| | |
- builtins.object
-
- OutputLevel
- PerNativeRRReporterHuman
- RRComparer
-
- RRComparerAutomorphicRMSD
- RRComparerChiDiff
- RRComparerElecDensDiff
- RRComparerRotBins
- RRComparerCreator
-
- RRComparerAutomorphicRMSDCreator
- RRComparerChiDiffCreator
- RRComparerElecDensDiffCreator
- RRComparerRotBinsCreator
- RRProtocol
-
- RRProtocolMinPack
- RRProtocolMover
- RRProtocolPackRotamers
- RRProtocolRTMin
- RRProtocolReferenceStructure
- RRProtocolRelax
- RRProtocolRotamerTrials
- RRProtocolCreator
-
- RRProtocolMinPackCreator
- RRProtocolMoverCreator
- RRProtocolPackRotamersCreator
- RRProtocolRTMinCreator
- RRProtocolReferenceStructureCreator
- RRProtocolRelaxCreator
- RRProtocolRotamerTrialsCreator
- RRReporter
-
- RRReporterHuman
- RRReporterSQLite
- RRReporterSimple
- RRReporterCreator
-
- RRReporterHumanCreator
- RRReporterSQLiteCreator
- RRReporterSimpleCreator
- RotamerRecovery
- rosetta.protocols.moves.Mover(builtins.object)
-
- RotamerRecoveryMover
- rosetta.protocols.moves.MoverCreator(builtins.object)
-
- RotamerRecoveryMoverCreator
- rosetta.utility.SingletonBase_protocols_rotamer_recovery_RotamerRecoveryFactory_t(builtins.object)
-
- RotamerRecoveryFactory
class PerNativeRRReporterHuman(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.rotamer_recovery.PerNativeRRReporterHuman) -> NoneType
2. __init__(self : rosetta.protocols.rotamer_recovery.PerNativeRRReporterHuman, native_pose : rosetta.core.pose.Pose) -> NoneType
3. __init__(self : rosetta.protocols.rotamer_recovery.PerNativeRRReporterHuman, src : rosetta.protocols.rotamer_recovery.PerNativeRRReporterHuman) -> 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.rotamer_recovery.PerNativeRRReporterHuman, : rosetta.protocols.rotamer_recovery.PerNativeRRReporterHuman) -> rosetta.protocols.rotamer_recovery.PerNativeRRReporterHuman
- initialized(...) from builtins.PyCapsule
- initialized(rosetta.protocols.rotamer_recovery.PerNativeRRReporterHuman) -> bool
- report_rotamer_recovery(...) from builtins.PyCapsule
- report_rotamer_recovery(self : rosetta.protocols.rotamer_recovery.PerNativeRRReporterHuman, : rosetta.core.pose.Pose, res : rosetta.core.conformation.Residue, score : float, recovered : bool) -> NoneType
- set_native(...) from builtins.PyCapsule
- set_native(self : rosetta.protocols.rotamer_recovery.PerNativeRRReporterHuman, native_pose : rosetta.core.pose.Pose) -> NoneType
|
class RRComparerAutomorphicRMSD(RRComparer) |
| | |
- Method resolution order:
- RRComparerAutomorphicRMSD
- RRComparer
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD) -> 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.rotamer_recovery.RRComparerAutomorphicRMSD, : rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD) -> rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD
- get_include_backbone_atoms(...) from builtins.PyCapsule
- get_include_backbone_atoms(rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD) -> bool
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD) -> str
- get_parameters(...) from builtins.PyCapsule
- get_parameters(rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD) -> str
- get_recovery_threshold(...) from builtins.PyCapsule
- get_recovery_threshold(rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD) -> float
- measure_rotamer_recovery(...) from builtins.PyCapsule
- measure_rotamer_recovery(self : rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, score : float, recovered : bool) -> bool
- set_include_backbone_atoms(...) from builtins.PyCapsule
- set_include_backbone_atoms(self : rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD, include_backbone_atoms : bool) -> NoneType
- set_recovery_threshold(...) from builtins.PyCapsule
