| | |
- builtins.object
-
- CALIBRATION_ATOM_TYPE
- CrossPeak
-
- CrossPeak3D
-
- CrossPeak4D
- CrossPeakInfo
- CrossPeakList
- FoldResonance
- FragsToAtomDist
- MethylNames
- NoesyModule
- PeakAssignment
- PeakAssignmentParameters
- PeakAssignmentResidueMap
- PeakCalibrator
-
- StructureDependentPeakCalibrator
- StructureIndependentPeakCalibrator
- PeakCalibratorMap
- PeakFileFormat_Base
-
- PeakFileFormat
-
- PeakFileFormat_Sparky
- PeakFileFormat_xeasy
- PeakFileFormat_xpk
- Resonance
-
- FloatingResonance
- LabelResonance
- ProtonResonance
- ResonanceList
- rosetta.protocols.moves.Mover(builtins.object)
-
- DistanceScoreMover
- rosetta.utility.SingletonBase_protocols_noesy_assign_CovalentCompliance_t(builtins.object)
-
- CovalentCompliance
- rosetta.utility.SingletonBase_protocols_noesy_assign_MethylNameLibrary_t(builtins.object)
-
- MethylNameLibrary
- rosetta.utility.excn.EXCN_Msg_Exception(rosetta.utility.excn.EXCN_Exception)
-
- EXCN_NoesyAssign
-
- EXCN_AssignmentNotFound
- EXCN_FileFormat
- EXCN_UnknownAtomname
- EXCN_UnknownResonance
class CovalentCompliance(rosetta.utility.SingletonBase_protocols_noesy_assign_CovalentCompliance_t) |
| |
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.
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- Method resolution order:
- CovalentCompliance
- rosetta.utility.SingletonBase_protocols_noesy_assign_CovalentCompliance_t
- builtins.object
Methods defined here:
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- distance(...) from builtins.PyCapsule
- distance(self : rosetta.protocols.noesy_assign.CovalentCompliance, atom1 : rosetta.core.id.NamedAtomID, atom2 : rosetta.core.id.NamedAtomID) -> float
- is_compliant(...) from builtins.PyCapsule
- is_compliant(*args, **kwargs)
Overloaded function.
1. is_compliant(self : rosetta.protocols.noesy_assign.CovalentCompliance, atom1 : rosetta.core.id.NamedAtomID, atom2 : rosetta.core.id.NamedAtomID) -> bool
2. is_compliant(self : rosetta.protocols.noesy_assign.CovalentCompliance, atom1 : rosetta.core.id.NamedAtomID, atom2 : rosetta.core.id.NamedAtomID, cutoff : float) -> bool
- load_dist_table(...) from builtins.PyCapsule
- load_dist_table(self : rosetta.protocols.noesy_assign.CovalentCompliance, file : str) -> NoneType
This is clearly thread-unsafe.
Methods inherited from rosetta.utility.SingletonBase_protocols_noesy_assign_CovalentCompliance_t:
- get_instance(...) from builtins.PyCapsule
- get_instance() -> protocols::noesy_assign::CovalentCompliance
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class CrossPeak(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, : protocols::noesy_assign::CrossPeak::Spin, : protocols::noesy_assign::CrossPeak::Spin, strength : float) -> NoneType
2. __init__(handle) -> NoneType
3. __init__(handle, rosetta.protocols.noesy_assign.CrossPeak) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.noesy_assign.CrossPeak) -> str
- ambiguous(...) from builtins.PyCapsule
- ambiguous(rosetta.protocols.noesy_assign.CrossPeak) -> bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.CrossPeak, : rosetta.protocols.noesy_assign.CrossPeak) -> rosetta.protocols.noesy_assign.CrossPeak
- assign_spin(...) from builtins.PyCapsule
- assign_spin(self : rosetta.protocols.noesy_assign.CrossPeak, spin_id : int) -> NoneType
- assigned(...) from builtins.PyCapsule
- assigned(rosetta.protocols.noesy_assign.CrossPeak) -> bool
- assignments(...) from builtins.PyCapsule
- assignments(rosetta.protocols.noesy_assign.CrossPeak) -> rosetta.utility.vector1_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t
- begin(...) from builtins.PyCapsule
- begin(*args, **kwargs)
Overloaded function.
1. begin(rosetta.protocols.noesy_assign.CrossPeak) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::noesy_assign::PeakAssignment> const*, std::vector<std::shared_ptr<protocols::noesy_assign::PeakAssignment>, std::allocator<std::shared_ptr<protocols::noesy_assign::PeakAssignment> > > >
2. begin(rosetta.protocols.noesy_assign.CrossPeak) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::noesy_assign::PeakAssignment>*, std::vector<std::shared_ptr<protocols::noesy_assign::PeakAssignment>, std::allocator<std::shared_ptr<protocols::noesy_assign::PeakAssignment> > > >
- create_fa_and_cen_constraint(...) from builtins.PyCapsule
- create_fa_and_cen_constraint(*args, **kwargs)
Overloaded function.
1. create_fa_and_cen_constraint(self : rosetta.protocols.noesy_assign.CrossPeak, fa_cst : rosetta.core.scoring.constraints.Constraint, cen_cst : rosetta.core.scoring.constraints.Constraint, pose : rosetta.core.pose.Pose, centroid_pose : rosetta.core.pose.Pose, normalization : int) -> NoneType
2. create_fa_and_cen_constraint(self : rosetta.protocols.noesy_assign.CrossPeak, fa_cst : rosetta.core.scoring.constraints.Constraint, cen_cst : rosetta.core.scoring.constraints.Constraint, pose : rosetta.core.pose.Pose, centroid_pose : rosetta.core.pose.Pose, normalization : int, padding : float) -> NoneType
3. create_fa_and_cen_constraint(self : rosetta.protocols.noesy_assign.CrossPeak, fa_cst : rosetta.core.scoring.constraints.Constraint, cen_cst : rosetta.core.scoring.constraints.Constraint, pose : rosetta.core.pose.Pose, centroid_pose : rosetta.core.pose.Pose, normalization : int, padding : float, fa_only : bool) -> NoneType
- cumulative_peak_volume(...) from builtins.PyCapsule
- cumulative_peak_volume(rosetta.protocols.noesy_assign.CrossPeak) -> float
the cumulative cyana-type weights for all assignments Vk
- dimension(...) from builtins.PyCapsule
- dimension(rosetta.protocols.noesy_assign.CrossPeak) -> int
- distance_bound(...) from builtins.PyCapsule
- distance_bound(rosetta.protocols.noesy_assign.CrossPeak) -> float
- eliminated(...) from builtins.PyCapsule
- eliminated(*args, **kwargs)
Overloaded function.
1. eliminated(rosetta.protocols.noesy_assign.CrossPeak) -> bool
returns true if this peak is to be ignored due to points (i)-(iv) on p215 of JMB 2002, 319,209-227
do_not_compute ... for outputter that does not want to change state...
2. eliminated(self : rosetta.protocols.noesy_assign.CrossPeak, recompute : bool) -> bool
returns true if this peak is to be ignored due to points (i)-(iv) on p215 of JMB 2002, 319,209-227
do_not_compute ... for outputter that does not want to change state...
3. eliminated(self : rosetta.protocols.noesy_assign.CrossPeak, recompute : bool, do_not_compute : bool) -> bool
returns true if this peak is to be ignored due to points (i)-(iv) on p215 of JMB 2002, 319,209-227
do_not_compute ... for outputter that does not want to change state...
- elimination_reason(...) from builtins.PyCapsule
- elimination_reason(rosetta.protocols.noesy_assign.CrossPeak) -> str
- empty_clone(...) from builtins.PyCapsule
- empty_clone(rosetta.protocols.noesy_assign.CrossPeak) -> rosetta.protocols.noesy_assign.CrossPeak
- end(...) from builtins.PyCapsule
- end(rosetta.protocols.noesy_assign.CrossPeak) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::noesy_assign::PeakAssignment> const*, std::vector<std::shared_ptr<protocols::noesy_assign::PeakAssignment>, std::allocator<std::shared_ptr<protocols::noesy_assign::PeakAssignment> > > >
- exp_hash(...) from builtins.PyCapsule
- exp_hash(rosetta.protocols.noesy_assign.CrossPeak) -> int
- filename(...) from builtins.PyCapsule
- filename(rosetta.protocols.noesy_assign.CrossPeak) -> str
- find_assignments(...) from builtins.PyCapsule
- find_assignments(rosetta.protocols.noesy_assign.CrossPeak) -> NoneType
- fold_resonance(...) from builtins.PyCapsule
- fold_resonance(self : rosetta.protocols.noesy_assign.CrossPeak, freq : float, i : int) -> float
- folder(...) from builtins.PyCapsule
- folder(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> rosetta.protocols.noesy_assign.FoldResonance
- has_label(...) from builtins.PyCapsule
- has_label(self : rosetta.protocols.noesy_assign.CrossPeak, : int) -> bool
- has_proton(...) from builtins.PyCapsule
- has_proton(self : rosetta.protocols.noesy_assign.CrossPeak, : int) -> bool
- info(...) from builtins.PyCapsule
- info(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> rosetta.protocols.noesy_assign.CrossPeakInfo
- is4D(...) from builtins.PyCapsule
- is4D(rosetta.protocols.noesy_assign.CrossPeak) -> bool
- is_elimination_candidate(...) from builtins.PyCapsule
- is_elimination_candidate(rosetta.protocols.noesy_assign.CrossPeak) -> bool
- label(...) from builtins.PyCapsule
- label(*args, **kwargs)
Overloaded function.
1. label(self : rosetta.protocols.noesy_assign.CrossPeak, : int) -> protocols::noesy_assign::CrossPeak::Spin
2. label(self : rosetta.protocols.noesy_assign.CrossPeak, : int) -> protocols::noesy_assign::CrossPeak::Spin
- max_volume_contribution(...) from builtins.PyCapsule
- max_volume_contribution(rosetta.protocols.noesy_assign.CrossPeak) -> float
the largest volume contribution (normalized) any of the assignments has
- min_seq_separation_residue_assignment(...) from builtins.PyCapsule
- min_seq_separation_residue_assignment(self : rosetta.protocols.noesy_assign.CrossPeak, volume_threshold : float) -> int
- n_Vmin_assignments(...) from builtins.PyCapsule
- n_Vmin_assignments(rosetta.protocols.noesy_assign.CrossPeak) -> int
number of assignments with peak volume higher than params.min_volume_
- n_assigned(...) from builtins.PyCapsule
- n_assigned(rosetta.protocols.noesy_assign.CrossPeak) -> int
- nudge_distance_bound(...) from builtins.PyCapsule
- nudge_distance_bound(self : rosetta.protocols.noesy_assign.CrossPeak, offset : float) -> NoneType
- peak_id(...) from builtins.PyCapsule
- peak_id(rosetta.protocols.noesy_assign.CrossPeak) -> int
- probability(...) from builtins.PyCapsule
- probability(rosetta.protocols.noesy_assign.CrossPeak) -> float
- proton(...) from builtins.PyCapsule
- proton(*args, **kwargs)
Overloaded function.
1. proton(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> protocols::noesy_assign::CrossPeak::Spin
2. proton(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> protocols::noesy_assign::CrossPeak::Spin
- quality_class(...) from builtins.PyCapsule
- quality_class(rosetta.protocols.noesy_assign.CrossPeak) -> rosetta.protocols.noesy_assign.QualityClass
- quality_class_str(...) from builtins.PyCapsule
- quality_class_str(rosetta.protocols.noesy_assign.CrossPeak) -> str
- resonances(...) from builtins.PyCapsule
- resonances(rosetta.protocols.noesy_assign.CrossPeak) -> rosetta.protocols.noesy_assign.ResonanceList
- same_peak(...) from builtins.PyCapsule
- same_peak(self : rosetta.protocols.noesy_assign.CrossPeak, other : rosetta.protocols.noesy_assign.CrossPeak) -> bool
- set_cumulative_peak_volume(...) from builtins.PyCapsule
- set_cumulative_peak_volume(self : rosetta.protocols.noesy_assign.CrossPeak, setting : float) -> NoneType
- set_eliminated_due_to_dist_violations(...) from builtins.PyCapsule
- set_eliminated_due_to_dist_violations(self : rosetta.protocols.noesy_assign.CrossPeak, setting : bool) -> NoneType
- set_elimination_candidate(...) from builtins.PyCapsule
- set_elimination_candidate(*args, **kwargs)
Overloaded function.
1. set_elimination_candidate(rosetta.protocols.noesy_assign.CrossPeak) -> NoneType
2. set_elimination_candidate(self : rosetta.protocols.noesy_assign.CrossPeak, setting : bool) -> NoneType
- set_elimination_comment(...) from builtins.PyCapsule
- set_elimination_comment(self : rosetta.protocols.noesy_assign.CrossPeak, str : str) -> NoneType
- set_info(...) from builtins.PyCapsule
- set_info(self : rosetta.protocols.noesy_assign.CrossPeak, i : int, info : rosetta.protocols.noesy_assign.CrossPeakInfo) -> NoneType
- set_peak_id(...) from builtins.PyCapsule
- set_peak_id(self : rosetta.protocols.noesy_assign.CrossPeak, val : int) -> NoneType
- set_resonances(...) from builtins.PyCapsule
- set_resonances(self : rosetta.protocols.noesy_assign.CrossPeak, res_in : rosetta.protocols.noesy_assign.ResonanceList) -> NoneType
- set_volume(...) from builtins.PyCapsule
- set_volume(self : rosetta.protocols.noesy_assign.CrossPeak, val : float) -> NoneType
- smallest_native_violation(...) from builtins.PyCapsule
- smallest_native_violation(rosetta.protocols.noesy_assign.CrossPeak) -> float
- spin(...) from builtins.PyCapsule
- spin(*args, **kwargs)
Overloaded function.
