| | |
- builtins.object
-
- boolean_operations
- rosetta.basic.datacache.CacheableData(builtins.object)
-
- STMStoredTask
- rosetta.core.pack.rotamer_set.RotamerSetOperation(builtins.object)
-
- LimitAromaChi2_RotamerSetOperation
- rosetta.core.pack.task.operation.ResFilter(builtins.object)
-
- ProteinCore
- rosetta.core.pack.task.operation.ResFilterCreator(builtins.object)
-
- ProteinCoreFilterCreator
- rosetta.core.pack.task.operation.TaskOperation(builtins.object)
-
- ConservativeDesignOperation
- CrystalContactsOperation
- DockingNoRepack1
- DockingNoRepack2
- DsspDesignOperation
- ImportUnboundRotamersOperation
- InteractingRotamerExplosion
- InterfaceTaskOperation
-
- RestrictToInterface
- RestrictToInterfaceVectorOperation
- JointSequenceOperation
- LimitAromaChi2Operation
- LinkResidues
- ModifyAnnealer
- MutationSetDesignOperation
- ReadResfileFromDB
- ResidueProbDesignOperation
- RestrictIdentitiesOperation
- RestrictInterGroupVectorOperation
- RestrictNativeResiduesOperation
- RestrictNonSurfaceToRepackingOperation
- RestrictOperationsBase
-
- AlignedThreadOperation
- DatabaseThread
- DesignAroundOperation
- PreventChainFromRepackingOperation
- PreventResiduesFromRepackingOperation
- ProteinInterfaceDesignOperation
- RestrictByCalculatorsOperation
- RestrictChainToRepackingOperation
- RestrictIdentitiesAtAlignedPositionsOperation
- RestrictResiduesToRepackingOperation
- RestrictToAlignedSegmentsOperation
- RestrictToInterfaceOperation
- RestrictToNeighborhoodOperation
- SelectResiduesWithinChainOperation
- ThreadSequenceOperation
- RestrictToCDRH3Loop
- RestrictToLoops
-
- RestrictToLoopsAndNeighbors
- RestrictToMoveMapChiOperation
- RestrictToTerminiOperation
- RetrieveStoredTaskOperation
- SelectByDeltaScoreOperation
- SelectByDensityFitOperation
- SelectBySASAOperation
- SeqprofConsensusOperation
-
- RestrictConservedLowDdgOperation
- SetIGTypeOperation
- rosetta.core.pack.task.operation.TaskOperationCreator(builtins.object)
-
- AlignedThreadOperationCreator
- CrystalContactsOperationCreator
- DatabaseThreadCreator
- DesignAroundOperationCreator
- DsspDesignOperationCreator
- ImportUnboundRotamersOperationCreator
- InteractingRotamerExplosionCreator
- JointSequenceOperationCreator
- LimitAromaChi2OperationCreator
- LinkResiduesCreator
- ModifyAnnealerCreator
- PreventChainFromRepackingOperationCreator
- PreventResiduesFromRepackingOperationCreator
- ProteinInterfaceDesignOperationCreator
- ReadResfileFromDBCreator
- RestrictByCalculatorsOperationCreator
- RestrictChainToRepackingOperationCreator
- RestrictConservedLowDdgOperationCreator
- RestrictIdentitiesAtAlignedPositionsOperationCreator
- RestrictIdentitiesOperationCreator
- RestrictInterGroupVectorOperationCreator
- RestrictNativeResiduesOperationCreator
- RestrictNonSurfaceToRepackingOperationCreator
- RestrictResiduesToRepackingOperationCreator
- RestrictToAlignedSegmentsOperationCreator
- RestrictToCDRH3LoopCreator
- RestrictToInterfaceCreator
- RestrictToInterfaceOperationCreator
- RestrictToInterfaceVectorOperationCreator
- RestrictToLoopsAndNeighborsCreator
- RestrictToLoopsCreator
- RestrictToNeighborhoodOperationCreator
- RestrictToTerminiOperationCreator
- RetrieveStoredTaskOperationCreator
- SelectByDeltaScoreOperationCreator
- SelectByDensityFitOperationCreator
- SelectBySASAOperationCreator
- SelectResiduesWithinChainOperationCreator
- SeqprofConsensusOperationCreator
- SetIGTypeOperationCreator
- ThreadSequenceOperationCreator
- rosetta.protocols.moves.Mover(builtins.object)
-
- StoreCombinedStoredTasksMover
- StoreCompoundTaskMover
- StoreTaskMover
- rosetta.protocols.moves.MoverCreator(builtins.object)
-
- StoreCombinedStoredTasksMoverCreator
- StoreCompoundTaskMoverCreator
- StoreTaskMoverCreator
class AlignedThreadOperation(RestrictOperationsBase) |
| |
this class is a TaskOperation to prevent repacking of residues not near an interface.
|
| |
- Method resolution order:
- AlignedThreadOperation
- RestrictOperationsBase
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.AlignedThreadOperation) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- alignment_file(...) from builtins.PyCapsule
- alignment_file(*args, **kwargs)
Overloaded function.
1. alignment_file(rosetta.protocols.toolbox.task_operations.AlignedThreadOperation) -> str
2. alignment_file(self : rosetta.protocols.toolbox.task_operations.AlignedThreadOperation, s : str) -> NoneType
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.toolbox.task_operations.AlignedThreadOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.AlignedThreadOperation, : rosetta.protocols.toolbox.task_operations.AlignedThreadOperation) -> rosetta.protocols.toolbox.task_operations.AlignedThreadOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.AlignedThreadOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.AlignedThreadOperation, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- query_name(...) from builtins.PyCapsule
- query_name(*args, **kwargs)
Overloaded function.
1. query_name(rosetta.protocols.toolbox.task_operations.AlignedThreadOperation) -> str
2. query_name(self : rosetta.protocols.toolbox.task_operations.AlignedThreadOperation, s : str) -> NoneType
- start_res(...) from builtins.PyCapsule
- start_res(*args, **kwargs)
Overloaded function.
1. start_res(self : rosetta.protocols.toolbox.task_operations.AlignedThreadOperation, s : int) -> NoneType
2. start_res(rosetta.protocols.toolbox.task_operations.AlignedThreadOperation) -> int
- template_name(...) from builtins.PyCapsule
- template_name(*args, **kwargs)
Overloaded function.
1. template_name(rosetta.protocols.toolbox.task_operations.AlignedThreadOperation) -> str
2. template_name(self : rosetta.protocols.toolbox.task_operations.AlignedThreadOperation, s : str) -> NoneType
|
class ConservativeDesignOperation(rosetta.core.pack.task.operation.TaskOperation) |
| |
A TaskOperation that sets the allowed amino acids of designable residues to the native amino acid's conservative mutations.
Default is to act on all designable residues. Use limit_to_positions to limit this.
Default is to replace the allowed_aas with these conservative mutations.
Data is loaded from database/sequence/resinfo.db.
|
| |
- Method resolution order:
- ConservativeDesignOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, data_source : str) -> NoneType
3. __init__(handle, rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_to_allowed_aas(...) from builtins.PyCapsule
- add_to_allowed_aas(self : rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation, setting : bool) -> NoneType
Add to the allowed amino acids list instead of replacing it. Default false.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation, rhs : rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation) -> rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation
- clear_positions(...) from builtins.PyCapsule
- clear_positions(rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation) -> NoneType
Clear any set positions.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation) -> rosetta.core.pack.task.operation.TaskOperation
- include_native_aa(...) from builtins.PyCapsule
- include_native_aa(self : rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation, setting : bool) -> NoneType
Include native amino acid in the allowed_aas list. Default true.
- include_residue(...) from builtins.PyCapsule
- include_residue(self : rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation, resnum : int) -> NoneType
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- limit_to_positions(...) from builtins.PyCapsule
- limit_to_positions(self : rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation, positions : rosetta.utility.vector1_unsigned_long) -> NoneType
Limit to a subset of residue positions, already set to designable.
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_data_source(...) from builtins.PyCapsule
- set_data_source(self : rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation, data_source : str) -> NoneType
Set the source of the data used to define what is conservative.
Options are: chothia_76, and the Blosum matrices from 30 to 100; designated as blosum30, 62, etc.
Default is blosum62. The higher the number, the more conservative the set of mutations (numbers are sequence identity cutoffs)
- set_native_sequence(...) from builtins.PyCapsule
- set_native_sequence(self : rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation, seq : str) -> NoneType
- use_pose_sequence_as_native(...) from builtins.PyCapsule
- use_pose_sequence_as_native(self : rosetta.protocols.toolbox.task_operations.ConservativeDesignOperation, pose : rosetta.core.pose.Pose) -> NoneType
Will use native residues from the this pose to determine conserved aa.
Methods inherited from rosetta.core.pack.task.operation.TaskOperation:
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.core.pack.task.operation.TaskOperation, : utility::tag::Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Used to parse an xml-like tag to load parameters and properties.
|
class CrystalContactsOperation(rosetta.core.pack.task.operation.TaskOperation) |
| | |
- Method resolution order:
- CrystalContactsOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
doc
2. __init__(handle, float) -> NoneType
doc
3. __init__(handle, float, float) -> NoneType
doc
4. __init__(handle, float, float, float) -> NoneType
doc
5. __init__(handle, float, float, float, bool) -> NoneType
doc
6. __init__(handle, float, float, float, bool, bool) -> NoneType
doc
7. __init__(handle, float, float, float, bool, bool, bool) -> NoneType
doc
8. __init__(self : handle, all_gap : float, polar_gap : float, max_buried_sasa_ : float, invert : bool, nbr_radius_to_nbr_radius : bool, nbr_radius_to_atoms : bool, atoms_to_atoms : bool) -> 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.toolbox.task_operations.CrystalContactsOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.CrystalContactsOperation, : rosetta.protocols.toolbox.task_operations.CrystalContactsOperation) -> rosetta.protocols.toolbox.task_operations.CrystalContactsOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.CrystalContactsOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.CrystalContactsOperation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
|
class DatabaseThread(RestrictOperationsBase) |
| |
this class is a TaskOperation to thread sequences from a database.
|
| |
- Method resolution order:
- DatabaseThread
- RestrictOperationsBase
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.DatabaseThread) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- allow_design_around(...) from builtins.PyCapsule
- allow_design_around(*args, **kwargs)
Overloaded function.
1. allow_design_around(rosetta.protocols.toolbox.task_operations.DatabaseThread) -> bool
2. allow_design_around(self : rosetta.protocols.toolbox.task_operations.DatabaseThread, b : bool) -> NoneType
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.toolbox.task_operations.DatabaseThread, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.DatabaseThread, : rosetta.protocols.toolbox.task_operations.DatabaseThread) -> rosetta.protocols.toolbox.task_operations.DatabaseThread
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.DatabaseThread) -> rosetta.core.pack.task.operation.TaskOperation
- database_fname(...) from builtins.PyCapsule
- database_fname(*args, **kwargs)
Overloaded function.