- set_recovery_threshold(self : rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD, recovery_threshold : float) -> NoneType
|
class RRComparerChiDiff(RRComparer) |
| | |
- Method resolution order:
- RRComparerChiDiff
- RRComparer
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.rotamer_recovery.RRComparerChiDiff) -> 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.rotamer_recovery.RRComparerChiDiff, : rosetta.protocols.rotamer_recovery.RRComparerChiDiff) -> rosetta.protocols.rotamer_recovery.RRComparerChiDiff
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.rotamer_recovery.RRComparerChiDiff) -> str
- get_parameters(...) from builtins.PyCapsule
- get_parameters(rosetta.protocols.rotamer_recovery.RRComparerChiDiff) -> str
- measure_rotamer_recovery(...) from builtins.PyCapsule
- measure_rotamer_recovery(self : rosetta.protocols.rotamer_recovery.RRComparerChiDiff, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, score : float, recovered : bool) -> bool
- set_max_chi_considered(...) from builtins.PyCapsule
- set_max_chi_considered(self : rosetta.protocols.rotamer_recovery.RRComparerChiDiff, max_chi : int) -> NoneType
- set_recovery_threshold(...) from builtins.PyCapsule
- set_recovery_threshold(self : rosetta.protocols.rotamer_recovery.RRComparerChiDiff, setting : float) -> NoneType
|
class RRComparerElecDensDiff(RRComparer) |
| | |
- Method resolution order:
- RRComparerElecDensDiff
- RRComparer
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff) -> 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.rotamer_recovery.RRComparerElecDensDiff, : rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff) -> rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff) -> str
- get_parameters(...) from builtins.PyCapsule
- get_parameters(rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff) -> str
- get_recovery_threshold(...) from builtins.PyCapsule
- get_recovery_threshold(rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff) -> float
- measure_rotamer_recovery(...) from builtins.PyCapsule
- measure_rotamer_recovery(self : rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, score : float, recovered : bool) -> bool
- set_recovery_threshold(...) from builtins.PyCapsule
- set_recovery_threshold(self : rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff, recovery_threshold : float) -> NoneType
|
class RRComparerRotBins(RRComparer) |
| | |
- Method resolution order:
- RRComparerRotBins
- RRComparer
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.rotamer_recovery.RRComparerRotBins) -> 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.rotamer_recovery.RRComparerRotBins, : rosetta.protocols.rotamer_recovery.RRComparerRotBins) -> rosetta.protocols.rotamer_recovery.RRComparerRotBins
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.rotamer_recovery.RRComparerRotBins) -> str
- get_parameters(...) from builtins.PyCapsule
- get_parameters(rosetta.protocols.rotamer_recovery.RRComparerRotBins) -> str
- measure_rotamer_recovery(...) from builtins.PyCapsule
- measure_rotamer_recovery(self : rosetta.protocols.rotamer_recovery.RRComparerRotBins, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, score : float, recovered : bool) -> bool
- set_recovery_threshold(...) from builtins.PyCapsule
- set_recovery_threshold(self : rosetta.protocols.rotamer_recovery.RRComparerRotBins, recovery_threshold : float) -> NoneType
|
class RRProtocol(builtins.object) |
| |
The protocol to run to compute the rotamer recovery the rotamer recovery test
Besides implementing the interface given in the base class
RRProtocol each RRProtocol should have an entry in the convenience
RotamerRecovery constructor so its use can be indicated by name.