1. spin(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> protocols::noesy_assign::CrossPeak::Spin
flat access to spins in [ a, b, h(a), h(b) ] order
2. spin(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> protocols::noesy_assign::CrossPeak::Spin
- tolerance(...) from builtins.PyCapsule
- tolerance(self : rosetta.protocols.noesy_assign.CrossPeak, d : int) -> float
- volume(...) from builtins.PyCapsule
- volume(rosetta.protocols.noesy_assign.CrossPeak) -> float
the measured integral of the peak
Data and other attributes defined here:
- BAD_LOW_PROB = QualityClass.BAD_LOW_PROB
- EL_DISTVIOL = EliminationReason.EL_DISTVIOL
- EL_MAXASSIGN = EliminationReason.EL_MAXASSIGN
- EL_MINPEAKVOL = EliminationReason.EL_MINPEAKVOL
- EL_NETWORK = EliminationReason.EL_NETWORK
- EliminationReason = <class 'rosetta.protocols.noesy_assign.CrossPeak.EliminationReason'>
- HI_AMBIG = QualityClass.HI_AMBIG
- HI_NEAR_UNAMBIG = QualityClass.HI_NEAR_UNAMBIG
- HI_UNAMBIG = QualityClass.HI_UNAMBIG
- MAX_CLASS = QualityClass.MAX_CLASS
- MED_AMBIG = QualityClass.MED_AMBIG
- NOT_ELIMINATED = EliminationReason.NOT_ELIMINATED
- QualityClass = <class 'rosetta.protocols.noesy_assign.CrossPeak.QualityClass'>
- UNAMBIG_MED_PROB = QualityClass.UNAMBIG_MED_PROB
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class CrossPeak3D(CrossPeak) |
| | |
- Method resolution order:
- CrossPeak3D
- CrossPeak
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, sp1 : protocols::noesy_assign::CrossPeak::Spin, sp2 : protocols::noesy_assign::CrossPeak::Spin, label1 : protocols::noesy_assign::CrossPeak::Spin, strength : float) -> NoneType
2. __init__(handle) -> NoneType
3. __init__(handle, rosetta.protocols.noesy_assign.CrossPeak3D) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.CrossPeak3D, : rosetta.protocols.noesy_assign.CrossPeak3D) -> rosetta.protocols.noesy_assign.CrossPeak3D
- assign_labelled_spin(...) from builtins.PyCapsule
- assign_labelled_spin(self : rosetta.protocols.noesy_assign.CrossPeak3D, proton : int) -> NoneType
- assign_spin(...) from builtins.PyCapsule
- assign_spin(self : rosetta.protocols.noesy_assign.CrossPeak3D, spin_id : int) -> NoneType
- empty_clone(...) from builtins.PyCapsule
- empty_clone(rosetta.protocols.noesy_assign.CrossPeak3D) -> rosetta.protocols.noesy_assign.CrossPeak
- has_label(...) from builtins.PyCapsule
- has_label(self : rosetta.protocols.noesy_assign.CrossPeak3D, i : int) -> bool
- label(...) from builtins.PyCapsule
- label(*args, **kwargs)
Overloaded function.
1. label(self : rosetta.protocols.noesy_assign.CrossPeak3D, : int) -> protocols::noesy_assign::CrossPeak::Spin
2. label(self : rosetta.protocols.noesy_assign.CrossPeak3D, : int) -> protocols::noesy_assign::CrossPeak::Spin
Methods inherited from CrossPeak:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.noesy_assign.CrossPeak) -> str
- ambiguous(...) from builtins.PyCapsule
- ambiguous(rosetta.protocols.noesy_assign.CrossPeak) -> bool
- assigned(...) from builtins.PyCapsule
- assigned(rosetta.protocols.noesy_assign.CrossPeak) -> bool
- assignments(...) from builtins.PyCapsule
- assignments(rosetta.protocols.noesy_assign.CrossPeak) -> rosetta.utility.vector1_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t
- begin(...) from builtins.PyCapsule
- begin(*args, **kwargs)
Overloaded function.
1. begin(rosetta.protocols.noesy_assign.CrossPeak) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::noesy_assign::PeakAssignment> const*, std::vector<std::shared_ptr<protocols::noesy_assign::PeakAssignment>, std::allocator<std::shared_ptr<protocols::noesy_assign::PeakAssignment> > > >
2. begin(rosetta.protocols.noesy_assign.CrossPeak) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::noesy_assign::PeakAssignment>*, std::vector<std::shared_ptr<protocols::noesy_assign::PeakAssignment>, std::allocator<std::shared_ptr<protocols::noesy_assign::PeakAssignment> > > >
- create_fa_and_cen_constraint(...) from builtins.PyCapsule
- create_fa_and_cen_constraint(*args, **kwargs)
Overloaded function.
1. create_fa_and_cen_constraint(self : rosetta.protocols.noesy_assign.CrossPeak, fa_cst : rosetta.core.scoring.constraints.Constraint, cen_cst : rosetta.core.scoring.constraints.Constraint, pose : rosetta.core.pose.Pose, centroid_pose : rosetta.core.pose.Pose, normalization : int) -> NoneType
2. create_fa_and_cen_constraint(self : rosetta.protocols.noesy_assign.CrossPeak, fa_cst : rosetta.core.scoring.constraints.Constraint, cen_cst : rosetta.core.scoring.constraints.Constraint, pose : rosetta.core.pose.Pose, centroid_pose : rosetta.core.pose.Pose, normalization : int, padding : float) -> NoneType
3. create_fa_and_cen_constraint(self : rosetta.protocols.noesy_assign.CrossPeak, fa_cst : rosetta.core.scoring.constraints.Constraint, cen_cst : rosetta.core.scoring.constraints.Constraint, pose : rosetta.core.pose.Pose, centroid_pose : rosetta.core.pose.Pose, normalization : int, padding : float, fa_only : bool) -> NoneType
- cumulative_peak_volume(...) from builtins.PyCapsule
- cumulative_peak_volume(rosetta.protocols.noesy_assign.CrossPeak) -> float
the cumulative cyana-type weights for all assignments Vk
- dimension(...) from builtins.PyCapsule
- dimension(rosetta.protocols.noesy_assign.CrossPeak) -> int
- distance_bound(...) from builtins.PyCapsule
- distance_bound(rosetta.protocols.noesy_assign.CrossPeak) -> float
- eliminated(...) from builtins.PyCapsule
- eliminated(*args, **kwargs)
Overloaded function.
1. eliminated(rosetta.protocols.noesy_assign.CrossPeak) -> bool
returns true if this peak is to be ignored due to points (i)-(iv) on p215 of JMB 2002, 319,209-227
do_not_compute ... for outputter that does not want to change state...
2. eliminated(self : rosetta.protocols.noesy_assign.CrossPeak, recompute : bool) -> bool
returns true if this peak is to be ignored due to points (i)-(iv) on p215 of JMB 2002, 319,209-227
do_not_compute ... for outputter that does not want to change state...
3. eliminated(self : rosetta.protocols.noesy_assign.CrossPeak, recompute : bool, do_not_compute : bool) -> bool
returns true if this peak is to be ignored due to points (i)-(iv) on p215 of JMB 2002, 319,209-227
do_not_compute ... for outputter that does not want to change state...
- elimination_reason(...) from builtins.PyCapsule
- elimination_reason(rosetta.protocols.noesy_assign.CrossPeak) -> str
- end(...) from builtins.PyCapsule
- end(rosetta.protocols.noesy_assign.CrossPeak) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::noesy_assign::PeakAssignment> const*, std::vector<std::shared_ptr<protocols::noesy_assign::PeakAssignment>, std::allocator<std::shared_ptr<protocols::noesy_assign::PeakAssignment> > > >
- exp_hash(...) from builtins.PyCapsule
- exp_hash(rosetta.protocols.noesy_assign.CrossPeak) -> int
- filename(...) from builtins.PyCapsule
- filename(rosetta.protocols.noesy_assign.CrossPeak) -> str
- find_assignments(...) from builtins.PyCapsule
- find_assignments(rosetta.protocols.noesy_assign.CrossPeak) -> NoneType
- fold_resonance(...) from builtins.PyCapsule
- fold_resonance(self : rosetta.protocols.noesy_assign.CrossPeak, freq : float, i : int) -> float
- folder(...) from builtins.PyCapsule
- folder(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> rosetta.protocols.noesy_assign.FoldResonance
- has_proton(...) from builtins.PyCapsule
- has_proton(self : rosetta.protocols.noesy_assign.CrossPeak, : int) -> bool
- info(...) from builtins.PyCapsule
- info(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> rosetta.protocols.noesy_assign.CrossPeakInfo
- is4D(...) from builtins.PyCapsule
- is4D(rosetta.protocols.noesy_assign.CrossPeak) -> bool
- is_elimination_candidate(...) from builtins.PyCapsule
- is_elimination_candidate(rosetta.protocols.noesy_assign.CrossPeak) -> bool
- max_volume_contribution(...) from builtins.PyCapsule
- max_volume_contribution(rosetta.protocols.noesy_assign.CrossPeak) -> float
the largest volume contribution (normalized) any of the assignments has
- min_seq_separation_residue_assignment(...) from builtins.PyCapsule
- min_seq_separation_residue_assignment(self : rosetta.protocols.noesy_assign.CrossPeak, volume_threshold : float) -> int
- n_Vmin_assignments(...) from builtins.PyCapsule
- n_Vmin_assignments(rosetta.protocols.noesy_assign.CrossPeak) -> int
number of assignments with peak volume higher than params.min_volume_
- n_assigned(...) from builtins.PyCapsule
- n_assigned(rosetta.protocols.noesy_assign.CrossPeak) -> int
- nudge_distance_bound(...) from builtins.PyCapsule
- nudge_distance_bound(self : rosetta.protocols.noesy_assign.CrossPeak, offset : float) -> NoneType
- peak_id(...) from builtins.PyCapsule
- peak_id(rosetta.protocols.noesy_assign.CrossPeak) -> int
- probability(...) from builtins.PyCapsule
- probability(rosetta.protocols.noesy_assign.CrossPeak) -> float
- proton(...) from builtins.PyCapsule
- proton(*args, **kwargs)
Overloaded function.
1. proton(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> protocols::noesy_assign::CrossPeak::Spin
2. proton(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> protocols::noesy_assign::CrossPeak::Spin
- quality_class(...) from builtins.PyCapsule
- quality_class(rosetta.protocols.noesy_assign.CrossPeak) -> rosetta.protocols.noesy_assign.QualityClass
- quality_class_str(...) from builtins.PyCapsule
- quality_class_str(rosetta.protocols.noesy_assign.CrossPeak) -> str
- resonances(...) from builtins.PyCapsule
- resonances(rosetta.protocols.noesy_assign.CrossPeak) -> rosetta.protocols.noesy_assign.ResonanceList
- same_peak(...) from builtins.PyCapsule
- same_peak(self : rosetta.protocols.noesy_assign.CrossPeak, other : rosetta.protocols.noesy_assign.CrossPeak) -> bool
- set_cumulative_peak_volume(...) from builtins.PyCapsule
- set_cumulative_peak_volume(self : rosetta.protocols.noesy_assign.CrossPeak, setting : float) -> NoneType
- set_eliminated_due_to_dist_violations(...) from builtins.PyCapsule
- set_eliminated_due_to_dist_violations(self : rosetta.protocols.noesy_assign.CrossPeak, setting : bool) -> NoneType
- set_elimination_candidate(...) from builtins.PyCapsule
- set_elimination_candidate(*args, **kwargs)
Overloaded function.
1. set_elimination_candidate(rosetta.protocols.noesy_assign.CrossPeak) -> NoneType
2. set_elimination_candidate(self : rosetta.protocols.noesy_assign.CrossPeak, setting : bool) -> NoneType
- set_elimination_comment(...) from builtins.PyCapsule
- set_elimination_comment(self : rosetta.protocols.noesy_assign.CrossPeak, str : str) -> NoneType
- set_info(...) from builtins.PyCapsule
- set_info(self : rosetta.protocols.noesy_assign.CrossPeak, i : int, info : rosetta.protocols.noesy_assign.CrossPeakInfo) -> NoneType
- set_peak_id(...) from builtins.PyCapsule
- set_peak_id(self : rosetta.protocols.noesy_assign.CrossPeak, val : int) -> NoneType
- set_resonances(...) from builtins.PyCapsule
- set_resonances(self : rosetta.protocols.noesy_assign.CrossPeak, res_in : rosetta.protocols.noesy_assign.ResonanceList) -> NoneType
- set_volume(...) from builtins.PyCapsule
- set_volume(self : rosetta.protocols.noesy_assign.CrossPeak, val : float) -> NoneType
- smallest_native_violation(...) from builtins.PyCapsule
- smallest_native_violation(rosetta.protocols.noesy_assign.CrossPeak) -> float
- spin(...) from builtins.PyCapsule
- spin(*args, **kwargs)
Overloaded function.
1. spin(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> protocols::noesy_assign::CrossPeak::Spin
flat access to spins in [ a, b, h(a), h(b) ] order
2. spin(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> protocols::noesy_assign::CrossPeak::Spin
- tolerance(...) from builtins.PyCapsule
- tolerance(self : rosetta.protocols.noesy_assign.CrossPeak, d : int) -> float
- volume(...) from builtins.PyCapsule
- volume(rosetta.protocols.noesy_assign.CrossPeak) -> float
the measured integral of the peak
Data and other attributes inherited from CrossPeak:
- BAD_LOW_PROB = QualityClass.BAD_LOW_PROB
- EL_DISTVIOL = EliminationReason.EL_DISTVIOL
- EL_MAXASSIGN = EliminationReason.EL_MAXASSIGN
- EL_MINPEAKVOL = EliminationReason.EL_MINPEAKVOL
- EL_NETWORK = EliminationReason.EL_NETWORK
- EliminationReason = <class 'rosetta.protocols.noesy_assign.CrossPeak.EliminationReason'>
- HI_AMBIG = QualityClass.HI_AMBIG
- HI_NEAR_UNAMBIG = QualityClass.HI_NEAR_UNAMBIG
- HI_UNAMBIG = QualityClass.HI_UNAMBIG
- MAX_CLASS = QualityClass.MAX_CLASS
- MED_AMBIG = QualityClass.MED_AMBIG
- NOT_ELIMINATED = EliminationReason.NOT_ELIMINATED
- QualityClass = <class 'rosetta.protocols.noesy_assign.CrossPeak.QualityClass'>
- UNAMBIG_MED_PROB = QualityClass.UNAMBIG_MED_PROB
|
class CrossPeak4D(CrossPeak3D) |
| | |
- Method resolution order:
- CrossPeak4D
- CrossPeak3D
- CrossPeak
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, sp1 : protocols::noesy_assign::CrossPeak::Spin, sp2 : protocols::noesy_assign::CrossPeak::Spin, label1 : protocols::noesy_assign::CrossPeak::Spin, label2 : protocols::noesy_assign::CrossPeak::Spin, strength : float) -> NoneType
2. __init__(handle) -> NoneType
3. __init__(handle, rosetta.protocols.noesy_assign.CrossPeak4D) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.CrossPeak4D, : rosetta.protocols.noesy_assign.CrossPeak4D) -> rosetta.protocols.noesy_assign.CrossPeak4D
- assign_spin(...) from builtins.PyCapsule
- assign_spin(self : rosetta.protocols.noesy_assign.CrossPeak4D, proton : int) -> NoneType
- empty_clone(...) from builtins.PyCapsule
- empty_clone(rosetta.protocols.noesy_assign.CrossPeak4D) -> rosetta.protocols.noesy_assign.CrossPeak
- has_label(...) from builtins.PyCapsule
- has_label(self : rosetta.protocols.noesy_assign.CrossPeak4D, : int) -> bool
- label(...) from builtins.PyCapsule
- label(*args, **kwargs)
Overloaded function.
