protocols::noesy_assign Namespace Reference

Classes
class	CovalentCompliance
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_AssignmentNotFound
class	EXCN_FileFormat
class	EXCN_NoesyAssign
class	EXCN_UnknownAtomname
class	EXCN_UnknownResonance
class	FloatingResonance
class	FoldResonance
class	FragsToAtomDist
class	MethylNameLibrary
class	MethylNames
class	NoesyModule
class	PeakAssignment
	fast access to assignments that are stored in CrossPeak – similar to FragID More...
class	PeakAssignmentParameters
class	PeakAssignmentResidueMap
	fast access to assignments by residue number More...
class	PeakCalibrator
class	PeakCalibratorMap
class	PeakFileFormat
class	PeakFileFormat_Base
class	PeakFileFormat_Sparky
class	PeakFileFormat_xeasy
class	PeakFileFormat_xpk
class	Resonance
class	ResonanceList
class	StructureDependentPeakCalibrator
class	StructureIndependentPeakCalibrator

Typedefs
typedef utility::pointer::owning_ptr < PeakAssignment >	PeakAssignmentOP
typedef utility::pointer::owning_ptr < PeakAssignment const >	PeakAssignmentCOP
typedef utility::pointer::access_ptr < PeakAssignment >	PeakAssignmentAP
typedef utility::pointer::access_ptr < PeakAssignment const >	PeakAssignmentCAP
typedef utility::pointer::owning_ptr < CrossPeak >	CrossPeakOP
typedef utility::pointer::owning_ptr < CrossPeak const >	CrossPeakCOP
typedef utility::pointer::access_ptr < CrossPeak >	CrossPeakAP
typedef utility::pointer::access_ptr < CrossPeak const >	CrossPeakCAP
typedef utility::pointer::owning_ptr < CrossPeakInfo >	CrossPeakInfoOP
typedef utility::pointer::owning_ptr < CrossPeakInfo const >	CrossPeakInfoCOP
typedef utility::pointer::access_ptr < CrossPeakInfo >	CrossPeakInfoAP
typedef utility::pointer::access_ptr < CrossPeakInfo const >	CrossPeakInfoCAP
typedef utility::pointer::owning_ptr < CrossPeakList >	CrossPeakListOP
typedef utility::pointer::owning_ptr < CrossPeakList const >	CrossPeakListCOP
typedef utility::pointer::access_ptr < CrossPeakList >	CrossPeakListAP
typedef utility::pointer::access_ptr < CrossPeakList const >	CrossPeakListCAP
typedef utility::pointer::owning_ptr < DistanceScoreMover >	DistanceScoreMoverOP
typedef utility::pointer::owning_ptr < DistanceScoreMover const >	DistanceScoreMoverCOP
typedef utility::pointer::access_ptr < DistanceScoreMover >	DistanceScoreMoverAP
typedef utility::pointer::access_ptr < DistanceScoreMover const >	DistanceScoreMoverCAP
typedef utility::pointer::owning_ptr < FloatingResonance >	FloatingResonanceOP
typedef utility::pointer::owning_ptr < FloatingResonance const >	FloatingResonanceCOP
typedef utility::pointer::access_ptr < FloatingResonance >	FloatingResonanceAP
typedef utility::pointer::access_ptr < FloatingResonance const >	FloatingResonanceCAP
typedef utility::vector1 < core::Size >	SizeList
typedef utility::vector1 < std::pair< std::string, SizeList > >	AtomGrps
typedef utility::vector1 < AtomGrps >	GroupList
typedef std::map < core::id::AtomID, FragsToAtomDist::DistanceRecord >	InnerMap
typedef std::map < core::id::AtomID, InnerMap >	DistanceMap
typedef utility::pointer::owning_ptr < FragsToAtomDist >	FragsToAtomDistOP
typedef utility::pointer::owning_ptr < FragsToAtomDist const >	FragsToAtomDistCOP
typedef utility::pointer::access_ptr < FragsToAtomDist >	FragsToAtomDistAP
typedef utility::pointer::access_ptr < FragsToAtomDist const >	FragsToAtomDistCAP
typedef utility::pointer::owning_ptr < NoesyModule >	NoesyModuleOP
typedef utility::pointer::owning_ptr < NoesyModule const >	NoesyModuleCOP
typedef utility::pointer::access_ptr < NoesyModule >	NoesyModuleAP
typedef utility::pointer::access_ptr < NoesyModule const >	NoesyModuleCAP
typedef PeakAssignmentResidueMap::PeakAssignments	PeakAssignments
typedef utility::pointer::owning_ptr < PeakAssignmentResidueMap >	PeakAssignmentResidueMapOP
typedef utility::pointer::owning_ptr < PeakAssignmentResidueMap const >	PeakAssignmentResidueMapCOP
typedef utility::pointer::access_ptr < PeakAssignmentResidueMap >	PeakAssignmentResidueMapAP
typedef utility::pointer::access_ptr < PeakAssignmentResidueMap const >	PeakAssignmentResidueMapCAP
typedef std::bitset< MAX_TYPE >	CalibrationTypeCumulator
typedef utility::pointer::owning_ptr < PeakCalibrator >	PeakCalibratorOP
typedef utility::pointer::owning_ptr < PeakCalibrator const >	PeakCalibratorCOP
typedef utility::pointer::access_ptr < PeakCalibrator >	PeakCalibratorAP
typedef utility::pointer::access_ptr < PeakCalibrator const >	PeakCalibratorCAP
typedef utility::pointer::owning_ptr < PeakFileFormat >	PeakFileFormatOP
typedef utility::pointer::owning_ptr < PeakFileFormat const >	PeakFileFormatCOP
typedef utility::pointer::owning_ptr < Resonance >	ResonanceOP
typedef utility::pointer::owning_ptr < Resonance const >	ResonanceCOP
typedef utility::pointer::access_ptr < Resonance >	ResonanceAP
typedef utility::pointer::access_ptr < Resonance const >	ResonanceCAP
typedef utility::pointer::owning_ptr < ResonanceList >	ResonanceListOP
typedef utility::pointer::owning_ptr < ResonanceList const >	ResonanceListCOP
typedef utility::pointer::access_ptr < ResonanceList >	ResonanceListAP
typedef utility::pointer::access_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, Size start, Size short_size, GroupList const &grps)
std::istream &	operator>> (std::istream &, FragsToAtomDist::DistanceRecord const &)
PeakAssignment const	BOGUS_ASSIGNMENT (NULL, 0, 0)
std::ostream &	operator<< (std::ostream &os, PeakAssignment const &pa)
void	retrieve_assignment (PeakAssignments const &list, Size resonance_id1, 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)
bool	covalent_compliance (core::id::NamedAtomID const &atom1, core::id::NamedAtomID const &atom2)