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.rotamer_recovery.RRProtocol) -> 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.rotamer_recovery.RRProtocol, : rosetta.protocols.rotamer_recovery.RRProtocol) -> rosetta.protocols.rotamer_recovery.RRProtocol
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.rotamer_recovery.RRProtocol) -> str
- get_parameters(...) from builtins.PyCapsule
- get_parameters(rosetta.protocols.rotamer_recovery.RRProtocol) -> str
- run(...) from builtins.PyCapsule
- run(self : rosetta.protocols.rotamer_recovery.RRProtocol, comparer : rosetta.protocols.rotamer_recovery.RRComparer, reporter : rosetta.protocols.rotamer_recovery.RRReporter, pose : rosetta.core.pose.Pose, score_function : rosetta.core.scoring.ScoreFunction, packer_task : rosetta.core.pack.task.PackerTask) -> NoneType
|
class RRProtocolMover(RRProtocol) |
| | |
- Method resolution order:
- RRProtocolMover
- RRProtocol
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, mover : rosetta.protocols.moves.Mover) -> NoneType
3. __init__(handle, rosetta.protocols.rotamer_recovery.RRProtocolMover) -> 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.rotamer_recovery.RRProtocolMover, : rosetta.protocols.rotamer_recovery.RRProtocolMover) -> rosetta.protocols.rotamer_recovery.RRProtocolMover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.rotamer_recovery.RRProtocolMover) -> str
- get_parameters(...) from builtins.PyCapsule
- get_parameters(rosetta.protocols.rotamer_recovery.RRProtocolMover) -> str
- run(...) from builtins.PyCapsule
- run(self : rosetta.protocols.rotamer_recovery.RRProtocolMover, comparer : rosetta.protocols.rotamer_recovery.RRComparer, reporter : rosetta.protocols.rotamer_recovery.RRReporter, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, packer_task : rosetta.core.pack.task.PackerTask) -> NoneType
|
class RRProtocolRTMin(RRProtocol) |
| | |
- Method resolution order:
- RRProtocolRTMin
- RRProtocol
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.rotamer_recovery.RRProtocolRTMin) -> 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.rotamer_recovery.RRProtocolRTMin, : rosetta.protocols.rotamer_recovery.RRProtocolRTMin) -> rosetta.protocols.rotamer_recovery.RRProtocolRTMin
- get_cartesian(...) from builtins.PyCapsule
- get_cartesian(rosetta.protocols.rotamer_recovery.RRProtocolRTMin) -> bool
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.rotamer_recovery.RRProtocolRTMin) -> str
- get_nonideal(...) from builtins.PyCapsule
- get_nonideal(rosetta.protocols.rotamer_recovery.RRProtocolRTMin) -> bool
- get_parameters(...) from builtins.PyCapsule
- get_parameters(rosetta.protocols.rotamer_recovery.RRProtocolRTMin) -> str
- run(...) from builtins.PyCapsule
- run(self : rosetta.protocols.rotamer_recovery.RRProtocolRTMin, comparer : rosetta.protocols.rotamer_recovery.RRComparer, reporter : rosetta.protocols.rotamer_recovery.RRReporter, pose : rosetta.core.pose.Pose, score_function : rosetta.core.scoring.ScoreFunction, packer_task : rosetta.core.pack.task.PackerTask) -> NoneType
- set_cartesian(...) from builtins.PyCapsule
- set_cartesian(self : rosetta.protocols.rotamer_recovery.RRProtocolRTMin, setting : bool) -> NoneType
- set_nonideal(...) from builtins.PyCapsule
- set_nonideal(self : rosetta.protocols.rotamer_recovery.RRProtocolRTMin, setting : bool) -> NoneType
|
class RRProtocolReferenceStructure(RRProtocol) |
| | |
- Method resolution order:
- RRProtocolReferenceStructure
- RRProtocol
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, reference_pose : rosetta.core.pose.Pose) -> NoneType
3. __init__(handle, rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructure) -> 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.rotamer_recovery.RRProtocolReferenceStructure, : rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructure) -> rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructure
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructure) -> str
- get_parameters(...) from builtins.PyCapsule
- get_parameters(rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructure) -> str
- reference_structure(...) from builtins.PyCapsule
- reference_structure(self : rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructure, reference_pose : rosetta.core.pose.Pose) -> NoneType
- run(...) from builtins.PyCapsule
- run(self : rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructure, comparer : rosetta.protocols.rotamer_recovery.RRComparer, reporter : rosetta.protocols.rotamer_recovery.RRReporter, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, packer_task : rosetta.core.pack.task.PackerTask) -> NoneType
|
class RRProtocolRelax(RRProtocol) |
| | |
- Method resolution order:
- RRProtocolRelax
- RRProtocol
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.rotamer_recovery.RRProtocolRelax) -> 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.rotamer_recovery.RRProtocolRelax, : rosetta.protocols.rotamer_recovery.RRProtocolRelax) -> rosetta.protocols.rotamer_recovery.RRProtocolRelax
- get_cartesian(...) from builtins.PyCapsule
- get_cartesian(rosetta.protocols.rotamer_recovery.RRProtocolRelax) -> bool
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.rotamer_recovery.RRProtocolRelax) -> str
- get_nonideal(...) from builtins.PyCapsule
- get_nonideal(rosetta.protocols.rotamer_recovery.RRProtocolRelax) -> bool
- get_parameters(...) from builtins.PyCapsule
- get_parameters(rosetta.protocols.rotamer_recovery.RRProtocolRelax) -> str
- run(...) from builtins.PyCapsule
- run(self : rosetta.protocols.rotamer_recovery.RRProtocolRelax, comparer : rosetta.protocols.rotamer_recovery.RRComparer, reporter : rosetta.protocols.rotamer_recovery.RRReporter, pose : rosetta.core.pose.Pose, score_function : rosetta.core.scoring.ScoreFunction, packer_task : rosetta.core.pack.task.PackerTask) -> NoneType
- set_cartesian(...) from builtins.PyCapsule
- set_cartesian(self : rosetta.protocols.rotamer_recovery.RRProtocolRelax, setting : bool) -> NoneType
- set_nonideal(...) from builtins.PyCapsule
- set_nonideal(self : rosetta.protocols.rotamer_recovery.RRProtocolRelax, setting : bool) -> NoneType
|
class RRReporter(builtins.object) |
| |
The reporting functionality for the rotamer recovery test
Besides implementing the interface given in the base class
RRReporter each RRReporter should have an entry in the conevience
RotamerRecovery constructor so its use can be indicated by name.
|
| |
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.rotamer_recovery.RRReporter, : rosetta.protocols.rotamer_recovery.RRReporter) -> rosetta.protocols.rotamer_recovery.RRReporter
- recovery_rate(...) from builtins.PyCapsule
- recovery_rate(rosetta.protocols.rotamer_recovery.RRReporter) -> float
- report_rotamer_recovery(...) from builtins.PyCapsule
- report_rotamer_recovery(self : rosetta.protocols.rotamer_recovery.RRReporter, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, score : float, recovered : bool) -> NoneType
- reset_recovery(...) from builtins.PyCapsule
- reset_recovery(rosetta.protocols.rotamer_recovery.RRReporter) -> NoneType
- set_comparer_info(...) from builtins.PyCapsule
- set_comparer_info(self : rosetta.protocols.rotamer_recovery.RRReporter, comparer_name : str, comparer_params : str) -> NoneType
- set_protocol_info(...) from builtins.PyCapsule
- set_protocol_info(self : rosetta.protocols.rotamer_recovery.RRReporter, protocol_name : str, protocol_params : str) -> NoneType
- show(...) from builtins.PyCapsule
- show(rosetta.protocols.rotamer_recovery.RRReporter) -> NoneType
|
class RRReporterHuman(RRReporter) |
| |
The reporting functionality for the rotamer recovery test in
a human readable format.