1. label(self : rosetta.protocols.noesy_assign.CrossPeak4D, i : int) -> protocols::noesy_assign::CrossPeak::Spin
2. label(self : rosetta.protocols.noesy_assign.CrossPeak4D, i : int) -> protocols::noesy_assign::CrossPeak::Spin
Methods inherited from CrossPeak3D:
- assign_labelled_spin(...) from builtins.PyCapsule
- assign_labelled_spin(self : rosetta.protocols.noesy_assign.CrossPeak3D, proton : int) -> NoneType
Methods inherited from CrossPeak:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.noesy_assign.CrossPeak) -> str
- ambiguous(...) from builtins.PyCapsule
- ambiguous(rosetta.protocols.noesy_assign.CrossPeak) -> bool
- assigned(...) from builtins.PyCapsule
- assigned(rosetta.protocols.noesy_assign.CrossPeak) -> bool
- assignments(...) from builtins.PyCapsule
- assignments(rosetta.protocols.noesy_assign.CrossPeak) -> rosetta.utility.vector1_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t
- begin(...) from builtins.PyCapsule
- begin(*args, **kwargs)
Overloaded function.
1. begin(rosetta.protocols.noesy_assign.CrossPeak) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::noesy_assign::PeakAssignment> const*, std::vector<std::shared_ptr<protocols::noesy_assign::PeakAssignment>, std::allocator<std::shared_ptr<protocols::noesy_assign::PeakAssignment> > > >
2. begin(rosetta.protocols.noesy_assign.CrossPeak) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::noesy_assign::PeakAssignment>*, std::vector<std::shared_ptr<protocols::noesy_assign::PeakAssignment>, std::allocator<std::shared_ptr<protocols::noesy_assign::PeakAssignment> > > >
- create_fa_and_cen_constraint(...) from builtins.PyCapsule
- create_fa_and_cen_constraint(*args, **kwargs)
Overloaded function.
1. create_fa_and_cen_constraint(self : rosetta.protocols.noesy_assign.CrossPeak, fa_cst : rosetta.core.scoring.constraints.Constraint, cen_cst : rosetta.core.scoring.constraints.Constraint, pose : rosetta.core.pose.Pose, centroid_pose : rosetta.core.pose.Pose, normalization : int) -> NoneType
2. create_fa_and_cen_constraint(self : rosetta.protocols.noesy_assign.CrossPeak, fa_cst : rosetta.core.scoring.constraints.Constraint, cen_cst : rosetta.core.scoring.constraints.Constraint, pose : rosetta.core.pose.Pose, centroid_pose : rosetta.core.pose.Pose, normalization : int, padding : float) -> NoneType
3. create_fa_and_cen_constraint(self : rosetta.protocols.noesy_assign.CrossPeak, fa_cst : rosetta.core.scoring.constraints.Constraint, cen_cst : rosetta.core.scoring.constraints.Constraint, pose : rosetta.core.pose.Pose, centroid_pose : rosetta.core.pose.Pose, normalization : int, padding : float, fa_only : bool) -> NoneType
- cumulative_peak_volume(...) from builtins.PyCapsule
- cumulative_peak_volume(rosetta.protocols.noesy_assign.CrossPeak) -> float
the cumulative cyana-type weights for all assignments Vk
- dimension(...) from builtins.PyCapsule
- dimension(rosetta.protocols.noesy_assign.CrossPeak) -> int
- distance_bound(...) from builtins.PyCapsule
- distance_bound(rosetta.protocols.noesy_assign.CrossPeak) -> float
- eliminated(...) from builtins.PyCapsule
- eliminated(*args, **kwargs)
Overloaded function.
1. eliminated(rosetta.protocols.noesy_assign.CrossPeak) -> bool
returns true if this peak is to be ignored due to points (i)-(iv) on p215 of JMB 2002, 319,209-227
do_not_compute ... for outputter that does not want to change state...
2. eliminated(self : rosetta.protocols.noesy_assign.CrossPeak, recompute : bool) -> bool
returns true if this peak is to be ignored due to points (i)-(iv) on p215 of JMB 2002, 319,209-227
do_not_compute ... for outputter that does not want to change state...
3. eliminated(self : rosetta.protocols.noesy_assign.CrossPeak, recompute : bool, do_not_compute : bool) -> bool
returns true if this peak is to be ignored due to points (i)-(iv) on p215 of JMB 2002, 319,209-227
do_not_compute ... for outputter that does not want to change state...
- elimination_reason(...) from builtins.PyCapsule
- elimination_reason(rosetta.protocols.noesy_assign.CrossPeak) -> str
- end(...) from builtins.PyCapsule
- end(rosetta.protocols.noesy_assign.CrossPeak) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::noesy_assign::PeakAssignment> const*, std::vector<std::shared_ptr<protocols::noesy_assign::PeakAssignment>, std::allocator<std::shared_ptr<protocols::noesy_assign::PeakAssignment> > > >
- exp_hash(...) from builtins.PyCapsule
- exp_hash(rosetta.protocols.noesy_assign.CrossPeak) -> int
- filename(...) from builtins.PyCapsule
- filename(rosetta.protocols.noesy_assign.CrossPeak) -> str
- find_assignments(...) from builtins.PyCapsule
- find_assignments(rosetta.protocols.noesy_assign.CrossPeak) -> NoneType
- fold_resonance(...) from builtins.PyCapsule
- fold_resonance(self : rosetta.protocols.noesy_assign.CrossPeak, freq : float, i : int) -> float
- folder(...) from builtins.PyCapsule
- folder(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> rosetta.protocols.noesy_assign.FoldResonance
- has_proton(...) from builtins.PyCapsule
- has_proton(self : rosetta.protocols.noesy_assign.CrossPeak, : int) -> bool
- info(...) from builtins.PyCapsule
- info(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> rosetta.protocols.noesy_assign.CrossPeakInfo
- is4D(...) from builtins.PyCapsule
- is4D(rosetta.protocols.noesy_assign.CrossPeak) -> bool
- is_elimination_candidate(...) from builtins.PyCapsule
- is_elimination_candidate(rosetta.protocols.noesy_assign.CrossPeak) -> bool
- max_volume_contribution(...) from builtins.PyCapsule
- max_volume_contribution(rosetta.protocols.noesy_assign.CrossPeak) -> float
the largest volume contribution (normalized) any of the assignments has
- min_seq_separation_residue_assignment(...) from builtins.PyCapsule
- min_seq_separation_residue_assignment(self : rosetta.protocols.noesy_assign.CrossPeak, volume_threshold : float) -> int
- n_Vmin_assignments(...) from builtins.PyCapsule
- n_Vmin_assignments(rosetta.protocols.noesy_assign.CrossPeak) -> int
number of assignments with peak volume higher than params.min_volume_
- n_assigned(...) from builtins.PyCapsule
- n_assigned(rosetta.protocols.noesy_assign.CrossPeak) -> int
- nudge_distance_bound(...) from builtins.PyCapsule
- nudge_distance_bound(self : rosetta.protocols.noesy_assign.CrossPeak, offset : float) -> NoneType
- peak_id(...) from builtins.PyCapsule
- peak_id(rosetta.protocols.noesy_assign.CrossPeak) -> int
- probability(...) from builtins.PyCapsule
- probability(rosetta.protocols.noesy_assign.CrossPeak) -> float
- proton(...) from builtins.PyCapsule
- proton(*args, **kwargs)
Overloaded function.
1. proton(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> protocols::noesy_assign::CrossPeak::Spin
2. proton(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> protocols::noesy_assign::CrossPeak::Spin
- quality_class(...) from builtins.PyCapsule
- quality_class(rosetta.protocols.noesy_assign.CrossPeak) -> rosetta.protocols.noesy_assign.QualityClass
- quality_class_str(...) from builtins.PyCapsule
- quality_class_str(rosetta.protocols.noesy_assign.CrossPeak) -> str
- resonances(...) from builtins.PyCapsule
- resonances(rosetta.protocols.noesy_assign.CrossPeak) -> rosetta.protocols.noesy_assign.ResonanceList
- same_peak(...) from builtins.PyCapsule
- same_peak(self : rosetta.protocols.noesy_assign.CrossPeak, other : rosetta.protocols.noesy_assign.CrossPeak) -> bool
- set_cumulative_peak_volume(...) from builtins.PyCapsule
- set_cumulative_peak_volume(self : rosetta.protocols.noesy_assign.CrossPeak, setting : float) -> NoneType
- set_eliminated_due_to_dist_violations(...) from builtins.PyCapsule
- set_eliminated_due_to_dist_violations(self : rosetta.protocols.noesy_assign.CrossPeak, setting : bool) -> NoneType
- set_elimination_candidate(...) from builtins.PyCapsule
- set_elimination_candidate(*args, **kwargs)
Overloaded function.
1. set_elimination_candidate(rosetta.protocols.noesy_assign.CrossPeak) -> NoneType
2. set_elimination_candidate(self : rosetta.protocols.noesy_assign.CrossPeak, setting : bool) -> NoneType
- set_elimination_comment(...) from builtins.PyCapsule
- set_elimination_comment(self : rosetta.protocols.noesy_assign.CrossPeak, str : str) -> NoneType
- set_info(...) from builtins.PyCapsule
- set_info(self : rosetta.protocols.noesy_assign.CrossPeak, i : int, info : rosetta.protocols.noesy_assign.CrossPeakInfo) -> NoneType
- set_peak_id(...) from builtins.PyCapsule
- set_peak_id(self : rosetta.protocols.noesy_assign.CrossPeak, val : int) -> NoneType
- set_resonances(...) from builtins.PyCapsule
- set_resonances(self : rosetta.protocols.noesy_assign.CrossPeak, res_in : rosetta.protocols.noesy_assign.ResonanceList) -> NoneType
- set_volume(...) from builtins.PyCapsule
- set_volume(self : rosetta.protocols.noesy_assign.CrossPeak, val : float) -> NoneType
- smallest_native_violation(...) from builtins.PyCapsule
- smallest_native_violation(rosetta.protocols.noesy_assign.CrossPeak) -> float
- spin(...) from builtins.PyCapsule
- spin(*args, **kwargs)
Overloaded function.
1. spin(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> protocols::noesy_assign::CrossPeak::Spin
flat access to spins in [ a, b, h(a), h(b) ] order
2. spin(self : rosetta.protocols.noesy_assign.CrossPeak, i : int) -> protocols::noesy_assign::CrossPeak::Spin
- tolerance(...) from builtins.PyCapsule
- tolerance(self : rosetta.protocols.noesy_assign.CrossPeak, d : int) -> float
- volume(...) from builtins.PyCapsule
- volume(rosetta.protocols.noesy_assign.CrossPeak) -> float
the measured integral of the peak
Data and other attributes inherited from CrossPeak:
- BAD_LOW_PROB = QualityClass.BAD_LOW_PROB
- EL_DISTVIOL = EliminationReason.EL_DISTVIOL
- EL_MAXASSIGN = EliminationReason.EL_MAXASSIGN
- EL_MINPEAKVOL = EliminationReason.EL_MINPEAKVOL
- EL_NETWORK = EliminationReason.EL_NETWORK
- EliminationReason = <class 'rosetta.protocols.noesy_assign.CrossPeak.EliminationReason'>
- HI_AMBIG = QualityClass.HI_AMBIG
- HI_NEAR_UNAMBIG = QualityClass.HI_NEAR_UNAMBIG
- HI_UNAMBIG = QualityClass.HI_UNAMBIG
- MAX_CLASS = QualityClass.MAX_CLASS
- MED_AMBIG = QualityClass.MED_AMBIG
- NOT_ELIMINATED = EliminationReason.NOT_ELIMINATED
- QualityClass = <class 'rosetta.protocols.noesy_assign.CrossPeak.QualityClass'>
- UNAMBIG_MED_PROB = QualityClass.UNAMBIG_MED_PROB
|
class CrossPeakInfo(builtins.object) |
| |
shared information about CrossPeak (one for each proton dimension)
|
| |
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.protocols.noesy_assign.CrossPeakInfo, cpi : rosetta.protocols.noesy_assign.CrossPeakInfo) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.noesy_assign.CrossPeakInfo, proton : str, label : str, max_noe_distance : float, proton_tolerance : float, label_tolerance : float) -> NoneType
2. __init__(self : rosetta.protocols.noesy_assign.CrossPeakInfo, : rosetta.protocols.noesy_assign.CrossPeakInfo) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.noesy_assign.CrossPeakInfo) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.CrossPeakInfo, : rosetta.protocols.noesy_assign.CrossPeakInfo) -> rosetta.protocols.noesy_assign.CrossPeakInfo
- exp_hash(...) from builtins.PyCapsule
- exp_hash(rosetta.protocols.noesy_assign.CrossPeakInfo) -> int
- filename(...) from builtins.PyCapsule
- filename(rosetta.protocols.noesy_assign.CrossPeakInfo) -> str
- fold_label_resonance(...) from builtins.PyCapsule
- fold_label_resonance(rosetta.protocols.noesy_assign.CrossPeakInfo) -> rosetta.protocols.noesy_assign.FoldResonance
- fold_proton_resonance(...) from builtins.PyCapsule
- fold_proton_resonance(rosetta.protocols.noesy_assign.CrossPeakInfo) -> rosetta.protocols.noesy_assign.FoldResonance
- has_label(...) from builtins.PyCapsule
- has_label(rosetta.protocols.noesy_assign.CrossPeakInfo) -> bool
- label_atom_name(...) from builtins.PyCapsule
- label_atom_name(self : rosetta.protocols.noesy_assign.CrossPeakInfo, proton_name : str, aa : rosetta.core.chemical.AA) -> str
- label_atom_type(...) from builtins.PyCapsule
- label_atom_type(rosetta.protocols.noesy_assign.CrossPeakInfo) -> str
- label_tolerance(...) from builtins.PyCapsule
- label_tolerance(rosetta.protocols.noesy_assign.CrossPeakInfo) -> float
- main_atom(...) from builtins.PyCapsule
- main_atom(rosetta.protocols.noesy_assign.CrossPeakInfo) -> str
- max_noe_distance(...) from builtins.PyCapsule
- max_noe_distance(rosetta.protocols.noesy_assign.CrossPeakInfo) -> float
- proton_tolerance(...) from builtins.PyCapsule
- proton_tolerance(rosetta.protocols.noesy_assign.CrossPeakInfo) -> float
- set_filename(...) from builtins.PyCapsule
- set_filename(self : rosetta.protocols.noesy_assign.CrossPeakInfo, filename : str) -> NoneType
- set_folding_window(...) from builtins.PyCapsule
- set_folding_window(*args, **kwargs)
Overloaded function.