1. database_fname(rosetta.protocols.toolbox.task_operations.DatabaseThread) -> str
2. database_fname(self : rosetta.protocols.toolbox.task_operations.DatabaseThread, d : str) -> NoneType
- designable(...) from builtins.PyCapsule
- designable(*args, **kwargs)
Overloaded function.
1. designable(rosetta.protocols.toolbox.task_operations.DatabaseThread) -> rosetta.utility.vector1_unsigned_long
2. designable(self : rosetta.protocols.toolbox.task_operations.DatabaseThread, vector : rosetta.utility.vector1_unsigned_long) -> NoneType
- end_res(...) from builtins.PyCapsule
- end_res(*args, **kwargs)
Overloaded function.
1. end_res(rosetta.protocols.toolbox.task_operations.DatabaseThread) -> int
2. end_res(self : rosetta.protocols.toolbox.task_operations.DatabaseThread, s : int) -> NoneType
- find_length(...) from builtins.PyCapsule
- find_length(self : rosetta.protocols.toolbox.task_operations.DatabaseThread, pose : rosetta.core.pose.Pose) -> int
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- leave_as_is(...) from builtins.PyCapsule
- leave_as_is(*args, **kwargs)
Overloaded function.
1. leave_as_is(rosetta.protocols.toolbox.task_operations.DatabaseThread) -> rosetta.utility.vector1_unsigned_long
2. leave_as_is(self : rosetta.protocols.toolbox.task_operations.DatabaseThread, vector : rosetta.utility.vector1_unsigned_long) -> NoneType
- mark_designable(...) from builtins.PyCapsule
- mark_designable(self : rosetta.protocols.toolbox.task_operations.DatabaseThread, sequence : str, : rosetta.core.pose.Pose) -> NoneType
- mark_leave_as_is(...) from builtins.PyCapsule
- mark_leave_as_is(self : rosetta.protocols.toolbox.task_operations.DatabaseThread, sequence : str, : rosetta.core.pose.Pose) -> NoneType
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.DatabaseThread, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- pick_sequence_from_database(...) from builtins.PyCapsule
- pick_sequence_from_database(self : rosetta.protocols.toolbox.task_operations.DatabaseThread, pose : rosetta.core.pose.Pose) -> str
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- start_res(...) from builtins.PyCapsule
- start_res(*args, **kwargs)
Overloaded function.
1. start_res(rosetta.protocols.toolbox.task_operations.DatabaseThread) -> int
2. start_res(self : rosetta.protocols.toolbox.task_operations.DatabaseThread, s : int) -> NoneType
- target_sequence(...) from builtins.PyCapsule
- target_sequence(*args, **kwargs)
Overloaded function.
1. target_sequence(self : rosetta.protocols.toolbox.task_operations.DatabaseThread, seq : str) -> NoneType
2. target_sequence(rosetta.protocols.toolbox.task_operations.DatabaseThread) -> str
- template_file(...) from builtins.PyCapsule
- template_file(*args, **kwargs)
Overloaded function.
1. template_file(rosetta.protocols.toolbox.task_operations.DatabaseThread) -> str
2. template_file(self : rosetta.protocols.toolbox.task_operations.DatabaseThread, s : str) -> NoneType
|
class DesignAroundOperation(RestrictOperationsBase) |
| | |
- Method resolution order:
- DesignAroundOperation
- RestrictOperationsBase
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.DesignAroundOperation) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- allow_design(...) from builtins.PyCapsule
- allow_design(*args, **kwargs)
Overloaded function.
1. allow_design(self : rosetta.protocols.toolbox.task_operations.DesignAroundOperation, a : bool) -> NoneType
2. allow_design(rosetta.protocols.toolbox.task_operations.DesignAroundOperation) -> bool
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.toolbox.task_operations.DesignAroundOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.DesignAroundOperation, : rosetta.protocols.toolbox.task_operations.DesignAroundOperation) -> rosetta.protocols.toolbox.task_operations.DesignAroundOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.DesignAroundOperation) -> rosetta.core.pack.task.operation.TaskOperation
- design_shell(...) from builtins.PyCapsule
- design_shell(*args, **kwargs)
Overloaded function.
1. design_shell(self : rosetta.protocols.toolbox.task_operations.DesignAroundOperation, radius : float) -> NoneType
2. design_shell(rosetta.protocols.toolbox.task_operations.DesignAroundOperation) -> float
- get_designable_residues(...) from builtins.PyCapsule
- get_designable_residues(rosetta.protocols.toolbox.task_operations.DesignAroundOperation) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t
- include_residue(...) from builtins.PyCapsule
- include_residue(self : rosetta.protocols.toolbox.task_operations.DesignAroundOperation, resid : int) -> NoneType
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.DesignAroundOperation, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- repack_shell(...) from builtins.PyCapsule
- repack_shell(*args, **kwargs)
Overloaded function.
1. repack_shell(self : rosetta.protocols.toolbox.task_operations.DesignAroundOperation, repack_shell : float) -> NoneType
2. repack_shell(rosetta.protocols.toolbox.task_operations.DesignAroundOperation) -> float
- resnums_allow_design(...) from builtins.PyCapsule
- resnums_allow_design(*args, **kwargs)
Overloaded function.
1. resnums_allow_design(self : rosetta.protocols.toolbox.task_operations.DesignAroundOperation, a : bool) -> NoneType
2. resnums_allow_design(rosetta.protocols.toolbox.task_operations.DesignAroundOperation) -> bool
|
class DsspDesignOperation(rosetta.core.pack.task.operation.TaskOperation) |
| |
TaskOperation that can be used to restrict AAs allowed at each position
based on DSSP-assigned secondary structure
|
| |
- Method resolution order:
- DsspDesignOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.DsspDesignOperation) -> 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.toolbox.task_operations.DsspDesignOperation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
apply
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.DsspDesignOperation, : rosetta.protocols.toolbox.task_operations.DsspDesignOperation) -> rosetta.protocols.toolbox.task_operations.DsspDesignOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.DsspDesignOperation) -> rosetta.core.pack.task.operation.TaskOperation
make clone
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.DsspDesignOperation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
parse RosettaScripts XML
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_blueprint(...) from builtins.PyCapsule
- set_blueprint(self : rosetta.protocols.toolbox.task_operations.DsspDesignOperation, bp : rosetta.protocols.jd2.parser.BluePrint) -> NoneType
define secondary structure from a blueprint
- set_restrictions_aa(...) from builtins.PyCapsule
- set_restrictions_aa(self : rosetta.protocols.toolbox.task_operations.DsspDesignOperation, sse : str, aas : str) -> NoneType
define allowed residues for some SSE
- set_restrictions_append(...) from builtins.PyCapsule
- set_restrictions_append(self : rosetta.protocols.toolbox.task_operations.DsspDesignOperation, sse : str, aas : str) -> NoneType
append allowed residues for some SSE
- set_restrictions_exclude(...) from builtins.PyCapsule
- set_restrictions_exclude(self : rosetta.protocols.toolbox.task_operations.DsspDesignOperation, sse : str, aas : str) -> NoneType
exclude allowed residues for some SSE
|
class InterfaceTaskOperation(rosetta.core.pack.task.operation.TaskOperation) |
| | |
- Method resolution order:
- InterfaceTaskOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.toolbox.task_operations.InterfaceTaskOperation) -> NoneType
2. __init__(rosetta.protocols.toolbox.task_operations.InterfaceTaskOperation, rosetta.protocols.toolbox.task_operations.InterfaceTaskOperation) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_movable_jump(...) from builtins.PyCapsule
- add_movable_jump(self : rosetta.protocols.toolbox.task_operations.InterfaceTaskOperation, additional_jump : int) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.InterfaceTaskOperation, : rosetta.protocols.toolbox.task_operations.InterfaceTaskOperation) -> rosetta.protocols.toolbox.task_operations.InterfaceTaskOperation
- keyname(...) from builtins.PyCapsule
- keyname(*args, **kwargs)
Overloaded function.
1. keyname() -> str
2. keyname() -> str
3. keyname() -> str
- movable_jumps(...) from builtins.PyCapsule
- movable_jumps(rosetta.protocols.toolbox.task_operations.InterfaceTaskOperation) -> rosetta.utility.vector1_int
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(*args, **kwargs)
Overloaded function.
1. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
2. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
3. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_movable_jumps(...) from builtins.PyCapsule
- set_movable_jumps(self : rosetta.protocols.toolbox.task_operations.InterfaceTaskOperation, movable_jumps : rosetta.utility.vector1_int) -> NoneType
Methods inherited from rosetta.core.pack.task.operation.TaskOperation:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.core.pack.task.operation.TaskOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
Change a packer task in some way. The input pose is the one to which the input
task will be later applied.
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.pack.task.operation.TaskOperation) -> rosetta.core.pack.task.operation.TaskOperation
Create another task operation of the type matching the most-derived
version of the class.
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.core.pack.task.operation.TaskOperation, : utility::tag::Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Used to parse an xml-like tag to load parameters and properties.
|
class JointSequenceOperation(rosetta.core.pack.task.operation.TaskOperation) |
| | |
- Method resolution order:
- JointSequenceOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_native_fasta(...) from builtins.PyCapsule
- add_native_fasta(self : rosetta.protocols.toolbox.task_operations.JointSequenceOperation, fasta_file : str) -> NoneType
Add the sequence from the given fasta filename to the set of allowed aas
- add_native_pdb(...) from builtins.PyCapsule
- add_native_pdb(self : rosetta.protocols.toolbox.task_operations.JointSequenceOperation, filename : str) -> NoneType
Add the sequence from the given filename to the set of allowed aas
and add the rotamers to the set of possible rotamers
- add_native_pose(...) from builtins.PyCapsule
- add_native_pose(self : rosetta.protocols.toolbox.task_operations.JointSequenceOperation, posecop : rosetta.core.pose.Pose) -> NoneType
Add the sequence from the given pose to the set of allowed aas
and add the rotamers to the set of possible rotamers
- add_pdb(...) from builtins.PyCapsule
- add_pdb(self : rosetta.protocols.toolbox.task_operations.JointSequenceOperation, filename : str) -> NoneType
Add the sequence from the given filename to the set of allowed aas.
- add_pose(...) from builtins.PyCapsule
- add_pose(self : rosetta.protocols.toolbox.task_operations.JointSequenceOperation, pose : rosetta.core.pose.Pose) -> NoneType
Add the sequence from the given pose to the set of allowed aas.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.toolbox.task_operations.JointSequenceOperation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
apply
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.JointSequenceOperation, : rosetta.protocols.toolbox.task_operations.JointSequenceOperation) -> rosetta.protocols.toolbox.task_operations.JointSequenceOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.JointSequenceOperation) -> rosetta.core.pack.task.operation.TaskOperation
make clone
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.JointSequenceOperation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_chain(...) from builtins.PyCapsule
- set_chain(self : rosetta.protocols.toolbox.task_operations.JointSequenceOperation, chain : int) -> NoneType
Return which chain to operate on with 0 meaning all
- use_current_pose(...) from builtins.PyCapsule
- use_current_pose(self : rosetta.protocols.toolbox.task_operations.JointSequenceOperation, ucp : bool) -> NoneType
Should the current pose (pose supplied to apply) be used in addition to the other ones?