|
| |
- Method resolution order:
- RRReporterHuman
- RRReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.rotamer_recovery.RRReporterHuman) -> 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.rotamer_recovery.RRReporterHuman, : rosetta.protocols.rotamer_recovery.RRReporterHuman) -> rosetta.protocols.rotamer_recovery.RRReporterHuman
- recovery_rate(...) from builtins.PyCapsule
- recovery_rate(rosetta.protocols.rotamer_recovery.RRReporterHuman) -> float
- report_rotamer_recovery(...) from builtins.PyCapsule
- report_rotamer_recovery(self : rosetta.protocols.rotamer_recovery.RRReporterHuman, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, score : float, recovered : bool) -> NoneType
- reset_recovery(...) from builtins.PyCapsule
- reset_recovery(rosetta.protocols.rotamer_recovery.RRReporterHuman) -> NoneType
- set_comparer_info(...) from builtins.PyCapsule
- set_comparer_info(self : rosetta.protocols.rotamer_recovery.RRReporterHuman, comparer_name : str, comparer_params : str) -> NoneType
- set_protocol_info(...) from builtins.PyCapsule
- set_protocol_info(self : rosetta.protocols.rotamer_recovery.RRReporterHuman, protocol_name : str, protocol_params : str) -> NoneType
- show(...) from builtins.PyCapsule
- show(rosetta.protocols.rotamer_recovery.RRReporterHuman) -> NoneType
|
class RRReporterSQLite(RRReporter) |
| | |
- Method resolution order:
- RRReporterSQLite
- RRReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, str) -> NoneType
doc
3. __init__(handle, str, str) -> NoneType
doc
4. __init__(self : handle, database_name : str, database_pq_schema : str, output_level : rosetta.protocols.rotamer_recovery.OutputLevel) -> NoneType
5. __init__(handle, rosetta.utility.sql_database.session) -> NoneType
doc
6. __init__(self : handle, db_session : rosetta.utility.sql_database.session, output_level : rosetta.protocols.rotamer_recovery.OutputLevel) -> NoneType
7. __init__(handle, rosetta.protocols.rotamer_recovery.RRReporterSQLite) -> 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.rotamer_recovery.RRReporterSQLite, : rosetta.protocols.rotamer_recovery.RRReporterSQLite) -> rosetta.protocols.rotamer_recovery.RRReporterSQLite
- db_session(...) from builtins.PyCapsule
- db_session(*args, **kwargs)
Overloaded function.
1. db_session(self : rosetta.protocols.rotamer_recovery.RRReporterSQLite, db_session : rosetta.utility.sql_database.session) -> NoneType
2. db_session(rosetta.protocols.rotamer_recovery.RRReporterSQLite) -> rosetta.utility.sql_database.session
- get_output_level(...) from builtins.PyCapsule
- get_output_level(rosetta.protocols.rotamer_recovery.RRReporterSQLite) -> rosetta.protocols.rotamer_recovery.OutputLevel
- get_struct_id1(...) from builtins.PyCapsule
- get_struct_id1(rosetta.protocols.rotamer_recovery.RRReporterSQLite) -> int
- recovery_rate(...) from builtins.PyCapsule
- recovery_rate(rosetta.protocols.rotamer_recovery.RRReporterSQLite) -> float
- report_predicted_features(...) from builtins.PyCapsule
- report_predicted_features(self : rosetta.protocols.rotamer_recovery.RRReporterSQLite, struct_id1 : int, res1 : rosetta.core.conformation.Residue, predicted_pose : rosetta.core.pose.Pose, predicted_res : rosetta.core.conformation.Residue) -> NoneType
- report_rotamer_recovery(...) from builtins.PyCapsule
- report_rotamer_recovery(self : rosetta.protocols.rotamer_recovery.RRReporterSQLite, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, score : float, recovered : bool) -> NoneType
- report_rotamer_recovery_features(...) from builtins.PyCapsule
- report_rotamer_recovery_features(self : rosetta.protocols.rotamer_recovery.RRReporterSQLite, struct_id1 : int, res1 : rosetta.core.conformation.Residue, score : float, recovered : bool) -> NoneType
- report_rotamer_recovery_full(...) from builtins.PyCapsule
- report_rotamer_recovery_full(self : rosetta.protocols.rotamer_recovery.RRReporterSQLite, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, score : float, recovered : bool) -> NoneType
- reset_recovery(...) from builtins.PyCapsule
- reset_recovery(rosetta.protocols.rotamer_recovery.RRReporterSQLite) -> NoneType
- set_comparer_info(...) from builtins.PyCapsule
- set_comparer_info(self : rosetta.protocols.rotamer_recovery.RRReporterSQLite, comparer_name : str, comparer_params : str) -> NoneType
- set_output_level(...) from builtins.PyCapsule
- set_output_level(self : rosetta.protocols.rotamer_recovery.RRReporterSQLite, output_level : rosetta.protocols.rotamer_recovery.OutputLevel) -> NoneType
- set_predicted_report_to_db(...) from builtins.PyCapsule
- set_predicted_report_to_db(self : rosetta.protocols.rotamer_recovery.RRReporterSQLite, report_to_db : rosetta.protocols.features.ReportToDB) -> NoneType