Variables
PeakAssignment const	BOGUS_ASSIGNMENT
static basic::Tracer	tr ("protocols.noesy_assign.parameters")

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

typedef utility::pointer::access_ptr< DistanceScoreMover > protocols::noesy_assign::DistanceScoreMoverAP

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

typedef PeakAssignmentResidueMap::PeakAssignments protocols::noesy_assign::PeakAssignments

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Enumeration Type Documentation

enum protocols::noesy_assign::CALIBRATION_ATOM_TYPE

Enumerator
BACKBONE
BETA_NON_METHYL
METHYL
SIDECHAIN
MAX_TYPE

Function Documentation

PeakAssignment const protocols::noesy_assign::BOGUS_ASSIGNMENT	(	NULL	,
		0	,
		0
	)

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

References protocols::noesy_assign::CovalentCompliance::get_instance(), and protocols::noesy_assign::CovalentCompliance::is_compliant().

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

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().

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

References core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and tr.

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

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

References utility::file::FileName::base(), filename(), and utility::io::ozstream::open().

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

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

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

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().

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

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

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

inline

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

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

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

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

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

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

References basic::NOESY_ASSIGN_NETWORK_RETRIEVE_ASSIGN.

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

Referenced by protocols::loophash::Mover_LoopHashRefine::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::loophash::MPI_LoopHashRefine_Master::check_library_expiry_dates(), protocols::noesy_assign::CrossPeak::create_fa_and_cen_constraint(), protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs(), protocols::features::strand_assembly::SandwichFeatures::report_avg_b_factor_CB_at_each_component(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), and protocols::dna::DnaInterfacePacker::reversion_scan().

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

References sign().

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

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

References numeric::xyzVector< class >::distance_squared(), and core::pose::Pose::xyz().

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

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().

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().

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

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

Size const protocols::noesy_assign::TOL_H_DIRECT

(

2

)

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

Size const protocols::noesy_assign::TOL_H_INDIRECT

(

1

)

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

Size const protocols::noesy_assign::TOL_LABEL

(

3

)

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

Variable Documentation

PeakAssignment const protocols::noesy_assign::BOGUS_ASSIGNMENT

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

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::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::NoesyModule::generate_constraint_files(), protocols::noesy_assign::CrossPeakList::generate_fa_and_cen_constraints(), protocols::noesy_assign::MethylNameLibrary::load_database_table(), protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis(), protocols::noesy_assign::CrossPeakList::network_analysis(), protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis2(), protocols::noesy_assign::NoesyModule::NoesyModule(), protocols::noesy_assign::CrossPeakList::read_from_stream(), protocols::noesy_assign::ResonanceList::read_from_stream(), protocols::noesy_assign::NoesyModule::read_input_files(), protocols::noesy_assign::CrossPeakList::set_trivial_decoy_compatibility_score(), protocols::noesy_assign::PeakAssignmentParameters::show_on_tracer(), 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().