- use_natro(...) from builtins.PyCapsule
- use_natro(self : rosetta.protocols.toolbox.task_operations.JointSequenceOperation, unr : bool) -> NoneType
Should the rotamers for the native poses be used?
|
class LimitAromaChi2Operation(rosetta.core.pack.task.operation.TaskOperation) |
| |
///////////////////////////////////////////////////////////////////////////////////////////
|
| |
- Method resolution order:
- LimitAromaChi2Operation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> 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.toolbox.task_operations.LimitAromaChi2Operation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
apply
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation, : rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation) -> rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation
- chi2max(...) from builtins.PyCapsule
- chi2max(*args, **kwargs)
Overloaded function.
1. chi2max(rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation) -> float
max chi2 for picking rotamers of YFH
2. chi2max(self : rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation, r : float) -> NoneType
max chi2 for picking rotamers of YFH
- chi2min(...) from builtins.PyCapsule
- chi2min(*args, **kwargs)
Overloaded function.
1. chi2min(rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation) -> float
min chi2 for picking rotamers of YFH
2. chi2min(self : rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation, r : float) -> NoneType
min chi2 for picking rotamers of YFH
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation) -> rosetta.core.pack.task.operation.TaskOperation
make clone
- include_trp(...) from builtins.PyCapsule
- include_trp(*args, **kwargs)
Overloaded function.
1. include_trp(rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation) -> bool
include TRP ?
2. include_trp(self : rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation, b : bool) -> NoneType
include TRP ?
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.LimitAromaChi2Operation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
|
class LimitAromaChi2_RotamerSetOperation(rosetta.core.pack.rotamer_set.RotamerSetOperation) |
| | |
- Method resolution order:
- LimitAromaChi2_RotamerSetOperation
- rosetta.core.pack.rotamer_set.RotamerSetOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, chi2max : float, chi2min : float) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- alter_rotamer_set(...) from builtins.PyCapsule
- alter_rotamer_set(self : rosetta.protocols.toolbox.task_operations.LimitAromaChi2_RotamerSetOperation, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, ptask : rosetta.core.pack.task.PackerTask, : rosetta.core.graph.Graph, rotamer_set : rosetta.core.pack.rotamer_set.RotamerSet) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.LimitAromaChi2_RotamerSetOperation, : rosetta.protocols.toolbox.task_operations.LimitAromaChi2_RotamerSetOperation) -> rosetta.protocols.toolbox.task_operations.LimitAromaChi2_RotamerSetOperation
- chi2max(...) from builtins.PyCapsule
- chi2max(self : rosetta.protocols.toolbox.task_operations.LimitAromaChi2_RotamerSetOperation, r : float) -> NoneType
max chi2 for picking rotamers of YFH
- chi2min(...) from builtins.PyCapsule
- chi2min(self : rosetta.protocols.toolbox.task_operations.LimitAromaChi2_RotamerSetOperation, r : float) -> NoneType
min chi2 for picking rotamers of YFH
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.LimitAromaChi2_RotamerSetOperation) -> rosetta.core.pack.rotamer_set.RotamerSetOperation
- include_trp(...) from builtins.PyCapsule
- include_trp(self : rosetta.protocols.toolbox.task_operations.LimitAromaChi2_RotamerSetOperation, b : bool) -> NoneType
include TRP ?
Methods inherited from rosetta.core.pack.rotamer_set.RotamerSetOperation:
- increase_packer_residue_radius(...) from builtins.PyCapsule
- increase_packer_residue_radius(self : rosetta.core.pack.rotamer_set.RotamerSetOperation, pose : rosetta.core.pose.Pose, the_task : rosetta.core.pack.task.PackerTask, residue_in : int) -> float
|
class ModifyAnnealer(rosetta.core.pack.task.operation.TaskOperation) |
| | |
- Method resolution order:
- ModifyAnnealer
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, disallow_quench : bool, high_temp : float, low_temp : float) -> 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.toolbox.task_operations.ModifyAnnealer, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.ModifyAnnealer, : rosetta.protocols.toolbox.task_operations.ModifyAnnealer) -> rosetta.protocols.toolbox.task_operations.ModifyAnnealer
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.ModifyAnnealer) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.ModifyAnnealer, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
|
class MutationSetDesignOperation(rosetta.core.pack.task.operation.TaskOperation) |
| |
Sample a set of mutations each time packer is generated.
A MutationSet is a simple map of resnum:aa.
Each apply will sample a set either at random, or with a set of weights.
Does not enable/disable packing or design by default. Simply controls what the design set will be.
Typically each set would be of the same resnums, but this is not necessary.
Iterative Sampling can be achieved somewhat by setting the sample index with each pack.
Does not touch any resnums not in a sampled mutation set.
|
| |
- Method resolution order:
- MutationSetDesignOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_to_allowed_aas(...) from builtins.PyCapsule
- add_to_allowed_aas(self : rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation, setting : bool) -> NoneType
Add to the allowed amino acids list instead of replacing them. Default false.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation, : rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation) -> rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation
- clear_mutation_sets(...) from builtins.PyCapsule
- clear_mutation_sets(rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation) -> NoneType
Clear any stored mutation sets and weights.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation) -> rosetta.core.pack.task.operation.TaskOperation
- get_sample_index(...) from builtins.PyCapsule
- get_sample_index(rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation) -> int
- get_total_mutation_sets(...) from builtins.PyCapsule
- get_total_mutation_sets(rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation) -> int
Get the total number of mutation sets housed.
- include_native_aa(...) from builtins.PyCapsule
- include_native_aa(self : rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation, setting : bool) -> NoneType
Include native amino acid in the allowed_aas list. Default False.
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- reset_sample_index(...) from builtins.PyCapsule
- reset_sample_index(rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation) -> NoneType
Set the sample index back to zero - which means we will sample from all of them according to weights.
- set_picking_rounds(...) from builtins.PyCapsule
- set_picking_rounds(self : rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation, picking_rounds : int) -> NoneType
Number of times we sample from our sets. Default 1/apply.
The more rounds, the closer the final amino acid set for each position will be to the full profile for that position.
If using weights for the residue sets, this would increase variability.
- set_sample_index(...) from builtins.PyCapsule
- set_sample_index(self : rosetta.protocols.toolbox.task_operations.MutationSetDesignOperation, sample_index : int) -> NoneType
Used to sample particular indexes, since we can't do this iteratively due to const apply. 1 through n
Set to 0 in order to sample from the weights.
Methods inherited from rosetta.core.pack.task.operation.TaskOperation:
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.core.pack.task.operation.TaskOperation, : utility::tag::Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Used to parse an xml-like tag to load parameters and properties.
|
class PreventChainFromRepackingOperation(RestrictOperationsBase) |
| |
this class is a TaskOperation to prevent repacking of residues not near an interface.
|
| |
- Method resolution order:
- PreventChainFromRepackingOperation
- RestrictOperationsBase
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, chain : int) -> 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.toolbox.task_operations.PreventChainFromRepackingOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation, : rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation) -> rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation
- chain(...) from builtins.PyCapsule
- chain(*args, **kwargs)
Overloaded function.
1. chain(self : rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation, chain : int) -> NoneType
2. chain(rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation) -> int
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.PreventChainFromRepackingOperation, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
|
class PreventResiduesFromRepackingOperation(RestrictOperationsBase) |
| |
this class is a TaskOperation to prevent repacking of residues not near an interface.
|
| |
- Method resolution order:
- PreventResiduesFromRepackingOperation
- RestrictOperationsBase
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, residues : rosetta.utility.vector1_unsigned_long) -> NoneType
3. __init__(handle, rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation) -> 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.toolbox.task_operations.PreventResiduesFromRepackingOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation, : rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation) -> rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation) -> rosetta.core.pack.task.operation.TaskOperation
- get_residues(...) from builtins.PyCapsule
- get_residues(rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation) -> rosetta.utility.vector1_unsigned_long
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- reference_pdb_id(...) from builtins.PyCapsule
- reference_pdb_id(*args, **kwargs)
Overloaded function.
1. reference_pdb_id(rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation) -> str
2. reference_pdb_id(self : rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation, s : str) -> NoneType
- set_residues(...) from builtins.PyCapsule
- set_residues(self : rosetta.protocols.toolbox.task_operations.PreventResiduesFromRepackingOperation, residues_vec : rosetta.utility.vector1_unsigned_long) -> NoneType
|
class ProteinInterfaceDesignOperation(RestrictOperationsBase) |
| |
this class is a TaskOperation to prevent repacking of residues not near an interface.
|
| |
- Method resolution order:
- ProteinInterfaceDesignOperation
- RestrictOperationsBase
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- allow_all_aas(...) from builtins.PyCapsule
- allow_all_aas(self : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation, allow : bool) -> NoneType
allow all amino acids to be designed at all positions, do not exclude C, G, P
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation, : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation) -> rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation) -> rosetta.core.pack.task.operation.TaskOperation
- design_all_aas(...) from builtins.PyCapsule
- design_all_aas(self : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation, design_all : bool) -> NoneType
allow design of all residues on input pose, do not exclude G,P
- design_chain1(...) from builtins.PyCapsule
- design_chain1(self : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation, design : bool) -> NoneType
- design_chain2(...) from builtins.PyCapsule
- design_chain2(self : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation, design : bool) -> NoneType
- interface_distance_cutoff(...) from builtins.PyCapsule
- interface_distance_cutoff(self : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation, dist : float) -> NoneType
distance cutoff for atom distance in an interface.
All residues an atoms less than the distance cutoff from an atom in the other chain are
defined as interface.
- jump(...) from builtins.PyCapsule
- jump(*args, **kwargs)
Overloaded function.
1. jump(self : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation, j : int) -> NoneType
2. jump(rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation) -> int
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- modify_after_jump(...) from builtins.PyCapsule
- modify_after_jump(*args, **kwargs)
Overloaded function.
1. modify_after_jump(rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation) -> bool
2. modify_after_jump(self : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation, m : bool) -> NoneType
- modify_before_jump(...) from builtins.PyCapsule
- modify_before_jump(*args, **kwargs)
Overloaded function.
1. modify_before_jump(rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation) -> bool
2. modify_before_jump(self : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation, m : bool) -> NoneType
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- repack_chain1(...) from builtins.PyCapsule
- repack_chain1(self : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation, repack : bool) -> NoneType
- repack_chain2(...) from builtins.PyCapsule
- repack_chain2(self : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation, repack : bool) -> NoneType
|
class ReadResfileFromDB(rosetta.core.pack.task.operation.TaskOperation) |
| | |
- Method resolution order:
- ReadResfileFromDB
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, db_session : rosetta.utility.sql_database.session, database_table : str) -> NoneType
3. __init__(handle, rosetta.protocols.toolbox.task_operations.ReadResfileFromDB) -> 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.toolbox.task_operations.ReadResfileFromDB, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.ReadResfileFromDB, : rosetta.protocols.toolbox.task_operations.ReadResfileFromDB) -> rosetta.protocols.toolbox.task_operations.ReadResfileFromDB
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.ReadResfileFromDB) -> rosetta.core.pack.task.operation.TaskOperation
- database_table(...) from builtins.PyCapsule
- database_table(*args, **kwargs)
Overloaded function.