- set_protocol_info(...) from builtins.PyCapsule
- set_protocol_info(self : rosetta.protocols.rotamer_recovery.RRReporterSQLite, protocol_name : str, protocol_params : str) -> NoneType
- set_struct_id1(...) from builtins.PyCapsule
- set_struct_id1(self : rosetta.protocols.rotamer_recovery.RRReporterSQLite, struct_id1 : int) -> NoneType
- show(...) from builtins.PyCapsule
- show(rosetta.protocols.rotamer_recovery.RRReporterSQLite) -> NoneType
- write_schema_to_db(...) from builtins.PyCapsule
- write_schema_to_db(self : rosetta.protocols.rotamer_recovery.RRReporterSQLite, db_session : rosetta.utility.sql_database.session) -> NoneType
generate the table schemas and write them to the database
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class RRReporterSimple(RRReporter) |
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- Method resolution order:
- RRReporterSimple
- RRReporter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.rotamer_recovery.RRReporterSimple) -> 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.rotamer_recovery.RRReporterSimple, : rosetta.protocols.rotamer_recovery.RRReporterSimple) -> rosetta.protocols.rotamer_recovery.RRReporterSimple
- recovery_rate(...) from builtins.PyCapsule
- recovery_rate(rosetta.protocols.rotamer_recovery.RRReporterSimple) -> float
- report_rotamer_recovery(...) from builtins.PyCapsule
- report_rotamer_recovery(self : rosetta.protocols.rotamer_recovery.RRReporterSimple, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, score : float, recovered : bool) -> NoneType
- reset_recovery(...) from builtins.PyCapsule
- reset_recovery(rosetta.protocols.rotamer_recovery.RRReporterSimple) -> NoneType
- set_comparer_info(...) from builtins.PyCapsule
- set_comparer_info(self : rosetta.protocols.rotamer_recovery.RRReporterSimple, : str, : str) -> NoneType
- set_protocol_info(...) from builtins.PyCapsule
- set_protocol_info(self : rosetta.protocols.rotamer_recovery.RRReporterSimple, : str, : str) -> NoneType
- show(...) from builtins.PyCapsule
- show(rosetta.protocols.rotamer_recovery.RRReporterSimple) -> NoneType
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class RotamerRecovery(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, protocol : rosetta.protocols.rotamer_recovery.RRProtocol, comparer : rosetta.protocols.rotamer_recovery.RRComparer, reporter : rosetta.protocols.rotamer_recovery.RRReporter) -> NoneType
3. __init__(handle, rosetta.protocols.rotamer_recovery.RotamerRecovery) -> 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.rotamer_recovery.RotamerRecovery, : rosetta.protocols.rotamer_recovery.RotamerRecovery) -> rosetta.protocols.rotamer_recovery.RotamerRecovery
- get_ignore_unrecognized_res(...) from builtins.PyCapsule
- get_ignore_unrecognized_res(rosetta.protocols.rotamer_recovery.RotamerRecovery) -> bool
- init_rotamer_recovery_with_options(...) from builtins.PyCapsule
- init_rotamer_recovery_with_options(self : rosetta.protocols.rotamer_recovery.RotamerRecovery, rotamer_recovery : rosetta.protocols.rotamer_recovery.RotamerRecovery) -> NoneType
- init_with_options(...) from builtins.PyCapsule
- init_with_options(rosetta.protocols.rotamer_recovery.RotamerRecovery) -> NoneType
- recovery_rate(...) from builtins.PyCapsule
- recovery_rate(rosetta.protocols.rotamer_recovery.RotamerRecovery) -> float
- register_options(...) from builtins.PyCapsule
- register_options(rosetta.protocols.rotamer_recovery.RotamerRecovery) -> NoneType
- reset_recovery(...) from builtins.PyCapsule
- reset_recovery(rosetta.protocols.rotamer_recovery.RotamerRecovery) -> NoneType
- run(...) from builtins.PyCapsule
- run(self : rosetta.protocols.rotamer_recovery.RotamerRecovery, pose : rosetta.core.pose.Pose, score_function : rosetta.core.scoring.ScoreFunction, packer_task : rosetta.core.pack.task.PackerTask) -> float
- set_ignore_unrecognized_res(...) from builtins.PyCapsule
- set_ignore_unrecognized_res(self : rosetta.protocols.rotamer_recovery.RotamerRecovery, ignore_unrecognized_res : bool) -> NoneType
- show(...) from builtins.PyCapsule
- show(rosetta.protocols.rotamer_recovery.RotamerRecovery) -> NoneType
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class RotamerRecoveryFactory(rosetta.utility.SingletonBase_protocols_rotamer_recovery_RotamerRecoveryFactory_t) |
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Create Rotamer_Recovery Reporters
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- Method resolution order:
- RotamerRecoveryFactory
- rosetta.utility.SingletonBase_protocols_rotamer_recovery_RotamerRecoveryFactory_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.