1. set_folding_window(self : rosetta.protocols.noesy_assign.CrossPeakInfo, start : float, end : float) -> NoneType
2. set_folding_window(self : rosetta.protocols.noesy_assign.CrossPeakInfo, start : float, end : float, label : bool) -> NoneType
- set_label(...) from builtins.PyCapsule
- set_label(self : rosetta.protocols.noesy_assign.CrossPeakInfo, label : str, tolerance : float) -> NoneType
- set_proton(...) from builtins.PyCapsule
- set_proton(self : rosetta.protocols.noesy_assign.CrossPeakInfo, name : str, tolerance : float) -> NoneType
|
class CrossPeakList(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.noesy_assign.CrossPeakList) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.CrossPeakList, : rosetta.protocols.noesy_assign.CrossPeakList) -> rosetta.protocols.noesy_assign.CrossPeakList
- assignments(...) from builtins.PyCapsule
- assignments(*args, **kwargs)
Overloaded function.
1. assignments(rosetta.protocols.noesy_assign.CrossPeakList) -> protocols::noesy_assign::PeakAssignmentResidueMap
2. assignments(rosetta.protocols.noesy_assign.CrossPeakList) -> protocols::noesy_assign::PeakAssignmentResidueMap
- begin(...) from builtins.PyCapsule
- begin(*args, **kwargs)
Overloaded function.
1. begin(rosetta.protocols.noesy_assign.CrossPeakList) -> std::_List_const_iterator<std::shared_ptr<protocols::noesy_assign::CrossPeak> >
2. begin(rosetta.protocols.noesy_assign.CrossPeakList) -> std::_List_iterator<std::shared_ptr<protocols::noesy_assign::CrossPeak> >
- count_assignments(...) from builtins.PyCapsule
- count_assignments(rosetta.protocols.noesy_assign.CrossPeakList) -> int
- delete_diagonal_peaks(...) from builtins.PyCapsule
- delete_diagonal_peaks(rosetta.protocols.noesy_assign.CrossPeakList) -> NoneType
- eliminate_spurious_peaks(...) from builtins.PyCapsule
- eliminate_spurious_peaks(rosetta.protocols.noesy_assign.CrossPeakList) -> NoneType
- end(...) from builtins.PyCapsule
- end(rosetta.protocols.noesy_assign.CrossPeakList) -> std::_List_const_iterator<std::shared_ptr<protocols::noesy_assign::CrossPeak> >
- find_assignments(...) from builtins.PyCapsule
- find_assignments(rosetta.protocols.noesy_assign.CrossPeakList) -> NoneType
- generate_fa_and_cen_constraints(...) from builtins.PyCapsule
- generate_fa_and_cen_constraints(*args, **kwargs)
Overloaded function.
1. generate_fa_and_cen_constraints(self : rosetta.protocols.noesy_assign.CrossPeakList, fa_set : rosetta.core.scoring.constraints.ConstraintSet, cen_set : rosetta.core.scoring.constraints.ConstraintSet, pose : rosetta.core.pose.Pose, centroid_pose : rosetta.core.pose.Pose, min_seq_separation : int, min_quali : int, max_quali : int) -> NoneType
2. generate_fa_and_cen_constraints(self : rosetta.protocols.noesy_assign.CrossPeakList, fa_set : rosetta.core.scoring.constraints.ConstraintSet, cen_set : rosetta.core.scoring.constraints.ConstraintSet, pose : rosetta.core.pose.Pose, centroid_pose : rosetta.core.pose.Pose, min_seq_separation : int, min_quali : int, max_quali : int, padding : float) -> NoneType
3. generate_fa_and_cen_constraints(self : rosetta.protocols.noesy_assign.CrossPeakList, fa_set : rosetta.core.scoring.constraints.ConstraintSet, cen_set : rosetta.core.scoring.constraints.ConstraintSet, pose : rosetta.core.pose.Pose, centroid_pose : rosetta.core.pose.Pose, min_seq_separation : int, min_quali : int, max_quali : int, padding : float, ignore_elimination_candidates : bool) -> NoneType
4. generate_fa_and_cen_constraints(self : rosetta.protocols.noesy_assign.CrossPeakList, fa_set : rosetta.core.scoring.constraints.ConstraintSet, cen_set : rosetta.core.scoring.constraints.ConstraintSet, pose : rosetta.core.pose.Pose, centroid_pose : rosetta.core.pose.Pose, min_seq_separation : int, min_quali : int, max_quali : int, padding : float, ignore_elimination_candidates : bool, elimination_candidates : bool) -> NoneType
- network_analysis(...) from builtins.PyCapsule
- network_analysis(rosetta.protocols.noesy_assign.CrossPeakList) -> NoneType
- peaks(...) from builtins.PyCapsule
- peaks(rosetta.protocols.noesy_assign.CrossPeakList) -> rosetta.std.list_std_shared_ptr_protocols_noesy_assign_CrossPeak_std_allocator_std_shared_ptr_protocols_noesy_assign_CrossPeak_t
- set_trivial_decoy_compatibility_score(...) from builtins.PyCapsule
- set_trivial_decoy_compatibility_score(rosetta.protocols.noesy_assign.CrossPeakList) -> NoneType
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.noesy_assign.CrossPeakList) -> int
- update_chemshiftscore(...) from builtins.PyCapsule
- update_chemshiftscore(rosetta.protocols.noesy_assign.CrossPeakList) -> NoneType
- update_peak_volumina(...) from builtins.PyCapsule
- update_peak_volumina(rosetta.protocols.noesy_assign.CrossPeakList) -> NoneType
- update_symmetry_score(...) from builtins.PyCapsule
- update_symmetry_score(rosetta.protocols.noesy_assign.CrossPeakList) -> NoneType
- update_upperdistance_score(...) from builtins.PyCapsule
- update_upperdistance_score(rosetta.protocols.noesy_assign.CrossPeakList) -> NoneType
- write_peak_files(...) from builtins.PyCapsule
- write_peak_files(self : rosetta.protocols.noesy_assign.CrossPeakList, prefix : str, output_adaptor : protocols::noesy_assign::PeakFileFormat) -> NoneType
|
class DistanceScoreMover(rosetta.protocols.moves.Mover) |
| |
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)
|
| |
- Method resolution order:
- DistanceScoreMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, : rosetta.protocols.noesy_assign.CrossPeakList, pose : rosetta.core.pose.Pose, dcut : float) -> NoneType
2. __init__(handle, rosetta.protocols.noesy_assign.DistanceScoreMover) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.noesy_assign.DistanceScoreMover, pose : rosetta.core.pose.Pose) -> NoneType
sum up decoy_compatibility score in PeakAssignments
- finalize_scoring(...) from builtins.PyCapsule
- finalize_scoring(rosetta.protocols.noesy_assign.DistanceScoreMover) -> NoneType
normalize decoy_compatibility of PeakAssignments by count_decoys_
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.noesy_assign.DistanceScoreMover) -> str
- prepare_scoring(...) from builtins.PyCapsule
- prepare_scoring(*args, **kwargs)
Overloaded function.
1. prepare_scoring(rosetta.protocols.noesy_assign.DistanceScoreMover) -> NoneType
set decoy_compatibility in PeakAssignments to zero
2. prepare_scoring(self : rosetta.protocols.noesy_assign.DistanceScoreMover, use_for_calibration : bool) -> NoneType
set decoy_compatibility in PeakAssignments to zero
- set_dcut(...) from builtins.PyCapsule
- set_dcut(self : rosetta.protocols.noesy_assign.DistanceScoreMover, setting : float) -> NoneType
Methods inherited from rosetta.protocols.moves.Mover:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.moves.Mover, other : rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class FloatingResonance(Resonance) |
| |
FloatingResonance combines resonanceID (label), chemical shift (freq), tolerance (error), and the assigned atom (atom, name, resid)
(provided accessor methods of "FloatingResonance": label, atom, resid, name, freq, error, tolerance, calibration_atom_type )
|
| |
- Method resolution order:
- FloatingResonance
- Resonance
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, res : rosetta.protocols.noesy_assign.Resonance, : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, : rosetta.protocols.noesy_assign.ResonanceList) -> NoneType
3. __init__(handle, rosetta.protocols.noesy_assign.FloatingResonance) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- ambiguity(...) from builtins.PyCapsule
- ambiguity(rosetta.protocols.noesy_assign.FloatingResonance) -> int
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.FloatingResonance, : rosetta.protocols.noesy_assign.FloatingResonance) -> rosetta.protocols.noesy_assign.FloatingResonance
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.noesy_assign.FloatingResonance) -> rosetta.protocols.noesy_assign.Resonance
- float_label(...) from builtins.PyCapsule
- float_label(self : rosetta.protocols.noesy_assign.FloatingResonance, ifloat : int) -> int
- match2D(...) from builtins.PyCapsule
- match2D(self : rosetta.protocols.noesy_assign.FloatingResonance, proton_freq : float, proton_error : float, proton_folder : rosetta.protocols.noesy_assign.FoldResonance, label_freq : float, label_error : float, label_folder : rosetta.protocols.noesy_assign.FoldResonance, matches : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> bool
match the proton and corresponding label atom at same time
- pmatch(...) from builtins.PyCapsule
- pmatch(self : rosetta.protocols.noesy_assign.FloatingResonance, peakfreq : float, error : float, folder : rosetta.protocols.noesy_assign.FoldResonance) -> float
Methods inherited from Resonance:
- aa(...) from builtins.PyCapsule
- aa(rosetta.protocols.noesy_assign.Resonance) -> rosetta.core.chemical.AA
- add_connected_resonance(...) from builtins.PyCapsule
- add_connected_resonance(self : rosetta.protocols.noesy_assign.Resonance, ptr : rosetta.std.weak_ptr_protocols_noesy_assign_Resonance_t) -> NoneType
- atom(...) from builtins.PyCapsule
- atom(rosetta.protocols.noesy_assign.Resonance) -> rosetta.core.id.NamedAtomID
Atom
- calibration_atom_type(...) from builtins.PyCapsule
- calibration_atom_type(rosetta.protocols.noesy_assign.Resonance) -> rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE
classification for calibration... e.g., Backbone, sidechain, etc..
- clear_connected_resonances(...) from builtins.PyCapsule
- clear_connected_resonances(rosetta.protocols.noesy_assign.Resonance) -> NoneType
- connected_resonance_ids(...) from builtins.PyCapsule
- connected_resonance_ids(rosetta.protocols.noesy_assign.Resonance) -> rosetta.utility.vector1_unsigned_long
- connected_resonances(...) from builtins.PyCapsule
- connected_resonances(rosetta.protocols.noesy_assign.Resonance) -> rosetta.utility.vector1_std_weak_ptr_protocols_noesy_assign_Resonance_t
- error(...) from builtins.PyCapsule
- error(rosetta.protocols.noesy_assign.Resonance) -> float
- first_connected_resonance(...) from builtins.PyCapsule
- first_connected_resonance(rosetta.protocols.noesy_assign.Resonance) -> rosetta.protocols.noesy_assign.Resonance
- freq(...) from builtins.PyCapsule
- freq(rosetta.protocols.noesy_assign.Resonance) -> float
resonance frequency (chemical shift)
- has_connected_resonances(...) from builtins.PyCapsule
- has_connected_resonances(rosetta.protocols.noesy_assign.Resonance) -> bool
- intensity(...) from builtins.PyCapsule
- intensity(rosetta.protocols.noesy_assign.Resonance) -> float
in ILV-labelled proteins, the both LV methyls are labelled randomly with 50% probability,
whereas I delta methyls are labelled 100%
- is_proton(...) from builtins.PyCapsule
- is_proton(rosetta.protocols.noesy_assign.Resonance) -> bool
- label(...) from builtins.PyCapsule
- label(rosetta.protocols.noesy_assign.Resonance) -> int
ResonanceID
- match(...) from builtins.PyCapsule
- match(self : rosetta.protocols.noesy_assign.Resonance, freq : float, error : float, folder : rosetta.protocols.noesy_assign.FoldResonance) -> bool
Resonance matches the given cross-peaks frequency
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.noesy_assign.Resonance) -> str
- resid(...) from builtins.PyCapsule
- resid(rosetta.protocols.noesy_assign.Resonance) -> int
- set_intensity(...) from builtins.PyCapsule
- set_intensity(self : rosetta.protocols.noesy_assign.Resonance, setting : float) -> NoneType
- tolerance(...) from builtins.PyCapsule
- tolerance(rosetta.protocols.noesy_assign.Resonance) -> float
|
class FoldResonance(builtins.object) |
| | |
Methods defined here:
- __call__(...) from builtins.PyCapsule
- __call__(self : rosetta.protocols.noesy_assign.FoldResonance, freq : float) -> float
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.noesy_assign.FoldResonance) -> NoneType
2. __init__(self : rosetta.protocols.noesy_assign.FoldResonance, : rosetta.protocols.noesy_assign.FoldResonance) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.FoldResonance, : rosetta.protocols.noesy_assign.FoldResonance) -> rosetta.protocols.noesy_assign.FoldResonance
- end(...) from builtins.PyCapsule
- end(rosetta.protocols.noesy_assign.FoldResonance) -> float
- is_folded(...) from builtins.PyCapsule
- is_folded(*args, **kwargs)
Overloaded function.
1. is_folded(self : rosetta.protocols.noesy_assign.FoldResonance, freq : float) -> bool
2. is_folded(rosetta.protocols.noesy_assign.FoldResonance) -> bool
- is_folded_down(...) from builtins.PyCapsule
- is_folded_down(self : rosetta.protocols.noesy_assign.FoldResonance, freq : float) -> bool
- is_folded_up(...) from builtins.PyCapsule
- is_folded_up(self : rosetta.protocols.noesy_assign.FoldResonance, freq : float) -> bool
- set_window(...) from builtins.PyCapsule
- set_window(self : rosetta.protocols.noesy_assign.FoldResonance, start : float, end : float) -> NoneType
- start(...) from builtins.PyCapsule
- start(rosetta.protocols.noesy_assign.FoldResonance) -> float
|
class FragsToAtomDist(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.noesy_assign.FragsToAtomDist) -> NoneType
2. __init__(self : rosetta.protocols.noesy_assign.FragsToAtomDist, filename : str) -> NoneType
3. __init__(self : rosetta.protocols.noesy_assign.FragsToAtomDist, : rosetta.protocols.noesy_assign.FragsToAtomDist) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.FragsToAtomDist, : rosetta.protocols.noesy_assign.FragsToAtomDist) -> rosetta.protocols.noesy_assign.FragsToAtomDist
- check_sequence(...) from builtins.PyCapsule
- check_sequence(self : rosetta.protocols.noesy_assign.FragsToAtomDist, other_sequence : str) -> bool
- distance(...) from builtins.PyCapsule
- distance(*args, **kwargs)
Overloaded function.