1. database_table(self : rosetta.protocols.toolbox.task_operations.ReadResfileFromDB, database_table : str) -> NoneType
2. database_table(rosetta.protocols.toolbox.task_operations.ReadResfileFromDB) -> str
- db_session(...) from builtins.PyCapsule
- db_session(self : rosetta.protocols.toolbox.task_operations.ReadResfileFromDB, db_session : rosetta.utility.sql_database.session) -> NoneType
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.ReadResfileFromDB, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
|
class ResidueProbDesignOperation(rosetta.core.pack.task.operation.TaskOperation) |
| |
A TaskOperation that allows amino acids at designable positions through a set of aa probabilities (aa profile).
Each time a task is generated, it will choose one amino acid from the set for that position and add it to (or replace)
the set of packable residues chosen for that position.
Decreases number of rotamers for packing and the space for design. Instead of using energy for profiles, we use selection of residues through
probabilities at each task generation. If picking rounds is higher can result in more than one additional residue in the task from the native.
Default is for the TaskOp to control the allowed amino acids only if the class has probabilities to use for that resnum.
If no probabilities were set in general, it will not do anything.
Probabilities should add to one, but if not, they will act as weights.
Does NOT control which positions are set to design or repack, only what can be designed into.
If probabilities/weights for a particular residue are not present in the map, will not modify that residues task.
|
| |
- Method resolution order:
- ResidueProbDesignOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation) -> 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.toolbox.task_operations.ResidueProbDesignOperation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation, : rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation) -> rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation
- clear_overall_prob_set(...) from builtins.PyCapsule
- clear_overall_prob_set(rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation) -> NoneType
Clears the overall probabilities if any are set.
- clear_prob_set(...) from builtins.PyCapsule
- clear_prob_set(rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation) -> NoneType
Clears the probability matrix
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation) -> rosetta.core.pack.task.operation.TaskOperation
- include_native_restype(...) from builtins.PyCapsule
- include_native_restype(rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation) -> bool
- keep_task_allowed_aas(...) from builtins.PyCapsule
- keep_task_allowed_aas(rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation) -> bool
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- picking_rounds(...) from builtins.PyCapsule
- picking_rounds(rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation) -> int
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- resnum_exists_in_set(...) from builtins.PyCapsule
- resnum_exists_in_set(self : rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation, resnum : int) -> bool
- sample_zero_probs_at(...) from builtins.PyCapsule
- sample_zero_probs_at(rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation) -> float
- set_aa_probabilities(...) from builtins.PyCapsule
- set_aa_probabilities(self : rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation, resnum : int, aa_probs : rosetta.std.map_core_chemical_AA_double) -> NoneType
Sets aa probabilities for a particular resnum
- set_aa_probability_set(...) from builtins.PyCapsule
- set_aa_probability_set(self : rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation, per_res_aa_probs : rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t) -> NoneType
Sets the whole aa probability set.
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation) -> NoneType
- set_include_native_restype(...) from builtins.PyCapsule
- set_include_native_restype(self : rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation, include : bool) -> NoneType
Include current residuetype in packer in addition to selected mutation. Default is true.
- set_keep_task_allowed_aas(...) from builtins.PyCapsule
- set_keep_task_allowed_aas(self : rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation, setting : bool) -> NoneType
Add the aa types chosen from the probabilities to the allowed aa at the position instead of overwriting it.
Will result in very different results.
- set_overall_aa_probabilities(...) from builtins.PyCapsule
- set_overall_aa_probabilities(self : rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation, aa_probs : rosetta.std.map_core_chemical_AA_double) -> NoneType
Sets aa probabilities for all positions not given specifically. All designable residues will use these probabilities this if not specified through other functions.
- set_picking_rounds(...) from builtins.PyCapsule
- set_picking_rounds(self : rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation, picking_rounds : int) -> NoneType
Max number of times to sample from the probability distribution. Default is once.
This is to increase variability.
Too many rounds will even out the distribution.
Can also run the PackRotamers mover or equivalent multiple times for sampling.
- set_sample_zero_probs_at(...) from builtins.PyCapsule
- set_sample_zero_probs_at(self : rosetta.protocols.toolbox.task_operations.ResidueProbDesignOperation, probability : float) -> NoneType
Sample any zero probabilities at this probability instead of not using them.
Methods inherited from rosetta.core.pack.task.operation.TaskOperation:
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.core.pack.task.operation.TaskOperation, : utility::tag::Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Used to parse an xml-like tag to load parameters and properties.
|
class RestrictChainToRepackingOperation(RestrictOperationsBase) |
| |
this class is a TaskOperation to prevent repacking of residues not near an interface.
|
| |
- Method resolution order:
- RestrictChainToRepackingOperation
- RestrictOperationsBase
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, chain : int) -> 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.toolbox.task_operations.RestrictChainToRepackingOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation, : rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation) -> rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation
- chain(...) from builtins.PyCapsule
- chain(*args, **kwargs)
Overloaded function.
1. chain(self : rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation, chain : int) -> NoneType
2. chain(rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation) -> int
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.RestrictChainToRepackingOperation, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
|
class RestrictConservedLowDdgOperation(SeqprofConsensusOperation) |
| |
a Task operation that will check whether the amino acid at a
position is conserved in the sequence profile and has an unfavorable
ddG when mutated to ala. all positions that match this criterion will
get set to repacking.
wt ala positions are set to repacking based on seqprof criterion
only.
If the input pose contains a forbidden (i.e. non wildtype ) residue
at an untouchable position, the residue currently in the pose is
also allowed.
|
| |
- Method resolution order:
- RestrictConservedLowDdgOperation
- SeqprofConsensusOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation) -> 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.toolbox.task_operations.RestrictConservedLowDdgOperation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation, : rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation) -> rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname(*args, **kwargs)
Overloaded function.
1. keyname() -> str
2. keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- position_ala_ddG(...) from builtins.PyCapsule
- position_ala_ddG(self : rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation, seqpos : int) -> float
convenience function to query
what the ddG is for a to ala mutation
at a certain position
- position_untouchable(...) from builtins.PyCapsule
- position_untouchable(self : rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation, seqpos : int, seqprof_wt : rosetta.core.chemical.AA) -> bool
returns true if seqpos has a sequence profile
frequency > conservation_cutoff_ and an X->A ddG of >
ddG_cutoff_
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(*args, **kwargs)
Overloaded function.
1. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
2. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- seqprof_wt_aa(...) from builtins.PyCapsule
- seqprof_wt_aa(self : rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation, seqpos : int) -> rosetta.core.chemical.AA
- verbose(...) from builtins.PyCapsule
- verbose(rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation) -> bool
Methods inherited from SeqprofConsensusOperation:
- chain_num(...) from builtins.PyCapsule
- chain_num(*args, **kwargs)
Overloaded function.
1. chain_num(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> int
2. chain_num(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, d : int) -> NoneType
- conservation_cutoff_aligned_segments(...) from builtins.PyCapsule
- conservation_cutoff_aligned_segments(*args, **kwargs)
Overloaded function.
1. conservation_cutoff_aligned_segments(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> float
2. conservation_cutoff_aligned_segments(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, c : float) -> NoneType
- conservation_cutoff_protein_interface_design(...) from builtins.PyCapsule
- conservation_cutoff_protein_interface_design(*args, **kwargs)
Overloaded function.
1. conservation_cutoff_protein_interface_design(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> float
2. conservation_cutoff_protein_interface_design(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, c : float) -> NoneType
- convert_scores_to_probabilities(...) from builtins.PyCapsule
- convert_scores_to_probabilities(*args, **kwargs)
Overloaded function.
1. convert_scores_to_probabilities(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, c : bool) -> NoneType
2. convert_scores_to_probabilities(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> bool
- create_complex_type_generator(...) from builtins.PyCapsule
- create_complex_type_generator(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> rosetta.utility.tag.XMLSchemaComplexTypeGenerator
- debug(...) from builtins.PyCapsule
- debug(*args, **kwargs)
Overloaded function.
1. debug(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, b : bool) -> NoneType
2. debug(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> bool
- keep_native(...) from builtins.PyCapsule
- keep_native(*args, **kwargs)
Overloaded function.
1. keep_native(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> bool
2. keep_native(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, b : bool) -> NoneType
- protein_interface_design(...) from builtins.PyCapsule
- protein_interface_design(*args, **kwargs)
Overloaded function.
1. protein_interface_design(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation
2. protein_interface_design(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, pido : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation) -> NoneType
- restrict_to_aligned_segments(...) from builtins.PyCapsule
- restrict_to_aligned_segments(*args, **kwargs)
Overloaded function.
1. restrict_to_aligned_segments(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation
2. restrict_to_aligned_segments(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, rtas : rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation) -> NoneType
- seqprof(...) from builtins.PyCapsule
- seqprof(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> rosetta.core.sequence.SequenceProfile
- set_ignore_pose_profile_length_mismatch(...) from builtins.PyCapsule
- set_ignore_pose_profile_length_mismatch(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, setting : bool) -> NoneType
- set_seqprof(...) from builtins.PyCapsule
- set_seqprof(*args, **kwargs)
Overloaded function.
1. set_seqprof(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, seqprof : rosetta.core.sequence.SequenceProfile) -> NoneType
Set the sequence profile. If reweight is true, convert the profile into per-residue probabilities first
2. set_seqprof(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, seqprof : rosetta.core.sequence.SequenceProfile, reweight : bool) -> NoneType
Set the sequence profile. If reweight is true, convert the profile into per-residue probabilities first
|
class RestrictIdentitiesAtAlignedPositionsOperation(RestrictOperationsBase) |
| |
this class is a TaskOperation to prevent repacking of residues not near an interface.
|
| |
- Method resolution order:
- RestrictIdentitiesAtAlignedPositionsOperation
- RestrictOperationsBase
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> 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.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, : rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation
- chain(...) from builtins.PyCapsule
- chain(*args, **kwargs)
Overloaded function.
1. chain(self : rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, c : int) -> NoneType
2. chain(rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> int
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> rosetta.core.pack.task.operation.TaskOperation
- design_only_target_residues(...) from builtins.PyCapsule
- design_only_target_residues(*args, **kwargs)
Overloaded function.
1. design_only_target_residues(self : rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, b : bool) -> NoneType
2. design_only_target_residues(rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> bool
- keep_aas(...) from builtins.PyCapsule
- keep_aas(*args, **kwargs)
Overloaded function.
1. keep_aas(self : rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, s : str) -> NoneType
2. keep_aas(rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> str
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- prevent_repacking(...) from builtins.PyCapsule
- prevent_repacking(*args, **kwargs)
Overloaded function.
1. prevent_repacking(rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> bool
2. prevent_repacking(self : rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, b : bool) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- res_ids(...) from builtins.PyCapsule
- res_ids(*args, **kwargs)
Overloaded function.