- get_rotamer_recovery(...) from builtins.PyCapsule
- get_rotamer_recovery(self : rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory, protocol : str, comparer : str, reporter : str) -> rosetta.protocols.rotamer_recovery.RotamerRecovery
- get_rotamer_recovery_comparer(...) from builtins.PyCapsule
- get_rotamer_recovery_comparer(self : rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory, type_name : str) -> rosetta.protocols.rotamer_recovery.RRComparer
- get_rotamer_recovery_protocol(...) from builtins.PyCapsule
- get_rotamer_recovery_protocol(self : rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory, type_name : str) -> rosetta.protocols.rotamer_recovery.RRProtocol
- get_rotamer_recovery_reporter(...) from builtins.PyCapsule
- get_rotamer_recovery_reporter(self : rosetta.protocols.rotamer_recovery.RotamerRecoveryFactory, type_name : str) -> rosetta.protocols.rotamer_recovery.RRReporter
Methods inherited from rosetta.utility.SingletonBase_protocols_rotamer_recovery_RotamerRecoveryFactory_t:
- get_instance(...) from builtins.PyCapsule
- get_instance() -> protocols::rotamer_recovery::RotamerRecoveryFactory
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class RotamerRecoveryMover(rosetta.protocols.moves.Mover) |
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- Method resolution order:
- RotamerRecoveryMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, rotamer_recovery : rosetta.protocols.rotamer_recovery.RotamerRecovery, scfxn : rosetta.core.scoring.ScoreFunction, task_factory : rosetta.core.pack.task.TaskFactory) -> NoneType
3. __init__(handle, rosetta.protocols.rotamer_recovery.RotamerRecoveryMover) -> 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.rotamer_recovery.RotamerRecoveryMover, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.rotamer_recovery.RotamerRecoveryMover, : rosetta.protocols.rotamer_recovery.RotamerRecoveryMover) -> rosetta.protocols.rotamer_recovery.RotamerRecoveryMover
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.rotamer_recovery.RotamerRecoveryMover) -> rosetta.protocols.moves.Mover
make a copy
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.rotamer_recovery.RotamerRecoveryMover) -> rosetta.protocols.moves.Mover
make a copy but use default constructor
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.rotamer_recovery.RotamerRecoveryMover) -> str
- register_options(...) from builtins.PyCapsule
- register_options(rosetta.protocols.rotamer_recovery.RotamerRecoveryMover) -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.rotamer_recovery.RotamerRecoveryMover) -> bool
this function informs 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.rotamer_recovery.RotamerRecoveryMover) -> bool
this function informs 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).
- score_function(...) from builtins.PyCapsule
- score_function(*args, **kwargs)
Overloaded function.
1. score_function(rosetta.protocols.rotamer_recovery.RotamerRecoveryMover) -> rosetta.core.scoring.ScoreFunction
2. score_function(self : rosetta.protocols.rotamer_recovery.RotamerRecoveryMover, : rosetta.core.scoring.ScoreFunction) -> NoneType
- show(...) from builtins.PyCapsule
- show(rosetta.protocols.rotamer_recovery.RotamerRecoveryMover) -> NoneType
Methods inherited from 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
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- 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
- 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
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