1. distance(self : rosetta.protocols.noesy_assign.FragsToAtomDist, atom1 : rosetta.core.id.NamedAtomID, atom2 : rosetta.core.id.NamedAtomID) -> float
2. distance(self : rosetta.protocols.noesy_assign.FragsToAtomDist, atom1 : rosetta.core.id.NamedAtomID, atom2 : rosetta.core.id.NamedAtomID, r6_averaged : bool) -> float
- distance_record(...) from builtins.PyCapsule
- distance_record(self : rosetta.protocols.noesy_assign.FragsToAtomDist, atom1 : rosetta.core.id.NamedAtomID, atom2 : rosetta.core.id.NamedAtomID) -> protocols::noesy_assign::FragsToAtomDist::DistanceRecord
- generate_from_frag_file(...) from builtins.PyCapsule
- generate_from_frag_file(self : rosetta.protocols.noesy_assign.FragsToAtomDist, filename : str, sequence : str, cycles : int, dump_freq : int) -> NoneType
- generate_from_fragments(...) from builtins.PyCapsule
- generate_from_fragments(self : rosetta.protocols.noesy_assign.FragsToAtomDist, fragments : rosetta.core.fragment.FragSet, sequence : str, cycles : int, dump_freq : int) -> NoneType
- read_from_file(...) from builtins.PyCapsule
- read_from_file(self : rosetta.protocols.noesy_assign.FragsToAtomDist, filename : str) -> NoneType
- sequence(...) from builtins.PyCapsule
- sequence(rosetta.protocols.noesy_assign.FragsToAtomDist) -> str
- write_hist_to_file(...) from builtins.PyCapsule
- write_hist_to_file(self : rosetta.protocols.noesy_assign.FragsToAtomDist, filename : str) -> NoneType
- write_to_file(...) from builtins.PyCapsule
- write_to_file(self : rosetta.protocols.noesy_assign.FragsToAtomDist, filename : str) -> NoneType
|
class LabelResonance(Resonance) |
| |
LabelResonance combines resonanceID (label), chemical shift (freq), tolerance (error), and the assigned atom (atom, name, resid)
(provided accessor methods of "LabelResonance": label, atom, resid, name, freq, error, tolerance, calibration_atom_type )
|
| |
- Method resolution order:
- LabelResonance
- Resonance
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, label : int, freq : float, error : float, id : rosetta.core.id.NamedAtomID, : rosetta.core.chemical.AA, intensity : float) -> NoneType
3. __init__(handle, rosetta.protocols.noesy_assign.LabelResonance) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.LabelResonance, : rosetta.protocols.noesy_assign.LabelResonance) -> rosetta.protocols.noesy_assign.LabelResonance
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.noesy_assign.LabelResonance) -> rosetta.protocols.noesy_assign.Resonance
- match2D(...) from builtins.PyCapsule
- match2D(self : rosetta.protocols.noesy_assign.LabelResonance, proton_freq : float, proton_error : float, proton_folder : rosetta.protocols.noesy_assign.FoldResonance, label_freq : float, label_error : float, label_folder : rosetta.protocols.noesy_assign.FoldResonance, matches : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> bool
match the proton and corresponding label atom at same time
Methods inherited from Resonance:
- aa(...) from builtins.PyCapsule
- aa(rosetta.protocols.noesy_assign.Resonance) -> rosetta.core.chemical.AA
- add_connected_resonance(...) from builtins.PyCapsule
- add_connected_resonance(self : rosetta.protocols.noesy_assign.Resonance, ptr : rosetta.std.weak_ptr_protocols_noesy_assign_Resonance_t) -> NoneType
- ambiguity(...) from builtins.PyCapsule
- ambiguity(rosetta.protocols.noesy_assign.Resonance) -> int
- atom(...) from builtins.PyCapsule
- atom(rosetta.protocols.noesy_assign.Resonance) -> rosetta.core.id.NamedAtomID
Atom
- calibration_atom_type(...) from builtins.PyCapsule
- calibration_atom_type(rosetta.protocols.noesy_assign.Resonance) -> rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE
classification for calibration... e.g., Backbone, sidechain, etc..
- clear_connected_resonances(...) from builtins.PyCapsule
- clear_connected_resonances(rosetta.protocols.noesy_assign.Resonance) -> NoneType
- connected_resonance_ids(...) from builtins.PyCapsule
- connected_resonance_ids(rosetta.protocols.noesy_assign.Resonance) -> rosetta.utility.vector1_unsigned_long
- connected_resonances(...) from builtins.PyCapsule
- connected_resonances(rosetta.protocols.noesy_assign.Resonance) -> rosetta.utility.vector1_std_weak_ptr_protocols_noesy_assign_Resonance_t
- error(...) from builtins.PyCapsule
- error(rosetta.protocols.noesy_assign.Resonance) -> float
- first_connected_resonance(...) from builtins.PyCapsule
- first_connected_resonance(rosetta.protocols.noesy_assign.Resonance) -> rosetta.protocols.noesy_assign.Resonance
- float_label(...) from builtins.PyCapsule
- float_label(self : rosetta.protocols.noesy_assign.Resonance, : int) -> int
- freq(...) from builtins.PyCapsule
- freq(rosetta.protocols.noesy_assign.Resonance) -> float
resonance frequency (chemical shift)
- has_connected_resonances(...) from builtins.PyCapsule
- has_connected_resonances(rosetta.protocols.noesy_assign.Resonance) -> bool
- intensity(...) from builtins.PyCapsule
- intensity(rosetta.protocols.noesy_assign.Resonance) -> float
in ILV-labelled proteins, the both LV methyls are labelled randomly with 50% probability,
whereas I delta methyls are labelled 100%
- is_proton(...) from builtins.PyCapsule
- is_proton(rosetta.protocols.noesy_assign.Resonance) -> bool
- label(...) from builtins.PyCapsule
- label(rosetta.protocols.noesy_assign.Resonance) -> int
ResonanceID
- match(...) from builtins.PyCapsule
- match(self : rosetta.protocols.noesy_assign.Resonance, freq : float, error : float, folder : rosetta.protocols.noesy_assign.FoldResonance) -> bool
Resonance matches the given cross-peaks frequency
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.noesy_assign.Resonance) -> str
- pmatch(...) from builtins.PyCapsule
- pmatch(self : rosetta.protocols.noesy_assign.Resonance, freq : float, error : float, folder : rosetta.protocols.noesy_assign.FoldResonance) -> float
- resid(...) from builtins.PyCapsule
- resid(rosetta.protocols.noesy_assign.Resonance) -> int
- set_intensity(...) from builtins.PyCapsule
- set_intensity(self : rosetta.protocols.noesy_assign.Resonance, setting : float) -> NoneType
- tolerance(...) from builtins.PyCapsule
- tolerance(rosetta.protocols.noesy_assign.Resonance) -> float
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class MethylNames(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.noesy_assign.MethylNames) -> NoneType
2. __init__(self : rosetta.protocols.noesy_assign.MethylNames, aa : rosetta.core.chemical.AA) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- aa(...) from builtins.PyCapsule
- aa(rosetta.protocols.noesy_assign.MethylNames) -> rosetta.core.chemical.AA
- aa_name(...) from builtins.PyCapsule
- aa_name(rosetta.protocols.noesy_assign.MethylNames) -> str
- add_methyl(...) from builtins.PyCapsule
- add_methyl(self : rosetta.protocols.noesy_assign.MethylNames, rosetta : str, methyl : str) -> NoneType
- add_proton(...) from builtins.PyCapsule
- add_proton(self : rosetta.protocols.noesy_assign.MethylNames, nmr : str, rosetta : str) -> NoneType
- begin(...) from builtins.PyCapsule
- begin(rosetta.protocols.noesy_assign.MethylNames) -> std::_Rb_tree_const_iterator<std::pair<std::string const, utility::vector1<std::string, std::allocator<std::string> > > >
- end(...) from builtins.PyCapsule
- end(rosetta.protocols.noesy_assign.MethylNames) -> std::_Rb_tree_const_iterator<std::pair<std::string const, utility::vector1<std::string, std::allocator<std::string> > > >
- nmr2rosetta(...) from builtins.PyCapsule
- nmr2rosetta(self : rosetta.protocols.noesy_assign.MethylNames, proton : str) -> rosetta.utility.vector1_std_string
- proton_index(...) from builtins.PyCapsule
- proton_index(self : rosetta.protocols.noesy_assign.MethylNames, : str) -> int
- rosetta2methyl(...) from builtins.PyCapsule
- rosetta2methyl(self : rosetta.protocols.noesy_assign.MethylNames, proton : str) -> rosetta.utility.vector1_std_string
- rosetta2nmr(...) from builtins.PyCapsule
- rosetta2nmr(self : rosetta.protocols.noesy_assign.MethylNames, proton : str) -> str
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class NoesyModule(builtins.object) |
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WARNING WARNING WARNING THREAD UNSAFE FOR USING THE COVALENTCOMPLIANCE CLASS IN A NON-CONST WAY
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.noesy_assign.NoesyModule, fasta_sequence : str) -> NoneType
2. __init__(self : rosetta.protocols.noesy_assign.NoesyModule, : rosetta.protocols.noesy_assign.NoesyModule) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_dist_viol_to_assignments(...) from builtins.PyCapsule
- add_dist_viol_to_assignments(self : rosetta.protocols.noesy_assign.NoesyModule, native_pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(*args, **kwargs)
Overloaded function.
1. assign(rosetta.protocols.noesy_assign.NoesyModule) -> NoneType
same as above, but decoy file will be determined from commandline and read directly
2. assign(self : rosetta.protocols.noesy_assign.NoesyModule, : rosetta.protocols.noesy_assign.NoesyModule) -> rosetta.protocols.noesy_assign.NoesyModule
- cmdline_options_activated(...) from builtins.PyCapsule
- cmdline_options_activated() -> bool
returns true if -noesy::in::resonances and -noesy::in::peaks are in cmd-line
- crosspeaks(...) from builtins.PyCapsule
- crosspeaks(rosetta.protocols.noesy_assign.NoesyModule) -> rosetta.protocols.noesy_assign.CrossPeakList
return (cross)peak-list (peak-file)
- generate_constraint_files(...) from builtins.PyCapsule
- generate_constraint_files(*args, **kwargs)
Overloaded function.
1. generate_constraint_files(self : rosetta.protocols.noesy_assign.NoesyModule, pose : rosetta.core.pose.Pose, cst_fa_file : str, cst_centroid_file : str, min_seq_separation : int) -> NoneType
after assignment --> create appropriate constraints
2. generate_constraint_files(self : rosetta.protocols.noesy_assign.NoesyModule, pose : rosetta.core.pose.Pose, cst_fa_file : str, cst_centroid_file : str, min_seq_separation : int, min_quali : int) -> NoneType
after assignment --> create appropriate constraints
3. generate_constraint_files(self : rosetta.protocols.noesy_assign.NoesyModule, pose : rosetta.core.pose.Pose, cst_fa_file : str, cst_centroid_file : str, min_seq_separation : int, min_quali : int, max_quali : int) -> NoneType
after assignment --> create appropriate constraints
4. generate_constraint_files(self : rosetta.protocols.noesy_assign.NoesyModule, pose : rosetta.core.pose.Pose, cst_fa_file : str, cst_centroid_file : str, min_seq_separation : int, min_quali : int, max_quali : int, ignore_elimination_candidates : bool) -> NoneType
after assignment --> create appropriate constraints
5. generate_constraint_files(self : rosetta.protocols.noesy_assign.NoesyModule, pose : rosetta.core.pose.Pose, cst_fa_file : str, cst_centroid_file : str, min_seq_separation : int, min_quali : int, max_quali : int, ignore_elimination_candidates : bool, elimination_candidates : bool) -> NoneType
after assignment --> create appropriate constraints
- register_options(...) from builtins.PyCapsule
- register_options() -> NoneType
register options
- reset(...) from builtins.PyCapsule
- reset(rosetta.protocols.noesy_assign.NoesyModule) -> NoneType
reset assignments... -- call before re-assigning peaks
- sequence(...) from builtins.PyCapsule
- sequence(rosetta.protocols.noesy_assign.NoesyModule) -> str
- write_assignments(...) from builtins.PyCapsule
- write_assignments(*args, **kwargs)
Overloaded function.
1. write_assignments(rosetta.protocols.noesy_assign.NoesyModule) -> NoneType
write assignments into peak-file...
2. write_assignments(self : rosetta.protocols.noesy_assign.NoesyModule, file : str) -> NoneType
write assignments into peak-file...
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class PeakAssignment(builtins.object) |
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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
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Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.protocols.noesy_assign.PeakAssignment, other : rosetta.protocols.noesy_assign.PeakAssignment) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.noesy_assign.PeakAssignment, : rosetta.protocols.noesy_assign.CrossPeak, assign_spin1 : int, assign_spin2 : int) -> NoneType
2. __init__(self : rosetta.protocols.noesy_assign.PeakAssignment, : rosetta.protocols.noesy_assign.PeakAssignment) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.noesy_assign.PeakAssignment) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.PeakAssignment, : rosetta.protocols.noesy_assign.PeakAssignment) -> rosetta.protocols.noesy_assign.PeakAssignment
- atom(...) from builtins.PyCapsule
- atom(self : rosetta.protocols.noesy_assign.PeakAssignment, iatom : int) -> rosetta.core.id.NamedAtomID
returns atom 1 or 2 of the assigned cross-peak. --- might throw Exception if atom not found in ResonanceList
- calibration_atom_type(...) from builtins.PyCapsule
- calibration_atom_type(self : rosetta.protocols.noesy_assign.PeakAssignment, iatom : int) -> rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE
- chemshift_compliance(...) from builtins.PyCapsule
- chemshift_compliance(rosetta.protocols.noesy_assign.PeakAssignment) -> float
- create_constraint(...) from builtins.PyCapsule
- create_constraint(*args, **kwargs)
Overloaded function.