1. res_ids(rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> rosetta.utility.vector1_unsigned_long
2. res_ids(self : rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, s : rosetta.utility.vector1_unsigned_long) -> NoneType
- restrict_identities(...) from builtins.PyCapsule
- restrict_identities(*args, **kwargs)
Overloaded function.
1. restrict_identities(self : rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, b : bool) -> NoneType
2. restrict_identities(rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> bool
- source_pose(...) from builtins.PyCapsule
- source_pose(self : rosetta.protocols.toolbox.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, s : str) -> NoneType
|
class RestrictIdentitiesOperation(rosetta.core.pack.task.operation.TaskOperation) |
| |
this class is a TaskOperation to prevent repacking of residues not near an interface.
|
| |
- Method resolution order:
- RestrictIdentitiesOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, identities : rosetta.utility.vector1_std_string, prevent_repacking : bool) -> NoneType
3. __init__(handle, rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation) -> 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.toolbox.task_operations.RestrictIdentitiesOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation, : rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation) -> rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation) -> rosetta.core.pack.task.operation.TaskOperation
- identities(...) from builtins.PyCapsule
- identities(*args, **kwargs)
Overloaded function.
1. identities(rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation) -> rosetta.utility.vector1_std_string
2. identities(self : rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation, residues_vec : rosetta.utility.vector1_std_string) -> NoneType
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- prevent_repacking(...) from builtins.PyCapsule
- prevent_repacking(*args, **kwargs)
Overloaded function.
1. prevent_repacking(rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation) -> bool
2. prevent_repacking(self : rosetta.protocols.toolbox.task_operations.RestrictIdentitiesOperation, prevent_repacking : bool) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
|
class RestrictInterGroupVectorOperation(rosetta.core.pack.task.operation.TaskOperation) |
| | |
- Method resolution order:
- RestrictInterGroupVectorOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- CB_dist_cutoff(...) from builtins.PyCapsule
- CB_dist_cutoff(self : rosetta.protocols.toolbox.task_operations.RestrictInterGroupVectorOperation, CB_dist_cutoff : float) -> NoneType
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, group : rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, CB_dist_cutoff : float, nearby_atom_cutoff : float, vector_angle_cutoff : float, vector_dist_cutoff : float) -> NoneType
3. __init__(self : handle, one_group : (rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t), CB_dist_cutoff : float, nearby_atom_cutoff : float, vector_angle_cutoff : float, vector_dist_cutoff : float) -> 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.toolbox.task_operations.RestrictInterGroupVectorOperation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
apply
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictInterGroupVectorOperation, : rosetta.protocols.toolbox.task_operations.RestrictInterGroupVectorOperation) -> rosetta.protocols.toolbox.task_operations.RestrictInterGroupVectorOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictInterGroupVectorOperation) -> rosetta.core.pack.task.operation.TaskOperation
make clone
- insert_pair(...) from builtins.PyCapsule
- insert_pair(self : rosetta.protocols.toolbox.task_operations.RestrictInterGroupVectorOperation, pair : (rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t)) -> NoneType
setters for member data
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- nearby_atom_cutoff(...) from builtins.PyCapsule
- nearby_atom_cutoff(self : rosetta.protocols.toolbox.task_operations.RestrictInterGroupVectorOperation, nearby_atom_cutoff : float) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- vector_angle_cutoff(...) from builtins.PyCapsule
- vector_angle_cutoff(self : rosetta.protocols.toolbox.task_operations.RestrictInterGroupVectorOperation, vector_angle_cutoff : float) -> NoneType
- vector_dist_cutoff(...) from builtins.PyCapsule
- vector_dist_cutoff(self : rosetta.protocols.toolbox.task_operations.RestrictInterGroupVectorOperation, vector_dist_cutoff : float) -> NoneType
Methods inherited from rosetta.core.pack.task.operation.TaskOperation:
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.core.pack.task.operation.TaskOperation, : utility::tag::Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Used to parse an xml-like tag to load parameters and properties.
|
class RestrictNativeResiduesOperation(rosetta.core.pack.task.operation.TaskOperation) |
| | |
- Method resolution order:
- RestrictNativeResiduesOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> 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.toolbox.task_operations.RestrictNativeResiduesOperation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
apply
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictNativeResiduesOperation, : rosetta.protocols.toolbox.task_operations.RestrictNativeResiduesOperation) -> rosetta.protocols.toolbox.task_operations.RestrictNativeResiduesOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictNativeResiduesOperation) -> rosetta.core.pack.task.operation.TaskOperation
make clone
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.RestrictNativeResiduesOperation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- prevent_repacking(...) from builtins.PyCapsule
- prevent_repacking(*args, **kwargs)
Overloaded function.
1. prevent_repacking(rosetta.protocols.toolbox.task_operations.RestrictNativeResiduesOperation) -> bool
2. prevent_repacking(self : rosetta.protocols.toolbox.task_operations.RestrictNativeResiduesOperation, prev : bool) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- reference_pose(...) from builtins.PyCapsule
- reference_pose(*args, **kwargs)
Overloaded function.
1. reference_pose(rosetta.protocols.toolbox.task_operations.RestrictNativeResiduesOperation) -> rosetta.core.pose.Pose
2. reference_pose(self : rosetta.protocols.toolbox.task_operations.RestrictNativeResiduesOperation, reference_pose : rosetta.core.pose.Pose) -> NoneType
3. reference_pose(self : rosetta.protocols.toolbox.task_operations.RestrictNativeResiduesOperation, pose : rosetta.core.pose.Pose) -> NoneType
- verbose(...) from builtins.PyCapsule
- verbose(*args, **kwargs)
Overloaded function.
1. verbose(rosetta.protocols.toolbox.task_operations.RestrictNativeResiduesOperation) -> bool
2. verbose(self : rosetta.protocols.toolbox.task_operations.RestrictNativeResiduesOperation, verb : bool) -> NoneType
|
class RestrictOperationsBase(rosetta.core.pack.task.operation.TaskOperation) |
| |
This base class defines an interface for TaskOperations which use PoseMetricCalculators to pick out certain residues in a pose. The apply function takes a vector of PoseMetricCalculators and a vector of calculation queries, and uses those queries to shape the PackerTask. This was designed to work with NeighborsByDistanceCalculator, NeighborhoodByDistanceCalculator, and InterfaceNeighborDefinitionCalculator; in general it works when the calculators can return MetricValue< std::set< core::Size > > (a std::set of resids).
|
| |
- Method resolution order:
- RestrictOperationsBase
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.toolbox.task_operations.RestrictOperationsBase) -> NoneType
2. __init__(rosetta.protocols.toolbox.task_operations.RestrictOperationsBase, rosetta.protocols.toolbox.task_operations.RestrictOperationsBase) -> 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.toolbox.task_operations.RestrictOperationsBase, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictOperationsBase, : rosetta.protocols.toolbox.task_operations.RestrictOperationsBase) -> rosetta.protocols.toolbox.task_operations.RestrictOperationsBase
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictOperationsBase) -> rosetta.core.pack.task.operation.TaskOperation
Methods inherited from rosetta.core.pack.task.operation.TaskOperation:
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.core.pack.task.operation.TaskOperation, : utility::tag::Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Used to parse an xml-like tag to load parameters and properties.
|
class RestrictResiduesToRepackingOperation(RestrictOperationsBase) |
| |
this class is a TaskOperation to prevent repacking of residues not near an interface.
|
| |
- Method resolution order:
- RestrictResiduesToRepackingOperation
- RestrictOperationsBase
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, residues : rosetta.utility.vector1_unsigned_long) -> NoneType
3. __init__(handle, rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation) -> 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.toolbox.task_operations.RestrictResiduesToRepackingOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation, : rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation) -> rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation) -> rosetta.core.pack.task.operation.TaskOperation
- get_residues(...) from builtins.PyCapsule
- get_residues(rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation) -> rosetta.utility.vector1_unsigned_long
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- reference_pdb_id(...) from builtins.PyCapsule
- reference_pdb_id(*args, **kwargs)
Overloaded function.
1. reference_pdb_id(rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation) -> str
2. reference_pdb_id(self : rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation, s : str) -> NoneType
- set_residues(...) from builtins.PyCapsule
- set_residues(self : rosetta.protocols.toolbox.task_operations.RestrictResiduesToRepackingOperation, residues_vec : rosetta.utility.vector1_unsigned_long) -> NoneType
|
class RestrictToAlignedSegmentsOperation(RestrictOperationsBase) |
| |
this class is a TaskOperation to prevent repacking of residues not near an interface.
|
| |
- Method resolution order:
- RestrictToAlignedSegmentsOperation
- RestrictOperationsBase
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> 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.toolbox.task_operations.RestrictToAlignedSegmentsOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation, : rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation) -> rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation
- chain(...) from builtins.PyCapsule
- chain(*args, **kwargs)
Overloaded function.
1. chain(rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation) -> int
2. chain(self : rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation, c : int) -> NoneType
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- repack_shell(...) from builtins.PyCapsule
- repack_shell(*args, **kwargs)
Overloaded function.
1. repack_shell(rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation) -> float
2. repack_shell(self : rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation, r : float) -> NoneType
- start_res(...) from builtins.PyCapsule
- start_res(*args, **kwargs)
Overloaded function.
1. start_res(rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation) -> rosetta.utility.vector1_unsigned_long
2. start_res(self : rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation, s : rosetta.utility.vector1_unsigned_long) -> NoneType
- stop_res(...) from builtins.PyCapsule
- stop_res(*args, **kwargs)
Overloaded function.
1. stop_res(rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation) -> rosetta.utility.vector1_unsigned_long
2. stop_res(self : rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation, s : rosetta.utility.vector1_unsigned_long) -> NoneType
|
class RestrictToInterface(InterfaceTaskOperation) |
| | |
- Method resolution order:
- RestrictToInterface
- InterfaceTaskOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, int) -> NoneType
doc
3. __init__(self : handle, rb_jump_in : int, distance_in : float) -> NoneType
4. __init__(handle, rosetta.utility.vector1_int) -> NoneType
doc
5. __init__(self : handle, rb_jump_in : rosetta.utility.vector1_int, distance_in : float) -> NoneType
6. __init__(self : handle, rb_jump_in : rosetta.utility.vector1_int, loop_residues : ObjexxFCL::FArray1D<bool>) -> NoneType
7. __init__(self : handle, loop_residues : ObjexxFCL::FArray1D<bool>) -> NoneType
8. __init__(self : handle, loop_residues : rosetta.utility.vector1_bool) -> NoneType
9. __init__(handle, rosetta.protocols.toolbox.task_operations.RestrictToInterface) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_jump(...) from builtins.PyCapsule
- add_jump(self : rosetta.protocols.toolbox.task_operations.RestrictToInterface, rb_jump_in : int) -> NoneType
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.toolbox.task_operations.RestrictToInterface, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictToInterface, : rosetta.protocols.toolbox.task_operations.RestrictToInterface) -> rosetta.protocols.toolbox.task_operations.RestrictToInterface
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictToInterface) -> rosetta.core.pack.task.operation.TaskOperation
- distance(...) from builtins.PyCapsule
- distance(self : rosetta.protocols.toolbox.task_operations.RestrictToInterface, distance_in : float) -> NoneType
- keyname(...) from builtins.PyCapsule
- keyname(*args, **kwargs)
Overloaded function.
