Rosetta Protocols  2014.35
Classes | Typedefs | Enumerations | Functions | Variables
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  LabelResonance
 
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  ProtonResonance
 
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
< LabelResonance
LabelResonanceOP
 
typedef
utility::pointer::owning_ptr
< LabelResonance const > 
LabelResonanceCOP
 
typedef
utility::pointer::access_ptr
< LabelResonance
LabelResonanceAP
 
typedef
utility::pointer::access_ptr
< LabelResonance const > 
LabelResonanceCAP
 
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_TYPECalibrationTypeCumulator
 
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
< ProtonResonance
ProtonResonanceOP
 
typedef
utility::pointer::owning_ptr
< ProtonResonance const > 
ProtonResonanceCOP
 
typedef
utility::pointer::access_ptr
< ProtonResonance
ProtonResonanceAP
 
typedef
utility::pointer::access_ptr
< ProtonResonance const > 
ProtonResonanceCAP
 
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)
 
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)
 

Variables

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

Typedef Documentation

Enumeration Type Documentation

Enumerator
BACKBONE 
BETA_NON_METHYL 
METHYL 
SIDECHAIN 
MAX_TYPE 

Function Documentation

PeakAssignment const protocols::noesy_assign::BOGUS_ASSIGNMENT ( NULL  ,
,
 
)
bool protocols::noesy_assign::covalent_compliance ( core::id::NamedAtomID const &  atom1,
core::id::NamedAtomID const &  atom2 
)
bool protocols::noesy_assign::fall_back ( core::id::NamedAtomID const &  _atom1,
core::id::NamedAtomID const &  _atom2 
)
void protocols::noesy_assign::initialize_group_list ( GroupList &  grp_list,
core::pose::Pose const &  pose 
)
std::string protocols::noesy_assign::label_atom_name ( std::string const &  proton_name,
core::chemical::AA  aa 
)
void protocols::noesy_assign::open_stream ( utility::io::ozstream os,
std::string const &  prefix,
std::string const &  peak_filename 
)
std::ostream & protocols::noesy_assign::operator<< ( std::ostream &  os,
CrossPeakInfo const &  cpi 
)
std::ostream & protocols::noesy_assign::operator<< ( std::ostream &  os,
FragsToAtomDist::DistanceRecord const &  dr 
)
std::ostream & protocols::noesy_assign::operator<< ( std::ostream &  os,
PeakAssignment const &  pa 
)
std::ostream& protocols::noesy_assign::operator<< ( std::ostream &  os,
CrossPeak const &  peak 
)
inline
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 
)
void protocols::noesy_assign::retrieve_assignment ( PeakAssignments const &  list,
Size  resonance_id1,
Size  resonance_id2,
PeakAssignments &  intra_res_NOEs 
)
core::Real protocols::noesy_assign::round ( core::Real  d,
core::Size  digits 
)
Real protocols::noesy_assign::sigmoid ( Real  x,
Real  tau,
Real  m,
int  sign = 1 
)
void protocols::noesy_assign::store_distance_snapshot ( DistanceMap &  distmap,
core::pose::Pose const &  short_pose,
Size  start,
Size  short_size,
GroupList const &  grps 
)
void protocols::noesy_assign::store_distmap_with_namedatoms ( FragsToAtomDist::NamedDistanceMap &  named_distmap,
DistanceMap const &  distmap,
GroupList const &  proton_groups 
)
Real protocols::noesy_assign::sum_IntraNOE ( PeakAssignments const &  list,
id::NamedAtomID const &  atom1,
id::NamedAtomID const &  atom2 
)
Real protocols::noesy_assign::sum_peak_volumes ( PeakAssignments const &  list,
core::Size  i,
core::Size  j 
)
Size const protocols::noesy_assign::TOL_H_DIRECT ( )
Size const protocols::noesy_assign::TOL_H_INDIRECT ( )
Size const protocols::noesy_assign::TOL_LABEL ( )

Variable Documentation

PeakAssignment const protocols::noesy_assign::BOGUS_ASSIGNMENT
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::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::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::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().