1. create_constraint(self : rosetta.protocols.noesy_assign.PeakAssignment, pose : rosetta.core.pose.Pose) -> rosetta.core.scoring.constraints.Constraint
2. create_constraint(self : rosetta.protocols.noesy_assign.PeakAssignment, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.func.Func) -> rosetta.core.scoring.constraints.Constraint
3. create_constraint(self : rosetta.protocols.noesy_assign.PeakAssignment, pose : rosetta.core.pose.Pose, ifloat : int) -> rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint
4. create_constraint(self : rosetta.protocols.noesy_assign.PeakAssignment, pose : rosetta.core.pose.Pose, ifloat : int, : rosetta.core.scoring.func.Func) -> rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint
- crosspeak(...) from builtins.PyCapsule
- crosspeak(*args, **kwargs)
Overloaded function.
1. crosspeak(rosetta.protocols.noesy_assign.PeakAssignment) -> rosetta.protocols.noesy_assign.CrossPeak
2. crosspeak(rosetta.protocols.noesy_assign.PeakAssignment) -> rosetta.protocols.noesy_assign.CrossPeak
- decoy_compatibility(...) from builtins.PyCapsule
- decoy_compatibility(rosetta.protocols.noesy_assign.PeakAssignment) -> float
- float_ambiguity(...) from builtins.PyCapsule
- float_ambiguity(rosetta.protocols.noesy_assign.PeakAssignment) -> int
- has_label(...) from builtins.PyCapsule
- has_label(self : rosetta.protocols.noesy_assign.PeakAssignment, select : int) -> bool
- has_proton(...) from builtins.PyCapsule
- has_proton(self : rosetta.protocols.noesy_assign.PeakAssignment, select : int) -> bool
- is_symmetric_partner_of(...) from builtins.PyCapsule
- is_symmetric_partner_of(self : rosetta.protocols.noesy_assign.PeakAssignment, other : rosetta.protocols.noesy_assign.PeakAssignment) -> bool
- label_atom(...) from builtins.PyCapsule
- label_atom(self : rosetta.protocols.noesy_assign.PeakAssignment, iatom : int) -> rosetta.core.id.NamedAtomID
- label_resonance(...) from builtins.PyCapsule
- label_resonance(self : rosetta.protocols.noesy_assign.PeakAssignment, iatom : int) -> rosetta.protocols.noesy_assign.Resonance
- label_resonance_id(...) from builtins.PyCapsule
- label_resonance_id(self : rosetta.protocols.noesy_assign.PeakAssignment, select : int) -> int
return resonance_id, i.e., pointer into Resonance list that will resolve in assigned atom
- native_distance_viol(...) from builtins.PyCapsule
- native_distance_viol(rosetta.protocols.noesy_assign.PeakAssignment) -> float
- network_anchoring(...) from builtins.PyCapsule
- network_anchoring(rosetta.protocols.noesy_assign.PeakAssignment) -> float
- network_anchoring_per_residue(...) from builtins.PyCapsule
- network_anchoring_per_residue(rosetta.protocols.noesy_assign.PeakAssignment) -> float
- normalized_peak_volume(...) from builtins.PyCapsule
- normalized_peak_volume(rosetta.protocols.noesy_assign.PeakAssignment) -> float
only correct if peak_volumes have been update in CrossPeaks.
- peak_volume(...) from builtins.PyCapsule
- peak_volume(rosetta.protocols.noesy_assign.PeakAssignment) -> float
this is not normalized
- resid(...) from builtins.PyCapsule
- resid(self : rosetta.protocols.noesy_assign.PeakAssignment, iatom : int) -> int
returns residue number of a1 or a2 of the assigned cross-peak, --- might throw Exception if atom not found
- resonance(...) from builtins.PyCapsule
- resonance(self : rosetta.protocols.noesy_assign.PeakAssignment, iatom : int) -> rosetta.protocols.noesy_assign.Resonance
- resonance_id(...) from builtins.PyCapsule
- resonance_id(self : rosetta.protocols.noesy_assign.PeakAssignment, select : int) -> int
return resonance_id, i.e., pointer into Resonance list that will resolve in assigned atom
- resonances(...) from builtins.PyCapsule
- resonances(rosetta.protocols.noesy_assign.PeakAssignment) -> rosetta.protocols.noesy_assign.ResonanceList
- set_decoy_compatibility(...) from builtins.PyCapsule
- set_decoy_compatibility(self : rosetta.protocols.noesy_assign.PeakAssignment, setting : float) -> NoneType
- set_native_distance_viol(...) from builtins.PyCapsule
- set_native_distance_viol(self : rosetta.protocols.noesy_assign.PeakAssignment, setting : float) -> NoneType
- set_network_anchoring(...) from builtins.PyCapsule
- set_network_anchoring(self : rosetta.protocols.noesy_assign.PeakAssignment, setting : float) -> NoneType
- set_network_anchoring_per_residue(...) from builtins.PyCapsule
- set_network_anchoring_per_residue(self : rosetta.protocols.noesy_assign.PeakAssignment, reswise_setting : float) -> NoneType
- set_symmetry(...) from builtins.PyCapsule
- set_symmetry(*args, **kwargs)
Overloaded function.
1. set_symmetry(rosetta.protocols.noesy_assign.PeakAssignment) -> NoneType
2. set_symmetry(self : rosetta.protocols.noesy_assign.PeakAssignment, setting : float) -> NoneType
- spin_id(...) from builtins.PyCapsule
- spin_id(self : rosetta.protocols.noesy_assign.PeakAssignment, select : int) -> int
- symmetry_compliance(...) from builtins.PyCapsule
- symmetry_compliance(rosetta.protocols.noesy_assign.PeakAssignment) -> float
- update_chemshiftscore_from_peak(...) from builtins.PyCapsule
- update_chemshiftscore_from_peak(rosetta.protocols.noesy_assign.PeakAssignment) -> NoneType
- update_upperdistance_score(...) from builtins.PyCapsule
- update_upperdistance_score(rosetta.protocols.noesy_assign.PeakAssignment) -> NoneType
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class PeakAssignmentResidueMap(builtins.object) |
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fast access to assignments by residue number
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.noesy_assign.PeakAssignmentResidueMap) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add(...) from builtins.PyCapsule
- add(*args, **kwargs)
Overloaded function.
1. add(self : rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, : rosetta.protocols.noesy_assign.CrossPeakList) -> NoneType
add all PeakAssignments in all Crosspeaks of list
2. add(self : rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, : rosetta.protocols.noesy_assign.PeakAssignment) -> NoneType
add individual PeakAssignment
- add_all_atoms(...) from builtins.PyCapsule
- add_all_atoms(self : rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, : rosetta.protocols.noesy_assign.ResonanceList) -> NoneType
add all resonances for backward compatibility in covalent-part of network-analysis
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, : rosetta.protocols.noesy_assign.PeakAssignmentResidueMap) -> rosetta.protocols.noesy_assign.PeakAssignmentResidueMap
- assignments(...) from builtins.PyCapsule
- assignments(*args, **kwargs)
Overloaded function.
1. assignments(self : rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, resi : int, resj : int) -> rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_std_allocator_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t
get list of PeakAssignments for pair of residues --- throws Exception
2. assignments(self : rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, resi : int, resj : int) -> rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_std_allocator_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t
3. assignments(self : rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, resi : int, resj : int, collector : rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_std_allocator_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t) -> NoneType
add assignments found between resi and resj to collector
- check_for_symmetric_peaks(...) from builtins.PyCapsule
- check_for_symmetric_peaks(self : rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, : rosetta.protocols.noesy_assign.CrossPeakList, accumulate_symmetry : bool) -> NoneType
invalidate non symmetric peaks
- has(...) from builtins.PyCapsule
- has(self : rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, resi : int, resj : int) -> bool
has some (valid or invalid) assignments between residue pair
- network_analysis(...) from builtins.PyCapsule
- network_analysis(self : rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, n_total_assignments : int) -> NoneType
- network_analysis2(...) from builtins.PyCapsule
- network_analysis2(rosetta.protocols.noesy_assign.PeakAssignmentResidueMap) -> NoneType
- remove(...) from builtins.PyCapsule
- remove(self : rosetta.protocols.noesy_assign.PeakAssignmentResidueMap, : rosetta.protocols.noesy_assign.PeakAssignment) -> NoneType
remove individual PeakAssignment
- total_residue(...) from builtins.PyCapsule
- total_residue(rosetta.protocols.noesy_assign.PeakAssignmentResidueMap) -> int
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class PeakCalibrator(builtins.object) |
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Methods defined here:
- __call__(...) from builtins.PyCapsule
- __call__(self : rosetta.protocols.noesy_assign.PeakCalibrator, atom : rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE) -> float
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_peak(...) from builtins.PyCapsule
- add_peak(self : rosetta.protocols.noesy_assign.PeakCalibrator, peak : rosetta.protocols.noesy_assign.CrossPeak) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.PeakCalibrator, : rosetta.protocols.noesy_assign.PeakCalibrator) -> rosetta.protocols.noesy_assign.PeakCalibrator
- atom_type(...) from builtins.PyCapsule
- atom_type(atom : rosetta.core.id.NamedAtomID, aa : rosetta.core.chemical.AA) -> rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE
- calibration_constant(...) from builtins.PyCapsule
- calibration_constant(self : rosetta.protocols.noesy_assign.PeakCalibrator, type : rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE) -> float
- do_calibration(...) from builtins.PyCapsule
- do_calibration(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- eliminate_violated_constraints(...) from builtins.PyCapsule
- eliminate_violated_constraints(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.noesy_assign.PeakCalibrator) -> rosetta.protocols.noesy_assign.PeakCalibrator
- init_calibrator(...) from builtins.PyCapsule
- init_calibrator(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- interpolate_on_statistics(...) from builtins.PyCapsule
- interpolate_on_statistics(rosetta.protocols.noesy_assign.PeakCalibrator) -> bool
- interpolate_too_big(...) from builtins.PyCapsule
- interpolate_too_big(self : rosetta.protocols.noesy_assign.PeakCalibrator, type : int) -> NoneType
- interpolate_too_small(...) from builtins.PyCapsule
- interpolate_too_small(self : rosetta.protocols.noesy_assign.PeakCalibrator, type : int) -> NoneType
- reset_calibration_constants(...) from builtins.PyCapsule
- reset_calibration_constants(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- reset_statistics(...) from builtins.PyCapsule
- reset_statistics(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- set_new_upper_bounds(...) from builtins.PyCapsule
- set_new_upper_bounds(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- set_target_and_tolerance(...) from builtins.PyCapsule
- set_target_and_tolerance(self : rosetta.protocols.noesy_assign.PeakCalibrator, target : float, tolerance : float) -> NoneType
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class PeakFileFormat(PeakFileFormat_Base) |
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- Method resolution order:
- PeakFileFormat
- PeakFileFormat_Base
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.noesy_assign.PeakFileFormat) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.PeakFileFormat, : rosetta.protocols.noesy_assign.PeakFileFormat) -> rosetta.protocols.noesy_assign.PeakFileFormat
- compatible_with_current_format(...) from builtins.PyCapsule
- compatible_with_current_format(self : rosetta.protocols.noesy_assign.PeakFileFormat, : rosetta.protocols.noesy_assign.CrossPeak) -> bool
- ncol(...) from builtins.PyCapsule
- ncol(rosetta.protocols.noesy_assign.PeakFileFormat) -> int
- register_options(...) from builtins.PyCapsule
- register_options() -> NoneType
- set_format_from_peak(...) from builtins.PyCapsule
- set_format_from_peak(self : rosetta.protocols.noesy_assign.PeakFileFormat, : rosetta.protocols.noesy_assign.CrossPeak) -> NoneType
- set_write_atom_names(...) from builtins.PyCapsule
- set_write_atom_names(*args, **kwargs)
Overloaded function.
1. set_write_atom_names(rosetta.protocols.noesy_assign.PeakFileFormat) -> NoneType
2. set_write_atom_names(self : rosetta.protocols.noesy_assign.PeakFileFormat, setting : bool) -> NoneType
- write_atom_names(...) from builtins.PyCapsule
- write_atom_names(rosetta.protocols.noesy_assign.PeakFileFormat) -> bool
Methods inherited from PeakFileFormat_Base:
- filename(...) from builtins.PyCapsule
- filename(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> str
- ignore_assignments(...) from builtins.PyCapsule
- ignore_assignments(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> bool
- ignore_negative_intensity(...) from builtins.PyCapsule
- ignore_negative_intensity(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> bool
- min_VC_to_write(...) from builtins.PyCapsule
- min_VC_to_write(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> float
- minimum_peak_intensity(...) from builtins.PyCapsule
- minimum_peak_intensity(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> float
- set_filename(...) from builtins.PyCapsule
- set_filename(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, str : str) -> NoneType
- set_ignore_assignments(...) from builtins.PyCapsule
- set_ignore_assignments(*args, **kwargs)
Overloaded function.
1. set_ignore_assignments(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> NoneType
2. set_ignore_assignments(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : bool) -> NoneType
- set_ignore_negative_intensity(...) from builtins.PyCapsule
- set_ignore_negative_intensity(*args, **kwargs)
Overloaded function.
1. set_ignore_negative_intensity(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> NoneType
2. set_ignore_negative_intensity(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : bool) -> NoneType
- set_min_VC_to_write(...) from builtins.PyCapsule
- set_min_VC_to_write(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : float) -> NoneType
- set_minimum_peak_intensity(...) from builtins.PyCapsule
- set_minimum_peak_intensity(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : float) -> NoneType
- set_write_only_highest_VC(...) from builtins.PyCapsule
- set_write_only_highest_VC(*args, **kwargs)
Overloaded function.
1. set_write_only_highest_VC(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> NoneType
2. set_write_only_highest_VC(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : bool) -> NoneType
- write_only_highest_VC(...) from builtins.PyCapsule
- write_only_highest_VC(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> bool
|
class PeakFileFormat_Base(builtins.object) |
| | |
Methods defined here:
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, : rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> rosetta.protocols.noesy_assign.PeakFileFormat_Base
- compatible_with_current_format(...) from builtins.PyCapsule
- compatible_with_current_format(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, : rosetta.protocols.noesy_assign.CrossPeak) -> bool
- filename(...) from builtins.PyCapsule
- filename(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> str
- ignore_assignments(...) from builtins.PyCapsule
- ignore_assignments(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> bool
- ignore_negative_intensity(...) from builtins.PyCapsule
- ignore_negative_intensity(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> bool
- min_VC_to_write(...) from builtins.PyCapsule
- min_VC_to_write(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> float
- minimum_peak_intensity(...) from builtins.PyCapsule
- minimum_peak_intensity(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> float
- set_filename(...) from builtins.PyCapsule
- set_filename(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, str : str) -> NoneType
- set_format_from_peak(...) from builtins.PyCapsule
- set_format_from_peak(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, : rosetta.protocols.noesy_assign.CrossPeak) -> NoneType
- set_ignore_assignments(...) from builtins.PyCapsule
- set_ignore_assignments(*args, **kwargs)
Overloaded function.