1. keyname() -> str
2. keyname() -> str
3. keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.RestrictToInterface, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(*args, **kwargs)
Overloaded function.
1. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
2. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
3. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- rb_jump(...) from builtins.PyCapsule
- rb_jump(self : rosetta.protocols.toolbox.task_operations.RestrictToInterface, jump_in : int) -> NoneType
- symmetric_task(...) from builtins.PyCapsule
- symmetric_task(self : rosetta.protocols.toolbox.task_operations.RestrictToInterface, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
Methods inherited from InterfaceTaskOperation:
- add_movable_jump(...) from builtins.PyCapsule
- add_movable_jump(self : rosetta.protocols.toolbox.task_operations.InterfaceTaskOperation, additional_jump : int) -> NoneType
- movable_jumps(...) from builtins.PyCapsule
- movable_jumps(rosetta.protocols.toolbox.task_operations.InterfaceTaskOperation) -> rosetta.utility.vector1_int
- set_movable_jumps(...) from builtins.PyCapsule
- set_movable_jumps(self : rosetta.protocols.toolbox.task_operations.InterfaceTaskOperation, movable_jumps : rosetta.utility.vector1_int) -> NoneType
|
class RestrictToInterfaceOperation(RestrictOperationsBase) |
| |
this class is a TaskOperation to prevent repacking of residues not near an interface.
|
| |
- Method resolution order:
- RestrictToInterfaceOperation
- RestrictOperationsBase
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
doc
2. __init__(handle, int) -> NoneType
doc
3. __init__(self : handle, upper_chain : int, lower_chain : int) -> NoneType
4. __init__(self : handle, calculator : str) -> NoneType
5. __init__(handle, rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation) -> 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.toolbox.task_operations.RestrictToInterfaceOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation, : rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation) -> rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictToInterfaceOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
Methods inherited from rosetta.core.pack.task.operation.TaskOperation:
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.core.pack.task.operation.TaskOperation, : utility::tag::Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Used to parse an xml-like tag to load parameters and properties.
|
class RestrictToInterfaceVectorOperation(InterfaceTaskOperation) |
| |
this class is a TaskOperation to prevent repacking of residues not near an interface.
|
| |
- Method resolution order:
- RestrictToInterfaceVectorOperation
- InterfaceTaskOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- CB_dist_cutoff(...) from builtins.PyCapsule
- CB_dist_cutoff(self : rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation, CB_dist_cutoff : float) -> NoneType
Commenting out to fix PyRosetta build void jump_num( int jump_num);
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, lower_chain_id : int, upper_chain_id : int) -> NoneType
3. __init__(self : handle, lower_chain : int, upper_chain : int, CB_dist_cutoff : float, nearby_atom_cutoff : float, vector_angle_cutoff : float, vector_dist_cutoff : float) -> NoneType
4. __init__(self : handle, movable_jumps : rosetta.utility.vector1_int) -> NoneType
5. __init__(self : handle, movable_jumps : rosetta.utility.vector1_int, CB_dist_cutoff : float, nearby_atom_cutoff : float, vector_angle_cutoff : float, vector_dist_cutoff : float) -> 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.toolbox.task_operations.RestrictToInterfaceVectorOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation, : rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation) -> rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname(*args, **kwargs)
Overloaded function.
1. keyname() -> str
2. keyname() -> str
3. keyname() -> str
- lower_chain(...) from builtins.PyCapsule
- lower_chain(*args, **kwargs)
Overloaded function.
1. lower_chain(self : rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation, lower_chain : int) -> NoneType
2. lower_chain(self : rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation, lower_chain : rosetta.utility.vector1_unsigned_long) -> NoneType
- nearby_atom_cutoff(...) from builtins.PyCapsule
- nearby_atom_cutoff(self : rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation, nearby_atom_cutoff : float) -> NoneType
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
parse_tag function for rosetta scripts
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(*args, **kwargs)
Overloaded function.
1. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
2. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
3. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- upper_chain(...) from builtins.PyCapsule
- upper_chain(*args, **kwargs)
Overloaded function.
1. upper_chain(self : rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation, upper_chain : int) -> NoneType
2. upper_chain(self : rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation, upper_chain : rosetta.utility.vector1_unsigned_long) -> NoneType
- vector_angle_cutoff(...) from builtins.PyCapsule
- vector_angle_cutoff(self : rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation, vector_angle_cutoff : float) -> NoneType
- vector_dist_cutoff(...) from builtins.PyCapsule
- vector_dist_cutoff(self : rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation, vector_dist_cutoff : float) -> NoneType
Methods inherited from InterfaceTaskOperation:
- add_movable_jump(...) from builtins.PyCapsule
- add_movable_jump(self : rosetta.protocols.toolbox.task_operations.InterfaceTaskOperation, additional_jump : int) -> NoneType
- movable_jumps(...) from builtins.PyCapsule
- movable_jumps(rosetta.protocols.toolbox.task_operations.InterfaceTaskOperation) -> rosetta.utility.vector1_int
- set_movable_jumps(...) from builtins.PyCapsule
- set_movable_jumps(self : rosetta.protocols.toolbox.task_operations.InterfaceTaskOperation, movable_jumps : rosetta.utility.vector1_int) -> NoneType
|
class RestrictToLoops(rosetta.core.pack.task.operation.TaskOperation) |
| | |
- Method resolution order:
- RestrictToLoops
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.RestrictToLoops) -> 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.toolbox.task_operations.RestrictToLoops, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
Apply this operation to the packer task.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictToLoops, rhs : rosetta.protocols.toolbox.task_operations.RestrictToLoops) -> rosetta.protocols.toolbox.task_operations.RestrictToLoops
Assignment operator.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictToLoops) -> rosetta.core.pack.task.operation.TaskOperation
Return a deep-copied OP.
- design_loop(...) from builtins.PyCapsule
- design_loop(rosetta.protocols.toolbox.task_operations.RestrictToLoops) -> bool
Return true if design is allowed.
- keyname(...) from builtins.PyCapsule
- keyname(*args, **kwargs)
Overloaded function.
1. keyname() -> str
2. keyname() -> str
- loops(...) from builtins.PyCapsule
- loops(rosetta.protocols.toolbox.task_operations.RestrictToLoops) -> rosetta.protocols.loops.Loops
Return the loops allowed to pack.
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.RestrictToLoops, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Configure from a RosettaScripts XML tag.
- provide_attributes(...) from builtins.PyCapsule
- provide_attributes(attributes : rosetta.std.list_utility_tag_XMLSchemaAttribute_std_allocator_utility_tag_XMLSchemaAttribute_t) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(*args, **kwargs)
Overloaded function.
1. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
2. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- restrict_only_design_to_loops(...) from builtins.PyCapsule
- restrict_only_design_to_loops(rosetta.protocols.toolbox.task_operations.RestrictToLoops) -> bool
Return true if we are restricting to only design.
AKA RestrictDesignToLoops.
- set_design_loop(...) from builtins.PyCapsule
- set_design_loop(self : rosetta.protocols.toolbox.task_operations.RestrictToLoops, design_loop : bool) -> NoneType
Specify whether or not design is allowed.
- set_loops(...) from builtins.PyCapsule
- set_loops(self : rosetta.protocols.toolbox.task_operations.RestrictToLoops, loops : rosetta.protocols.loops.Loops) -> NoneType
Specify the loops that will be allowed to pack.
- set_loops_from_file(...) from builtins.PyCapsule
- set_loops_from_file(self : rosetta.protocols.toolbox.task_operations.RestrictToLoops, loops_file : str) -> NoneType
Specify the loops that will be allowed to pack.
- set_restrict_only_design_to_loops(...) from builtins.PyCapsule
- set_restrict_only_design_to_loops(self : rosetta.protocols.toolbox.task_operations.RestrictToLoops, restrict_only_design : bool) -> NoneType
Specify whether to restrict only design to loops/neighbors
AKA RestrictDesignToLoops. Does not disable packing for any residue.
Implies and sets design_loop to true.
|
class RestrictToLoopsAndNeighbors(RestrictToLoops) |
| |
This class allows the selection for packing (and possibly design) of residues contained in a Loops object as
well as the neighbors within a specified cutoff distance, with the default and maximum cutoff at 10.0 A.
|
| |
- Method resolution order:
- RestrictToLoopsAndNeighbors
- RestrictToLoops
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors) -> 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.toolbox.task_operations.RestrictToLoopsAndNeighbors, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors, rhs : rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors) -> rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors
Assignment operator.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors) -> rosetta.core.pack.task.operation.TaskOperation
RestrictToLoops::clone
- cutoff_distance(...) from builtins.PyCapsule
- cutoff_distance(rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors) -> float
- design_neighbors(...) from builtins.PyCapsule
- design_neighbors(rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors) -> bool
- include_neighbors(...) from builtins.PyCapsule
- include_neighbors(rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors) -> bool
- keyname(...) from builtins.PyCapsule
- keyname(*args, **kwargs)
Overloaded function.
1. keyname() -> str
2. keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
RestrictToLoops::parse_tag
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(*args, **kwargs)
Overloaded function.
1. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
2. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_cutoff_distance(...) from builtins.PyCapsule
- set_cutoff_distance(self : rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors, cutoff_distance : float) -> NoneType
- set_design_neighbors(...) from builtins.PyCapsule
- set_design_neighbors(self : rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors, design_neighbors : bool) -> NoneType
- set_include_neighbors(...) from builtins.PyCapsule
- set_include_neighbors(self : rosetta.protocols.toolbox.task_operations.RestrictToLoopsAndNeighbors, include_neighbors : bool) -> NoneType
Methods inherited from RestrictToLoops:
- design_loop(...) from builtins.PyCapsule
- design_loop(rosetta.protocols.toolbox.task_operations.RestrictToLoops) -> bool
Return true if design is allowed.
- loops(...) from builtins.PyCapsule
- loops(rosetta.protocols.toolbox.task_operations.RestrictToLoops) -> rosetta.protocols.loops.Loops
Return the loops allowed to pack.
- provide_attributes(...) from builtins.PyCapsule
- provide_attributes(attributes : rosetta.std.list_utility_tag_XMLSchemaAttribute_std_allocator_utility_tag_XMLSchemaAttribute_t) -> NoneType
- restrict_only_design_to_loops(...) from builtins.PyCapsule
- restrict_only_design_to_loops(rosetta.protocols.toolbox.task_operations.RestrictToLoops) -> bool
Return true if we are restricting to only design.
AKA RestrictDesignToLoops.
- set_design_loop(...) from builtins.PyCapsule
- set_design_loop(self : rosetta.protocols.toolbox.task_operations.RestrictToLoops, design_loop : bool) -> NoneType
Specify whether or not design is allowed.
