_ptr< Resonance >	ResonanceAP
typedef utility::pointer::weak_ptr< Resonance const >	ResonanceCAP
typedef utility::pointer::shared_ptr< ResonanceList >	ResonanceListOP
typedef utility::pointer::shared_ptr< ResonanceList const >	ResonanceListCOP
typedef utility::pointer::weak_ptr< ResonanceList >	ResonanceListAP
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

typedef std::bitset< MAX_TYPE > protocols::noesy_assign::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

typedef std::map< core::id::AtomID, InnerMap > protocols::noesy_assign::DistanceMap

DistanceScoreMoverAP

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

typedef std::map< core::id::AtomID, FragsToAtomDist::DistanceRecord > protocols::noesy_assign::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

typedef utility::pointer::weak_ptr< PeakAssignmentResidueMap > protocols::noesy_assign::PeakAssignmentResidueMapAP

PeakAssignmentResidueMapCAP

typedef utility::pointer::weak_ptr< PeakAssignmentResidueMap const > protocols::noesy_assign::PeakAssignmentResidueMapCAP

PeakAssignmentResidueMapCOP

typedef utility::pointer::shared_ptr< PeakAssignmentResidueMap const > protocols::noesy_assign::PeakAssignmentResidueMapCOP

PeakAssignmentResidueMapOP

typedef utility::pointer::shared_ptr< PeakAssignmentResidueMap > protocols::noesy_assign::PeakAssignmentResidueMapOP

PeakAssignments

using protocols::noesy_assign::PeakAssignments = typedef PeakAssignmentResidueMap::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

enum protocols::noesy_assign::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
	)

References core::id::NamedAtomID::atom(), and core::id::NamedAtomID::rsd().

Referenced by protocols::noesy_assign::CovalentCompliance::distance(), and protocols::noesy_assign::CovalentCompliance::is_compliant().

initialize_group_list()

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

References core::chemical::ResidueTypeBase::aa(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and tr().

Referenced by protocols::noesy_assign::FragsToAtomDist::compute_average_distances().

label_atom_name()

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

References protocols::cluster::calibur::aa, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_gln, core::chemical::aa_his, core::chemical::aa_lys, core::chemical::aa_phe, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::name_from_aa(), and tr().

Referenced by protocols::noesy_assign::ResonanceList::update_bond_connections().

open_stream()

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

References protocols::abinitio::filename().

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

operator<<() [1/4]

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

inline

References protocols::noesy_assign::CrossPeak::print_peak_info().

operator<<() [2/4]

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

References protocols::noesy_assign::CrossPeakInfo::show().

operator<<() [3/4]

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

References protocols::noesy_assign::FragsToAtomDist::DistanceRecord::average_dist(), protocols::noesy_assign::FragsToAtomDist::DistanceRecord::average_dist6(), and protocols::noesy_assign::FragsToAtomDist::DistanceRecord::min_dist().

operator<<() [4/4]

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

References protocols::noesy_assign::PeakAssignment::show().

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
	)

Referenced by protocols::noesy_assign::ResonanceList::read_from_stream().

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::simple_moves::SaveProbabilitiesMetricMover::save_aa_probabilities_to_file(), 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
	)

Referenced by protocols::noesy_assign::CrossPeak::probability().

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
	)

References protocols::loops::start, and core::pose::Pose::xyz().

Referenced by protocols::noesy_assign::FragsToAtomDist::compute_average_distances().

store_distmap_with_namedatoms()

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

References core::id::AtomID::atomno(), and core::id::AtomID::rsd().

Referenced by protocols::noesy_assign::FragsToAtomDist::compute_average_distances().

sum_IntraNOE()

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

References core::id::NamedAtomID::atom().

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

sum_peak_volumes()

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

Referenced by protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis2().

TOL_H_DIRECT()

Size const protocols::noesy_assign::TOL_H_DIRECT

(

2

)

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

TOL_H_INDIRECT()

Size const protocols::noesy_assign::TOL_H_INDIRECT

(

1

)

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

TOL_LABEL()

Size const protocols::noesy_assign::TOL_LABEL

(

3

)

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

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	,
		0	,
		0
	)

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