1. set_ignore_assignments(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> NoneType
2. set_ignore_assignments(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : bool) -> NoneType
- set_ignore_negative_intensity(...) from builtins.PyCapsule
- set_ignore_negative_intensity(*args, **kwargs)
Overloaded function.
1. set_ignore_negative_intensity(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> NoneType
2. set_ignore_negative_intensity(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : bool) -> NoneType
- set_min_VC_to_write(...) from builtins.PyCapsule
- set_min_VC_to_write(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : float) -> NoneType
- set_minimum_peak_intensity(...) from builtins.PyCapsule
- set_minimum_peak_intensity(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : float) -> NoneType
- set_write_only_highest_VC(...) from builtins.PyCapsule
- set_write_only_highest_VC(*args, **kwargs)
Overloaded function.
1. set_write_only_highest_VC(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> NoneType
2. set_write_only_highest_VC(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : bool) -> NoneType
- write_only_highest_VC(...) from builtins.PyCapsule
- write_only_highest_VC(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> bool
|
class PeakFileFormat_Sparky(PeakFileFormat) |
| | |
- Method resolution order:
- PeakFileFormat_Sparky
- PeakFileFormat
- PeakFileFormat_Base
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.noesy_assign.PeakFileFormat_Sparky) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.PeakFileFormat_Sparky, : rosetta.protocols.noesy_assign.PeakFileFormat_Sparky) -> rosetta.protocols.noesy_assign.PeakFileFormat_Sparky
- set_format_from_peak(...) from builtins.PyCapsule
- set_format_from_peak(self : rosetta.protocols.noesy_assign.PeakFileFormat_Sparky, : rosetta.protocols.noesy_assign.CrossPeak) -> NoneType
Methods inherited from PeakFileFormat:
- compatible_with_current_format(...) from builtins.PyCapsule
- compatible_with_current_format(self : rosetta.protocols.noesy_assign.PeakFileFormat, : rosetta.protocols.noesy_assign.CrossPeak) -> bool
- ncol(...) from builtins.PyCapsule
- ncol(rosetta.protocols.noesy_assign.PeakFileFormat) -> int
- register_options(...) from builtins.PyCapsule
- register_options() -> NoneType
- set_write_atom_names(...) from builtins.PyCapsule
- set_write_atom_names(*args, **kwargs)
Overloaded function.
1. set_write_atom_names(rosetta.protocols.noesy_assign.PeakFileFormat) -> NoneType
2. set_write_atom_names(self : rosetta.protocols.noesy_assign.PeakFileFormat, setting : bool) -> NoneType
- write_atom_names(...) from builtins.PyCapsule
- write_atom_names(rosetta.protocols.noesy_assign.PeakFileFormat) -> bool
Methods inherited from PeakFileFormat_Base:
- filename(...) from builtins.PyCapsule
- filename(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> str
- ignore_assignments(...) from builtins.PyCapsule
- ignore_assignments(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> bool
- ignore_negative_intensity(...) from builtins.PyCapsule
- ignore_negative_intensity(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> bool
- min_VC_to_write(...) from builtins.PyCapsule
- min_VC_to_write(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> float
- minimum_peak_intensity(...) from builtins.PyCapsule
- minimum_peak_intensity(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> float
- set_filename(...) from builtins.PyCapsule
- set_filename(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, str : str) -> NoneType
- set_ignore_assignments(...) from builtins.PyCapsule
- set_ignore_assignments(*args, **kwargs)
Overloaded function.
1. set_ignore_assignments(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> NoneType
2. set_ignore_assignments(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : bool) -> NoneType
- set_ignore_negative_intensity(...) from builtins.PyCapsule
- set_ignore_negative_intensity(*args, **kwargs)
Overloaded function.
1. set_ignore_negative_intensity(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> NoneType
2. set_ignore_negative_intensity(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : bool) -> NoneType
- set_min_VC_to_write(...) from builtins.PyCapsule
- set_min_VC_to_write(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : float) -> NoneType
- set_minimum_peak_intensity(...) from builtins.PyCapsule
- set_minimum_peak_intensity(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : float) -> NoneType
- set_write_only_highest_VC(...) from builtins.PyCapsule
- set_write_only_highest_VC(*args, **kwargs)
Overloaded function.
1. set_write_only_highest_VC(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> NoneType
2. set_write_only_highest_VC(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : bool) -> NoneType
- write_only_highest_VC(...) from builtins.PyCapsule
- write_only_highest_VC(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> bool
|
class PeakFileFormat_xeasy(PeakFileFormat) |
| | |
- Method resolution order:
- PeakFileFormat_xeasy
- PeakFileFormat
- PeakFileFormat_Base
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.noesy_assign.PeakFileFormat_xeasy) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.PeakFileFormat_xeasy, : rosetta.protocols.noesy_assign.PeakFileFormat_xeasy) -> rosetta.protocols.noesy_assign.PeakFileFormat_xeasy
Methods inherited from PeakFileFormat:
- compatible_with_current_format(...) from builtins.PyCapsule
- compatible_with_current_format(self : rosetta.protocols.noesy_assign.PeakFileFormat, : rosetta.protocols.noesy_assign.CrossPeak) -> bool
- ncol(...) from builtins.PyCapsule
- ncol(rosetta.protocols.noesy_assign.PeakFileFormat) -> int
- register_options(...) from builtins.PyCapsule
- register_options() -> NoneType
- set_format_from_peak(...) from builtins.PyCapsule
- set_format_from_peak(self : rosetta.protocols.noesy_assign.PeakFileFormat, : rosetta.protocols.noesy_assign.CrossPeak) -> NoneType
- set_write_atom_names(...) from builtins.PyCapsule
- set_write_atom_names(*args, **kwargs)
Overloaded function.
1. set_write_atom_names(rosetta.protocols.noesy_assign.PeakFileFormat) -> NoneType
2. set_write_atom_names(self : rosetta.protocols.noesy_assign.PeakFileFormat, setting : bool) -> NoneType
- write_atom_names(...) from builtins.PyCapsule
- write_atom_names(rosetta.protocols.noesy_assign.PeakFileFormat) -> bool
Methods inherited from PeakFileFormat_Base:
- filename(...) from builtins.PyCapsule
- filename(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> str
- ignore_assignments(...) from builtins.PyCapsule
- ignore_assignments(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> bool
- ignore_negative_intensity(...) from builtins.PyCapsule
- ignore_negative_intensity(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> bool
- min_VC_to_write(...) from builtins.PyCapsule
- min_VC_to_write(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> float
- minimum_peak_intensity(...) from builtins.PyCapsule
- minimum_peak_intensity(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> float
- set_filename(...) from builtins.PyCapsule
- set_filename(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, str : str) -> NoneType
- set_ignore_assignments(...) from builtins.PyCapsule
- set_ignore_assignments(*args, **kwargs)
Overloaded function.
1. set_ignore_assignments(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> NoneType
2. set_ignore_assignments(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : bool) -> NoneType
- set_ignore_negative_intensity(...) from builtins.PyCapsule
- set_ignore_negative_intensity(*args, **kwargs)
Overloaded function.
1. set_ignore_negative_intensity(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> NoneType
2. set_ignore_negative_intensity(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : bool) -> NoneType
- set_min_VC_to_write(...) from builtins.PyCapsule
- set_min_VC_to_write(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : float) -> NoneType
- set_minimum_peak_intensity(...) from builtins.PyCapsule
- set_minimum_peak_intensity(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : float) -> NoneType
- set_write_only_highest_VC(...) from builtins.PyCapsule
- set_write_only_highest_VC(*args, **kwargs)
Overloaded function.
1. set_write_only_highest_VC(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> NoneType
2. set_write_only_highest_VC(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : bool) -> NoneType
- write_only_highest_VC(...) from builtins.PyCapsule
- write_only_highest_VC(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> bool
|
class PeakFileFormat_xpk(PeakFileFormat) |
| | |
- Method resolution order:
- PeakFileFormat_xpk
- PeakFileFormat
- PeakFileFormat_Base
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.noesy_assign.PeakFileFormat_xpk) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.PeakFileFormat_xpk, : rosetta.protocols.noesy_assign.PeakFileFormat_xpk) -> rosetta.protocols.noesy_assign.PeakFileFormat_xpk
- set_format_from_peak(...) from builtins.PyCapsule
- set_format_from_peak(self : rosetta.protocols.noesy_assign.PeakFileFormat_xpk, : rosetta.protocols.noesy_assign.CrossPeak) -> NoneType
Methods inherited from PeakFileFormat:
- compatible_with_current_format(...) from builtins.PyCapsule
- compatible_with_current_format(self : rosetta.protocols.noesy_assign.PeakFileFormat, : rosetta.protocols.noesy_assign.CrossPeak) -> bool
- ncol(...) from builtins.PyCapsule
- ncol(rosetta.protocols.noesy_assign.PeakFileFormat) -> int
- register_options(...) from builtins.PyCapsule
- register_options() -> NoneType
- set_write_atom_names(...) from builtins.PyCapsule
- set_write_atom_names(*args, **kwargs)
Overloaded function.
1. set_write_atom_names(rosetta.protocols.noesy_assign.PeakFileFormat) -> NoneType
2. set_write_atom_names(self : rosetta.protocols.noesy_assign.PeakFileFormat, setting : bool) -> NoneType
- write_atom_names(...) from builtins.PyCapsule
- write_atom_names(rosetta.protocols.noesy_assign.PeakFileFormat) -> bool
Methods inherited from PeakFileFormat_Base:
- filename(...) from builtins.PyCapsule
- filename(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> str
- ignore_assignments(...) from builtins.PyCapsule
- ignore_assignments(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> bool
- ignore_negative_intensity(...) from builtins.PyCapsule
- ignore_negative_intensity(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> bool
- min_VC_to_write(...) from builtins.PyCapsule
- min_VC_to_write(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> float
- minimum_peak_intensity(...) from builtins.PyCapsule
- minimum_peak_intensity(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> float
- set_filename(...) from builtins.PyCapsule
- set_filename(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, str : str) -> NoneType
- set_ignore_assignments(...) from builtins.PyCapsule
- set_ignore_assignments(*args, **kwargs)
Overloaded function.
1. set_ignore_assignments(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> NoneType
2. set_ignore_assignments(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : bool) -> NoneType
- set_ignore_negative_intensity(...) from builtins.PyCapsule
- set_ignore_negative_intensity(*args, **kwargs)
Overloaded function.
1. set_ignore_negative_intensity(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> NoneType
2. set_ignore_negative_intensity(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : bool) -> NoneType
- set_min_VC_to_write(...) from builtins.PyCapsule
- set_min_VC_to_write(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : float) -> NoneType
- set_minimum_peak_intensity(...) from builtins.PyCapsule
- set_minimum_peak_intensity(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : float) -> NoneType
- set_write_only_highest_VC(...) from builtins.PyCapsule
- set_write_only_highest_VC(*args, **kwargs)
Overloaded function.
1. set_write_only_highest_VC(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> NoneType
2. set_write_only_highest_VC(self : rosetta.protocols.noesy_assign.PeakFileFormat_Base, setting : bool) -> NoneType
- write_only_highest_VC(...) from builtins.PyCapsule
- write_only_highest_VC(rosetta.protocols.noesy_assign.PeakFileFormat_Base) -> bool
|
class ProtonResonance(Resonance) |
| |
ProtonResonance combines resonanceID (label), chemical shift (freq), tolerance (error), and the assigned atom (atom, name, resid)
(provided accessor methods of "ProtonResonance": label, atom, resid, name, freq, error, tolerance, calibration_atom_type )
|
| |
- Method resolution order:
- ProtonResonance
- Resonance
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, label : int, freq : float, error : float, id : rosetta.core.id.NamedAtomID, : rosetta.core.chemical.AA, intensity : float) -> NoneType
3. __init__(handle, rosetta.protocols.noesy_assign.ProtonResonance) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.ProtonResonance, : rosetta.protocols.noesy_assign.ProtonResonance) -> rosetta.protocols.noesy_assign.ProtonResonance
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.noesy_assign.ProtonResonance) -> rosetta.protocols.noesy_assign.Resonance
- match2D(...) from builtins.PyCapsule
- match2D(self : rosetta.protocols.noesy_assign.ProtonResonance, proton_freq : float, proton_error : float, proton_folder : rosetta.protocols.noesy_assign.FoldResonance, label_freq : float, label_error : float, label_folder : rosetta.protocols.noesy_assign.FoldResonance, matches : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> bool
match the proton and corresponding label atom at same time
Methods inherited from Resonance:
- aa(...) from builtins.PyCapsule
- aa(rosetta.protocols.noesy_assign.Resonance) -> rosetta.core.chemical.AA
- add_connected_resonance(...) from builtins.PyCapsule
- add_connected_resonance(self : rosetta.protocols.noesy_assign.Resonance, ptr : rosetta.std.weak_ptr_protocols_noesy_assign_Resonance_t) -> NoneType
- ambiguity(...) from builtins.PyCapsule
- ambiguity(rosetta.protocols.noesy_assign.Resonance) -> int
- atom(...) from builtins.PyCapsule
- atom(rosetta.protocols.noesy_assign.Resonance) -> rosetta.core.id.NamedAtomID
Atom
- calibration_atom_type(...) from builtins.PyCapsule
- calibration_atom_type(rosetta.protocols.noesy_assign.Resonance) -> rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE
classification for calibration... e.g., Backbone, sidechain, etc..