- set_loops(...) from builtins.PyCapsule
- set_loops(self : rosetta.protocols.toolbox.task_operations.RestrictToLoops, loops : rosetta.protocols.loops.Loops) -> NoneType
Specify the loops that will be allowed to pack.
- set_loops_from_file(...) from builtins.PyCapsule
- set_loops_from_file(self : rosetta.protocols.toolbox.task_operations.RestrictToLoops, loops_file : str) -> NoneType
Specify the loops that will be allowed to pack.
- set_restrict_only_design_to_loops(...) from builtins.PyCapsule
- set_restrict_only_design_to_loops(self : rosetta.protocols.toolbox.task_operations.RestrictToLoops, restrict_only_design : bool) -> NoneType
Specify whether to restrict only design to loops/neighbors
AKA RestrictDesignToLoops. Does not disable packing for any residue.
Implies and sets design_loop to true.
|
class RestrictToMoveMapChiOperation(rosetta.core.pack.task.operation.TaskOperation) |
| |
A TaskOperation that accepts a movemap and restricts chi that are false to either packing or design.
Does not turn anything on, just like the rest of the RestrictTo operations.
|
| |
- Method resolution order:
- RestrictToMoveMapChiOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, movemap : rosetta.core.kinematics.MoveMap) -> NoneType
3. __init__(handle, rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation) -> 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.toolbox.task_operations.RestrictToMoveMapChiOperation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation, : rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation) -> rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_cutoff_distance(...) from builtins.PyCapsule
- set_cutoff_distance(self : rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation, cutoff : float) -> NoneType
Cutoff distance for neighbor detection. Default is 10 A.
- set_design(...) from builtins.PyCapsule
- set_design(self : rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation, setting : bool) -> NoneType
Set residues from movemap to designable. Default false.
- set_include_neighbors(...) from builtins.PyCapsule
- set_include_neighbors(self : rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation, setting : bool) -> NoneType
Set to use neighbor residues in vacinity of movemap chi residues for packing. Default False.
- set_movemap(...) from builtins.PyCapsule
- set_movemap(self : rosetta.protocols.toolbox.task_operations.RestrictToMoveMapChiOperation, movemap : rosetta.core.kinematics.MoveMap) -> NoneType
Methods inherited from rosetta.core.pack.task.operation.TaskOperation:
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.core.pack.task.operation.TaskOperation, : utility::tag::Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Used to parse an xml-like tag to load parameters and properties.
|
class RestrictToNeighborhoodOperation(RestrictOperationsBase) |
| |
this class is a TaskOperation to prevent repacking of residues not near a neighborhood. Internally it just user NeighborhoodByDistanceCalculator to do all the work. You are allowed a "calculator name" interface to tell it which you-constructed calculator to use, or you can give it a set of residues and a desired distance cutoff to have it define the calculator itself. (There is no need to use both interfaces).
|
| |
- Method resolution order:
- RestrictToNeighborhoodOperation
- RestrictOperationsBase
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation) -> NoneType
3. __init__(self : handle, central_residues : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, dist_cutoff : float) -> NoneType
4. __init__(self : handle, central_residues : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType
5. __init__(self : handle, calculator : str) -> 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.toolbox.task_operations.RestrictToNeighborhoodOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation, rhs : rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation) -> rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation
assignment operator
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation) -> rosetta.core.pack.task.operation.TaskOperation
- get_calculator(...) from builtins.PyCapsule
- get_calculator(rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation) -> rosetta.protocols.toolbox.pose_metric_calculators.NeighborhoodByDistanceCalculator
look up actual calculator object
- get_calculator_name(...) from builtins.PyCapsule
- get_calculator_name(rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation) -> str
trivially returns underlying calculator string name
- get_central_residues(...) from builtins.PyCapsule
- get_central_residues(rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t
this nontrivially checks the underlying calculator
- get_distance_cutoff(...) from builtins.PyCapsule
- get_distance_cutoff(rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation) -> float
this nontrivially checks the underlying calculator
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- set_calculator_by_name(...) from builtins.PyCapsule
- set_calculator_by_name(self : rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation, calculator_name : str) -> NoneType
- set_neighborhood_parameters(...) from builtins.PyCapsule
- set_neighborhood_parameters(*args, **kwargs)
Overloaded function.
1. set_neighborhood_parameters(self : rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation, central_residues : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, dist_cutoff : float) -> NoneType
reskin of normal make_calculator
2. set_neighborhood_parameters(self : rosetta.protocols.toolbox.task_operations.RestrictToNeighborhoodOperation, central_residues : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType
reskin of normal make_calculator
Methods inherited from rosetta.core.pack.task.operation.TaskOperation:
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.core.pack.task.operation.TaskOperation, : utility::tag::Tag, : rosetta.basic.datacache.DataMap) -> NoneType
Used to parse an xml-like tag to load parameters and properties.
|
class RestrictToTerminiOperation(rosetta.core.pack.task.operation.TaskOperation) |
| | |
- Method resolution order:
- RestrictToTerminiOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, chain : int, restrict_n_terminus : bool, restrict_c_terminus : bool) -> NoneType
3. __init__(handle, rosetta.protocols.toolbox.task_operations.RestrictToTerminiOperation) -> 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.toolbox.task_operations.RestrictToTerminiOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.RestrictToTerminiOperation, : rosetta.protocols.toolbox.task_operations.RestrictToTerminiOperation) -> rosetta.protocols.toolbox.task_operations.RestrictToTerminiOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.RestrictToTerminiOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.RestrictToTerminiOperation, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
|
class STMStoredTask(rosetta.basic.datacache.CacheableData) |
| | |
- Method resolution order:
- STMStoredTask
- rosetta.basic.datacache.CacheableData
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.STMStoredTask) -> 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.toolbox.task_operations.STMStoredTask, : rosetta.protocols.toolbox.task_operations.STMStoredTask) -> rosetta.protocols.toolbox.task_operations.STMStoredTask
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.STMStoredTask) -> rosetta.basic.datacache.CacheableData
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.toolbox.task_operations.STMStoredTask) -> rosetta.basic.datacache.CacheableData
- get_task(...) from builtins.PyCapsule
- get_task(self : rosetta.protocols.toolbox.task_operations.STMStoredTask, task_name : str) -> rosetta.core.pack.task.PackerTask
- has_task(...) from builtins.PyCapsule
- has_task(self : rosetta.protocols.toolbox.task_operations.STMStoredTask, task_name : str) -> bool
- set_task(...) from builtins.PyCapsule
- set_task(self : rosetta.protocols.toolbox.task_operations.STMStoredTask, task : rosetta.core.pack.task.PackerTask, task_name : str) -> NoneType
Methods inherited from rosetta.basic.datacache.CacheableData:
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData
self pointers
2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t
2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t
|
class SelectByDeltaScoreOperation(rosetta.core.pack.task.operation.TaskOperation) |
| | |
- Method resolution order:
- SelectByDeltaScoreOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation) -> 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.toolbox.task_operations.SelectByDeltaScoreOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation, : rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation) -> rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation) -> rosetta.core.pack.task.operation.TaskOperation
make clone
- individual_hbonds(...) from builtins.PyCapsule
- individual_hbonds(*args, **kwargs)
Overloaded function.
1. individual_hbonds(rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation) -> bool
2. individual_hbonds(self : rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation, individual_hbonds : bool) -> NoneType
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- lower(...) from builtins.PyCapsule
- lower(*args, **kwargs)
Overloaded function.
1. lower(rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation) -> bool
2. lower(self : rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation, lower : bool) -> NoneType
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- reference_pose(...) from builtins.PyCapsule
- reference_pose(*args, **kwargs)
Overloaded function.
1. reference_pose(rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation) -> rosetta.core.pose.Pose
2. reference_pose(self : rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation, reference_pose : rosetta.core.pose.Pose) -> NoneType
- score_type(...) from builtins.PyCapsule
- score_type(*args, **kwargs)
Overloaded function.
1. score_type(rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation) -> rosetta.core.scoring.ScoreType
2. score_type(self : rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation, st : rosetta.core.scoring.ScoreType) -> NoneType
- score_type_name(...) from builtins.PyCapsule
- score_type_name(*args, **kwargs)
Overloaded function.
1. score_type_name(rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation) -> str
2. score_type_name(self : rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation, name : str) -> NoneType
- scorefxn(...) from builtins.PyCapsule
- scorefxn(*args, **kwargs)
Overloaded function.
1. scorefxn(rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation) -> rosetta.core.scoring.ScoreFunction
2. scorefxn(self : rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- threshold(...) from builtins.PyCapsule
- threshold(*args, **kwargs)
Overloaded function.
1. threshold(rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation) -> float
2. threshold(self : rosetta.protocols.toolbox.task_operations.SelectByDeltaScoreOperation, threshold : float) -> NoneType
|
class SelectByDensityFitOperation(rosetta.core.pack.task.operation.TaskOperation) |
| | |
- Method resolution order:
- SelectByDensityFitOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
doc
2. __init__(handle, float) -> NoneType
doc
3. __init__(self : handle, threshold : float, invert : bool) -> 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.toolbox.task_operations.SelectByDensityFitOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.SelectByDensityFitOperation, : rosetta.protocols.toolbox.task_operations.SelectByDensityFitOperation) -> rosetta.protocols.toolbox.task_operations.SelectByDensityFitOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.SelectByDensityFitOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.SelectByDensityFitOperation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
|
class SelectBySASAOperation(rosetta.core.pack.task.operation.TaskOperation) |
| | |
- Method resolution order:
- SelectBySASAOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
doc
2. __init__(handle, str) -> NoneType
doc
3. __init__(handle, str, str) -> NoneType
doc
4. __init__(handle, str, str, float) -> NoneType
doc
5. __init__(handle, str, str, float, float) -> NoneType
doc
6. __init__(handle, str, str, float, float, float) -> NoneType
doc
7. __init__(handle, str, str, float, float, float, str) -> NoneType
doc
8. __init__(handle, str, str, float, float, float, str, str) -> NoneType
doc
9. __init__(handle, str, str, float, float, float, str, str, bool) -> NoneType
doc
10. __init__(handle, str, str, float, float, float, str, str, bool, bool) -> NoneType
doc
11. __init__(handle, str, str, float, float, float, str, str, bool, bool, bool) -> NoneType
doc
12. __init__(self : handle, mode : str, state : str, probe_radius : float, core_asa : float, surface_asa : float, jump_nums : str, sym_dof_names : str, core : bool, boundary : bool, surface : bool, verbose : bool) -> NoneType
13. __init__(handle, rosetta.protocols.toolbox.task_operations.SelectBySASAOperation) -> 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.toolbox.task_operations.SelectBySASAOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.SelectBySASAOperation, : rosetta.protocols.toolbox.task_operations.SelectBySASAOperation) -> rosetta.protocols.toolbox.task_operations.SelectBySASAOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.SelectBySASAOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.SelectBySASAOperation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
|
class SelectResiduesWithinChainOperation(RestrictOperationsBase) |
| |
this class is a TaskOperation to prevent repacking of residues not near an interface.
|
| |
- Method resolution order:
- SelectResiduesWithinChainOperation
- RestrictOperationsBase
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_res(...) from builtins.PyCapsule
- add_res(self : rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation, resid : int) -> NoneType
- allow_design(...) from builtins.PyCapsule
- allow_design(*args, **kwargs)
Overloaded function.
