Classes
class	CovalentCompliance

class	CrossPeak

class	CrossPeak3D

class	CrossPeak4D

class	CrossPeakInfo
	shared information about CrossPeak (one for each proton dimension) More...

class	CrossPeakList

class	NoesyModule

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	MethylNames

class	MethylNameLibrary

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_Base

class	PeakFileFormat

class	PeakFileFormat_xeasy

class	PeakFileFormat_Sparky

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 &)

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 (NULL, 0, 0)

Typedef Documentation

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

Definition at line 84 of file FragsToAtomDist.cc.

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

Definition at line 45 of file PeakCalibrator.fwd.hh.

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

Definition at line 34 of file CrossPeak.fwd.hh.

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

Definition at line 35 of file CrossPeak.fwd.hh.

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

Definition at line 32 of file CrossPeak.fwd.hh.

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

Definition at line 34 of file CrossPeakInfo.fwd.hh.

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

Definition at line 35 of file CrossPeakInfo.fwd.hh.

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

Definition at line 32 of file CrossPeakInfo.fwd.hh.

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

Definition at line 28 of file CrossPeakInfo.fwd.hh.

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

Definition at line 34 of file CrossPeakList.fwd.hh.

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

Definition at line 35 of file CrossPeakList.fwd.hh.

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

Definition at line 32 of file CrossPeakList.fwd.hh.

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

Definition at line 28 of file CrossPeakList.fwd.hh.

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

Definition at line 28 of file CrossPeak.fwd.hh.

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

Definition at line 87 of file FragsToAtomDist.cc.

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

Definition at line 34 of file DistanceScoreMover.fwd.hh.

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

Definition at line 35 of file DistanceScoreMover.fwd.hh.

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

Definition at line 32 of file DistanceScoreMover.fwd.hh.

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

Definition at line 28 of file DistanceScoreMover.fwd.hh.

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

Definition at line 34 of file FloatingResonance.fwd.hh.

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

Definition at line 35 of file FloatingResonance.fwd.hh.

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

Definition at line 32 of file FloatingResonance.fwd.hh.

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

Definition at line 28 of file FloatingResonance.fwd.hh.

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

Definition at line 35 of file FragsToAtomDist.fwd.hh.

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

Definition at line 36 of file FragsToAtomDist.fwd.hh.

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

Definition at line 33 of file FragsToAtomDist.fwd.hh.

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

Definition at line 29 of file FragsToAtomDist.fwd.hh.

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

Definition at line 85 of file FragsToAtomDist.cc.

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

Definition at line 86 of file FragsToAtomDist.cc.

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

Definition at line 34 of file NoesyModule.fwd.hh.

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

Definition at line 35 of file NoesyModule.fwd.hh.

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

Definition at line 32 of file NoesyModule.fwd.hh.

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

Definition at line 28 of file NoesyModule.fwd.hh.

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

Definition at line 34 of file Assignment.fwd.hh.

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

Definition at line 35 of file Assignment.fwd.hh.

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

Definition at line 32 of file Assignment.fwd.hh.

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

Definition at line 28 of file Assignment.fwd.hh.

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

Definition at line 34 of file PeakAssignmentResidueMap.fwd.hh.

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

Definition at line 35 of file PeakAssignmentResidueMap.fwd.hh.

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

Definition at line 32 of file PeakAssignmentResidueMap.fwd.hh.

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

Definition at line 28 of file PeakAssignmentResidueMap.fwd.hh.

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

Definition at line 258 of file PeakAssignmentResidueMap.cc.

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

Definition at line 51 of file PeakCalibrator.fwd.hh.

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

Definition at line 52 of file PeakCalibrator.fwd.hh.

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

Definition at line 49 of file PeakCalibrator.fwd.hh.

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

Definition at line 48 of file PeakCalibrator.fwd.hh.

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

Definition at line 32 of file PeakFileFormat.fwd.hh.

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

Definition at line 28 of file PeakFileFormat.fwd.hh.

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

Definition at line 34 of file Resonance.fwd.hh.

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

Definition at line 35 of file Resonance.fwd.hh.

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

Definition at line 32 of file Resonance.fwd.hh.

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

Definition at line 34 of file ResonanceList.fwd.hh.

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

Definition at line 35 of file ResonanceList.fwd.hh.

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

Definition at line 32 of file ResonanceList.fwd.hh.

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

Definition at line 28 of file ResonanceList.fwd.hh.

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

Definition at line 28 of file Resonance.fwd.hh.

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

Definition at line 83 of file FragsToAtomDist.cc.

Enumeration Type Documentation

enum protocols::noesy_assign::CALIBRATION_ATOM_TYPE

Enumerator
BACKBONE
BETA_NON_METHYL
METHYL
SIDECHAIN
MAX_TYPE

Definition at line 31 of file PeakCalibrator.fwd.hh.

Function Documentation

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

Definition at line 66 of file util.cc.

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
	)

Definition at line 27 of file CovalentCompliance.cc.

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
	)

Definition at line 145 of file FragsToAtomDist.cc.

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
	)

Definition at line 155 of file CrossPeakList.cc.

References protocols::abinitio::filename().

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

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

Definition at line 87 of file CrossPeakInfo.cc.

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

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

Definition at line 109 of file FragsToAtomDist.cc.

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

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

Definition at line 216 of file PeakAssignment.cc.

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

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

inline

Definition at line 340 of file CrossPeak.hh.

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

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

Definition at line 115 of file FragsToAtomDist.cc.

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`
	)

Definition at line 95 of file ResonanceList.cc.

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
	)

Definition at line 259 of file PeakAssignmentResidueMap.cc.

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

Definition at line 176 of file CrossPeak.cc.

Referenced by protocols::loophash::Mover_LoopHashRefine::apply(), protocols::swa::rna::StepWiseRNA_Minimizer::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(), core::scoring::orbitals::OrbitalsStatistics::increment_histogram_bin(), 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`
	)

Definition at line 308 of file CrossPeak.cc.

Referenced by core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), and 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
	)

Definition at line 333 of file FragsToAtomDist.cc.

References 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
	)