- clear_connected_resonances(...) from builtins.PyCapsule
- clear_connected_resonances(rosetta.protocols.noesy_assign.Resonance) -> NoneType
- connected_resonance_ids(...) from builtins.PyCapsule
- connected_resonance_ids(rosetta.protocols.noesy_assign.Resonance) -> rosetta.utility.vector1_unsigned_long
- connected_resonances(...) from builtins.PyCapsule
- connected_resonances(rosetta.protocols.noesy_assign.Resonance) -> rosetta.utility.vector1_std_weak_ptr_protocols_noesy_assign_Resonance_t
- error(...) from builtins.PyCapsule
- error(rosetta.protocols.noesy_assign.Resonance) -> float
- first_connected_resonance(...) from builtins.PyCapsule
- first_connected_resonance(rosetta.protocols.noesy_assign.Resonance) -> rosetta.protocols.noesy_assign.Resonance
- float_label(...) from builtins.PyCapsule
- float_label(self : rosetta.protocols.noesy_assign.Resonance, : int) -> int
- freq(...) from builtins.PyCapsule
- freq(rosetta.protocols.noesy_assign.Resonance) -> float
resonance frequency (chemical shift)
- has_connected_resonances(...) from builtins.PyCapsule
- has_connected_resonances(rosetta.protocols.noesy_assign.Resonance) -> bool
- intensity(...) from builtins.PyCapsule
- intensity(rosetta.protocols.noesy_assign.Resonance) -> float
in ILV-labelled proteins, the both LV methyls are labelled randomly with 50% probability,
whereas I delta methyls are labelled 100%
- is_proton(...) from builtins.PyCapsule
- is_proton(rosetta.protocols.noesy_assign.Resonance) -> bool
- label(...) from builtins.PyCapsule
- label(rosetta.protocols.noesy_assign.Resonance) -> int
ResonanceID
- match(...) from builtins.PyCapsule
- match(self : rosetta.protocols.noesy_assign.Resonance, freq : float, error : float, folder : rosetta.protocols.noesy_assign.FoldResonance) -> bool
Resonance matches the given cross-peaks frequency
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.noesy_assign.Resonance) -> str
- pmatch(...) from builtins.PyCapsule
- pmatch(self : rosetta.protocols.noesy_assign.Resonance, freq : float, error : float, folder : rosetta.protocols.noesy_assign.FoldResonance) -> float
- resid(...) from builtins.PyCapsule
- resid(rosetta.protocols.noesy_assign.Resonance) -> int
- set_intensity(...) from builtins.PyCapsule
- set_intensity(self : rosetta.protocols.noesy_assign.Resonance, setting : float) -> NoneType
- tolerance(...) from builtins.PyCapsule
- tolerance(rosetta.protocols.noesy_assign.Resonance) -> float
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class Resonance(builtins.object) |
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Resonance combines resonanceID (label), chemical shift (freq), tolerance (error), and the assigned atom (atom, name, resid)
(provided accessor methods of "Resonance": label, atom, resid, name, freq, error, tolerance, calibration_atom_type )
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.noesy_assign.Resonance) -> NoneType
2. __init__(rosetta.protocols.noesy_assign.Resonance, int, float, float, rosetta.core.id.NamedAtomID, rosetta.core.chemical.AA) -> NoneType
doc
3. __init__(self : rosetta.protocols.noesy_assign.Resonance, label : int, freq : float, error : float, id : rosetta.core.id.NamedAtomID, : rosetta.core.chemical.AA, intensity : float) -> NoneType
4. __init__(rosetta.protocols.noesy_assign.Resonance, rosetta.protocols.noesy_assign.Resonance) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- aa(...) from builtins.PyCapsule
- aa(rosetta.protocols.noesy_assign.Resonance) -> rosetta.core.chemical.AA
- add_connected_resonance(...) from builtins.PyCapsule
- add_connected_resonance(self : rosetta.protocols.noesy_assign.Resonance, ptr : rosetta.std.weak_ptr_protocols_noesy_assign_Resonance_t) -> NoneType
- ambiguity(...) from builtins.PyCapsule
- ambiguity(rosetta.protocols.noesy_assign.Resonance) -> int
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.Resonance, : rosetta.protocols.noesy_assign.Resonance) -> rosetta.protocols.noesy_assign.Resonance
- atom(...) from builtins.PyCapsule
- atom(rosetta.protocols.noesy_assign.Resonance) -> rosetta.core.id.NamedAtomID
Atom
- calibration_atom_type(...) from builtins.PyCapsule
- calibration_atom_type(rosetta.protocols.noesy_assign.Resonance) -> rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE
classification for calibration... e.g., Backbone, sidechain, etc..
- clear_connected_resonances(...) from builtins.PyCapsule
- clear_connected_resonances(rosetta.protocols.noesy_assign.Resonance) -> NoneType
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.noesy_assign.Resonance) -> rosetta.protocols.noesy_assign.Resonance
- connected_resonance_ids(...) from builtins.PyCapsule
- connected_resonance_ids(rosetta.protocols.noesy_assign.Resonance) -> rosetta.utility.vector1_unsigned_long
- connected_resonances(...) from builtins.PyCapsule
- connected_resonances(rosetta.protocols.noesy_assign.Resonance) -> rosetta.utility.vector1_std_weak_ptr_protocols_noesy_assign_Resonance_t
- error(...) from builtins.PyCapsule
- error(rosetta.protocols.noesy_assign.Resonance) -> float
- first_connected_resonance(...) from builtins.PyCapsule
- first_connected_resonance(rosetta.protocols.noesy_assign.Resonance) -> rosetta.protocols.noesy_assign.Resonance
- float_label(...) from builtins.PyCapsule
- float_label(self : rosetta.protocols.noesy_assign.Resonance, : int) -> int
- freq(...) from builtins.PyCapsule
- freq(rosetta.protocols.noesy_assign.Resonance) -> float
resonance frequency (chemical shift)
- has_connected_resonances(...) from builtins.PyCapsule
- has_connected_resonances(rosetta.protocols.noesy_assign.Resonance) -> bool
- intensity(...) from builtins.PyCapsule
- intensity(rosetta.protocols.noesy_assign.Resonance) -> float
in ILV-labelled proteins, the both LV methyls are labelled randomly with 50% probability,
whereas I delta methyls are labelled 100%
- is_proton(...) from builtins.PyCapsule
- is_proton(rosetta.protocols.noesy_assign.Resonance) -> bool
- label(...) from builtins.PyCapsule
- label(rosetta.protocols.noesy_assign.Resonance) -> int
ResonanceID
- match(...) from builtins.PyCapsule
- match(self : rosetta.protocols.noesy_assign.Resonance, freq : float, error : float, folder : rosetta.protocols.noesy_assign.FoldResonance) -> bool
Resonance matches the given cross-peaks frequency
- match2D(...) from builtins.PyCapsule
- match2D(self : rosetta.protocols.noesy_assign.Resonance, proton_freq : float, proton_error : float, proton_folder : rosetta.protocols.noesy_assign.FoldResonance, label_freq : float, label_error : float, label_folder : rosetta.protocols.noesy_assign.FoldResonance, matches : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> bool
match the proton and corresponding label atom at same time
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.noesy_assign.Resonance) -> str
- pmatch(...) from builtins.PyCapsule
- pmatch(self : rosetta.protocols.noesy_assign.Resonance, freq : float, error : float, folder : rosetta.protocols.noesy_assign.FoldResonance) -> float
- resid(...) from builtins.PyCapsule
- resid(rosetta.protocols.noesy_assign.Resonance) -> int
- set_intensity(...) from builtins.PyCapsule
- set_intensity(self : rosetta.protocols.noesy_assign.Resonance, setting : float) -> NoneType
- tolerance(...) from builtins.PyCapsule
- tolerance(rosetta.protocols.noesy_assign.Resonance) -> float
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class ResonanceList(builtins.object) |
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:
the ResonanceList provides a map of chemical shifts.
each atom-chemical shift tupel has a "resonanceID" as a key. (integer)
used classes:
Resonance is an atom with chemical shift information
ResonanceIDs (typedef) is a map from ID to Resonance
ResidueMap (typedef) is a map from residue number to a vector of Resonances.
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Methods defined here:
- __getitem__(...) from builtins.PyCapsule
- __getitem__(*args, **kwargs)
Overloaded function.
1. __getitem__(self : rosetta.protocols.noesy_assign.ResonanceList, key : int) -> rosetta.protocols.noesy_assign.Resonance
retrieve a Resonance by ResonanceID --- throws EXCN_UnknonwResonance if atom not found
2. __getitem__(self : rosetta.protocols.noesy_assign.ResonanceList, : rosetta.core.id.NamedAtomID) -> rosetta.protocols.noesy_assign.Resonance
retrive a Resonance by atom --- throws EXCN_UnknonwResonance if atom not found
- __init__(...) from builtins.PyCapsule
- __init__(self : rosetta.protocols.noesy_assign.ResonanceList, sequence : str) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- aa_from_resid(...) from builtins.PyCapsule
- aa_from_resid(self : rosetta.protocols.noesy_assign.ResonanceList, resi : int) -> rosetta.core.chemical.AA
retrieve aminoacid of residue "resi"
- begin(...) from builtins.PyCapsule
- begin(rosetta.protocols.noesy_assign.ResonanceList) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, std::shared_ptr<protocols::noesy_assign::Resonance> > >
- end(...) from builtins.PyCapsule
- end(rosetta.protocols.noesy_assign.ResonanceList) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, std::shared_ptr<protocols::noesy_assign::Resonance> > >
- has_residue(...) from builtins.PyCapsule
- has_residue(self : rosetta.protocols.noesy_assign.ResonanceList, resi : int) -> bool
have at least one resonance for residue "resi"
- last_key(...) from builtins.PyCapsule
- last_key(rosetta.protocols.noesy_assign.ResonanceList) -> int
last ResonanceID ( given by input file )
- resonances_at_residue(...) from builtins.PyCapsule
- resonances_at_residue(self : rosetta.protocols.noesy_assign.ResonanceList, resid : int) -> rosetta.utility.vector1_std_shared_ptr_protocols_noesy_assign_Resonance_t
all resonances of a certain residue
--- requires that update_residue_map() has been called (which is done by read_from_stream() )
- sequence(...) from builtins.PyCapsule
- sequence(rosetta.protocols.noesy_assign.ResonanceList) -> str
retrieve the protein sequence
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.noesy_assign.ResonanceList) -> int
number of Resonances
- start_key(...) from builtins.PyCapsule
- start_key(rosetta.protocols.noesy_assign.ResonanceList) -> int
first ResonanceID (given by input file)
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class StructureDependentPeakCalibrator(PeakCalibrator) |
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- Method resolution order:
- StructureDependentPeakCalibrator
- PeakCalibrator
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, structures : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, dcalibrate : float) -> NoneType
2. __init__(handle, rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator, : rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator) -> rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator
- eliminate_violated_constraints(...) from builtins.PyCapsule
- eliminate_violated_constraints(rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator) -> NoneType
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator) -> rosetta.protocols.noesy_assign.PeakCalibrator
- generate_constraints(...) from builtins.PyCapsule
- generate_constraints(rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator) -> NoneType
- init_calibrator(...) from builtins.PyCapsule
- init_calibrator(rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator) -> NoneType
Methods inherited from PeakCalibrator:
- __call__(...) from builtins.PyCapsule
- __call__(self : rosetta.protocols.noesy_assign.PeakCalibrator, atom : rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE) -> float
- add_peak(...) from builtins.PyCapsule
- add_peak(self : rosetta.protocols.noesy_assign.PeakCalibrator, peak : rosetta.protocols.noesy_assign.CrossPeak) -> NoneType
- atom_type(...) from builtins.PyCapsule
- atom_type(atom : rosetta.core.id.NamedAtomID, aa : rosetta.core.chemical.AA) -> rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE
- calibration_constant(...) from builtins.PyCapsule
- calibration_constant(self : rosetta.protocols.noesy_assign.PeakCalibrator, type : rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE) -> float
- do_calibration(...) from builtins.PyCapsule
- do_calibration(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- interpolate_on_statistics(...) from builtins.PyCapsule
- interpolate_on_statistics(rosetta.protocols.noesy_assign.PeakCalibrator) -> bool
- interpolate_too_big(...) from builtins.PyCapsule
- interpolate_too_big(self : rosetta.protocols.noesy_assign.PeakCalibrator, type : int) -> NoneType
- interpolate_too_small(...) from builtins.PyCapsule
- interpolate_too_small(self : rosetta.protocols.noesy_assign.PeakCalibrator, type : int) -> NoneType
- reset_calibration_constants(...) from builtins.PyCapsule
- reset_calibration_constants(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- reset_statistics(...) from builtins.PyCapsule
- reset_statistics(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- set_new_upper_bounds(...) from builtins.PyCapsule
- set_new_upper_bounds(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- set_target_and_tolerance(...) from builtins.PyCapsule
- set_target_and_tolerance(self : rosetta.protocols.noesy_assign.PeakCalibrator, target : float, tolerance : float) -> NoneType
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class StructureIndependentPeakCalibrator(PeakCalibrator) |
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- Method resolution order:
- StructureIndependentPeakCalibrator
- PeakCalibrator
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator, : rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator) -> rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator) -> rosetta.protocols.noesy_assign.PeakCalibrator
Methods inherited from PeakCalibrator:
- __call__(...) from builtins.PyCapsule
- __call__(self : rosetta.protocols.noesy_assign.PeakCalibrator, atom : rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE) -> float
- add_peak(...) from builtins.PyCapsule
- add_peak(self : rosetta.protocols.noesy_assign.PeakCalibrator, peak : rosetta.protocols.noesy_assign.CrossPeak) -> NoneType
- atom_type(...) from builtins.PyCapsule
- atom_type(atom : rosetta.core.id.NamedAtomID, aa : rosetta.core.chemical.AA) -> rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE
- calibration_constant(...) from builtins.PyCapsule
- calibration_constant(self : rosetta.protocols.noesy_assign.PeakCalibrator, type : rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE) -> float
- do_calibration(...) from builtins.PyCapsule
- do_calibration(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- eliminate_violated_constraints(...) from builtins.PyCapsule
- eliminate_violated_constraints(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- init_calibrator(...) from builtins.PyCapsule
- init_calibrator(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- interpolate_on_statistics(...) from builtins.PyCapsule
- interpolate_on_statistics(rosetta.protocols.noesy_assign.PeakCalibrator) -> bool
- interpolate_too_big(...) from builtins.PyCapsule
- interpolate_too_big(self : rosetta.protocols.noesy_assign.PeakCalibrator, type : int) -> NoneType
- interpolate_too_small(...) from builtins.PyCapsule
- interpolate_too_small(self : rosetta.protocols.noesy_assign.PeakCalibrator, type : int) -> NoneType
- reset_calibration_constants(...) from builtins.PyCapsule
- reset_calibration_constants(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- reset_statistics(...) from builtins.PyCapsule
- reset_statistics(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- set_new_upper_bounds(...) from builtins.PyCapsule
- set_new_upper_bounds(rosetta.protocols.noesy_assign.PeakCalibrator) -> NoneType
- set_target_and_tolerance(...) from builtins.PyCapsule
- set_target_and_tolerance(self : rosetta.protocols.noesy_assign.PeakCalibrator, target : float, tolerance : float) -> NoneType
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