1. allow_design(self : rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation, b : bool) -> NoneType
2. allow_design(rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation) -> bool
- allow_repacking(...) from builtins.PyCapsule
- allow_repacking(*args, **kwargs)
Overloaded function.
1. allow_repacking(self : rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation, b : bool) -> NoneType
2. allow_repacking(rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation) -> bool
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation, : rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation) -> rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation
- chain(...) from builtins.PyCapsule
- chain(*args, **kwargs)
Overloaded function.
1. chain(rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation) -> int
2. chain(self : rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation, c : int) -> NoneType
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- modify_unselected_residues(...) from builtins.PyCapsule
- modify_unselected_residues(*args, **kwargs)
Overloaded function.
1. modify_unselected_residues(self : rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation, b : bool) -> NoneType
2. modify_unselected_residues(rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation) -> bool
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- resid(...) from builtins.PyCapsule
- resid(rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation) -> rosetta.utility.vector1_unsigned_long
|
class SeqprofConsensusOperation(rosetta.core.pack.task.operation.TaskOperation) |
| | |
- Method resolution order:
- SeqprofConsensusOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> 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.toolbox.task_operations.SeqprofConsensusOperation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
apply
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation
- chain_num(...) from builtins.PyCapsule
- chain_num(*args, **kwargs)
Overloaded function.
1. chain_num(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> int
2. chain_num(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, d : int) -> NoneType
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> rosetta.core.pack.task.operation.TaskOperation
make clone
- conservation_cutoff_aligned_segments(...) from builtins.PyCapsule
- conservation_cutoff_aligned_segments(*args, **kwargs)
Overloaded function.
1. conservation_cutoff_aligned_segments(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> float
2. conservation_cutoff_aligned_segments(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, c : float) -> NoneType
- conservation_cutoff_protein_interface_design(...) from builtins.PyCapsule
- conservation_cutoff_protein_interface_design(*args, **kwargs)
Overloaded function.
1. conservation_cutoff_protein_interface_design(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> float
2. conservation_cutoff_protein_interface_design(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, c : float) -> NoneType
- convert_scores_to_probabilities(...) from builtins.PyCapsule
- convert_scores_to_probabilities(*args, **kwargs)
Overloaded function.
1. convert_scores_to_probabilities(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, c : bool) -> NoneType
2. convert_scores_to_probabilities(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> bool
- create_complex_type_generator(...) from builtins.PyCapsule
- create_complex_type_generator(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> rosetta.utility.tag.XMLSchemaComplexTypeGenerator
- debug(...) from builtins.PyCapsule
- debug(*args, **kwargs)
Overloaded function.
1. debug(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, b : bool) -> NoneType
2. debug(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> bool
- keep_native(...) from builtins.PyCapsule
- keep_native(*args, **kwargs)
Overloaded function.
1. keep_native(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> bool
2. keep_native(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, b : bool) -> NoneType
- keyname(...) from builtins.PyCapsule
- keyname(*args, **kwargs)
Overloaded function.
1. keyname() -> str
2. keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- protein_interface_design(...) from builtins.PyCapsule
- protein_interface_design(*args, **kwargs)
Overloaded function.
1. protein_interface_design(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation
2. protein_interface_design(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, pido : rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(*args, **kwargs)
Overloaded function.
1. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
2. provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- restrict_to_aligned_segments(...) from builtins.PyCapsule
- restrict_to_aligned_segments(*args, **kwargs)
Overloaded function.
1. restrict_to_aligned_segments(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation
2. restrict_to_aligned_segments(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, rtas : rosetta.protocols.toolbox.task_operations.RestrictToAlignedSegmentsOperation) -> NoneType
- seqprof(...) from builtins.PyCapsule
- seqprof(rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation) -> rosetta.core.sequence.SequenceProfile
- set_ignore_pose_profile_length_mismatch(...) from builtins.PyCapsule
- set_ignore_pose_profile_length_mismatch(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, setting : bool) -> NoneType
- set_seqprof(...) from builtins.PyCapsule
- set_seqprof(*args, **kwargs)
Overloaded function.
1. set_seqprof(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, seqprof : rosetta.core.sequence.SequenceProfile) -> NoneType
Set the sequence profile. If reweight is true, convert the profile into per-residue probabilities first
2. set_seqprof(self : rosetta.protocols.toolbox.task_operations.SeqprofConsensusOperation, seqprof : rosetta.core.sequence.SequenceProfile, reweight : bool) -> NoneType
Set the sequence profile. If reweight is true, convert the profile into per-residue probabilities first
|
class StoreCombinedStoredTasksMover(rosetta.protocols.moves.Mover) |
| |
mover that can be used to save or restore a task at an arbitrary
point during a rosetta scripts protocol. other task operations, movers,
or filters can be set up to access tasks saved by this mover during their
apply calls.
|
| |
- Method resolution order:
- StoreCombinedStoredTasksMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover) -> 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.toolbox.task_operations.StoreCombinedStoredTasksMover, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover, : rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover) -> rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover) -> str
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
- 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 StoreCompoundTaskMover(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- StoreCompoundTaskMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- CompoundDesignableTask(...) from builtins.PyCapsule
- CompoundDesignableTask(self : rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover, pose : rosetta.core.pose.Pose, total_residue : int, task : rosetta.core.pack.task.PackerTask) -> NoneType
- CompoundPackableTask(...) from builtins.PyCapsule
- CompoundPackableTask(self : rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover, pose : rosetta.core.pose.Pose, total_residue : int, task : rosetta.core.pack.task.PackerTask) -> NoneType
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover) -> 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.toolbox.task_operations.StoreCompoundTaskMover, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover, : rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover) -> rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover) -> rosetta.protocols.moves.Mover
- factory_begin(...) from builtins.PyCapsule
- factory_begin(rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover) -> __gnu_cxx::__normal_iterator<std::pair<std::shared_ptr<core::pack::task::TaskFactory>, protocols::toolbox::task_operations::boolean_operations> const*, std::vector<std::pair<std::shared_ptr<core::pack::task::TaskFactory>, protocols::toolbox::task_operations::boolean_operations>, std::allocator<std::pair<std::shared_ptr<core::pack::task::TaskFactory>, protocols::toolbox::task_operations::boolean_operations> > > >
- factory_clear(...) from builtins.PyCapsule
- factory_clear(rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover) -> NoneType
- factory_end(...) from builtins.PyCapsule
- factory_end(rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover) -> __gnu_cxx::__normal_iterator<std::pair<std::shared_ptr<core::pack::task::TaskFactory>, protocols::toolbox::task_operations::boolean_operations> const*, std::vector<std::pair<std::shared_ptr<core::pack::task::TaskFactory>, protocols::toolbox::task_operations::boolean_operations>, std::allocator<std::pair<std::shared_ptr<core::pack::task::TaskFactory>, protocols::toolbox::task_operations::boolean_operations> > > >
- false_behavior(...) from builtins.PyCapsule
- false_behavior(self : rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover, fb : str) -> NoneType
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover) -> str
- invert(...) from builtins.PyCapsule
- invert(self : rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover, inv : bool) -> NoneType
- mode(...) from builtins.PyCapsule
- mode(self : rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover, md : str) -> NoneType
- overwrite(...) from builtins.PyCapsule
- overwrite(self : rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover, ow : bool) -> NoneType
- task_begin(...) from builtins.PyCapsule
- task_begin(rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover) -> __gnu_cxx::__normal_iterator<std::pair<std::shared_ptr<core::pack::task::PackerTask>, protocols::toolbox::task_operations::boolean_operations> const*, std::vector<std::pair<std::shared_ptr<core::pack::task::PackerTask>, protocols::toolbox::task_operations::boolean_operations>, std::allocator<std::pair<std::shared_ptr<core::pack::task::PackerTask>, protocols::toolbox::task_operations::boolean_operations> > > >
- task_clear(...) from builtins.PyCapsule
- task_clear(rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover) -> NoneType
- task_end(...) from builtins.PyCapsule
- task_end(rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover) -> __gnu_cxx::__normal_iterator<std::pair<std::shared_ptr<core::pack::task::PackerTask>, protocols::toolbox::task_operations::boolean_operations> const*, std::vector<std::pair<std::shared_ptr<core::pack::task::PackerTask>, protocols::toolbox::task_operations::boolean_operations>, std::allocator<std::pair<std::shared_ptr<core::pack::task::PackerTask>, protocols::toolbox::task_operations::boolean_operations> > > >
- task_name(...) from builtins.PyCapsule
- task_name(self : rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover, tn : str) -> NoneType
- true_behavior(...) from builtins.PyCapsule
- true_behavior(self : rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover, tb : str) -> NoneType
- verbose(...) from builtins.PyCapsule
- verbose(self : rosetta.protocols.toolbox.task_operations.StoreCompoundTaskMover, verb : bool) -> 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
- 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
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class StoreTaskMover(rosetta.protocols.moves.Mover) |
| |
mover that can be used to save or restore a task at an arbitrary
point during a rosetta scripts protocol. other task operations, movers,
or filters can be set up to access tasks saved by this mover during their
apply calls.
|
| |
- Method resolution order:
- StoreTaskMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.task_operations.StoreTaskMover) -> 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.toolbox.task_operations.StoreTaskMover, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.StoreTaskMover, : rosetta.protocols.toolbox.task_operations.StoreTaskMover) -> rosetta.protocols.toolbox.task_operations.StoreTaskMover
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.StoreTaskMover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.toolbox.task_operations.StoreTaskMover) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.toolbox.task_operations.StoreTaskMover) -> str
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
- 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 ThreadSequenceOperation(RestrictOperationsBase) |
| |
this class is a TaskOperation to prevent repacking of residues not near an interface.
|
| |
- Method resolution order:
- ThreadSequenceOperation
- RestrictOperationsBase
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, seq : str) -> NoneType
3. __init__(handle, rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- allow_design_around(...) from builtins.PyCapsule
- allow_design_around(*args, **kwargs)
Overloaded function.
1. allow_design_around(rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation) -> bool
2. allow_design_around(self : rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation, b : bool) -> NoneType
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation, : rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation) -> rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- start_res(...) from builtins.PyCapsule
- start_res(*args, **kwargs)
Overloaded function.
1. start_res(rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation) -> int
2. start_res(self : rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation, s : int) -> NoneType
- target_sequence(...) from builtins.PyCapsule
- target_sequence(*args, **kwargs)
Overloaded function.
1. target_sequence(self : rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation, seq : str) -> NoneType
2. target_sequence(rosetta.protocols.toolbox.task_operations.ThreadSequenceOperation) -> str
|
|