| | |
- builtins.object
-
- CstAction
- DesignVsNativeComparison
- EnzdesConstraintReporter
- PoseFoundResiduesCombination
- ValueEvaluator
- rosetta.core.fragment.Frame(builtins.object)
-
- EnzdesFlexibleRegion
- rosetta.core.pack.task.operation.TaskOperation(builtins.object)
-
- AddLigandMotifRotamers
- AddRigidBodyLigandConfs
- DetectProteinLigandInterface
- ProteinLigandInterfaceUpweighter
- SetCatalyticResPackBehavior
- rosetta.core.pack.task.operation.TaskOperationCreator(builtins.object)
-
- AddLigandMotifRotamersOperationCreator
- AddRigidBodyLigandConfsCreator
- DetectProteinLigandInterfaceOperationCreator
- ProteinLigandInterfaceUpweighterOperationCreator
- SetCatalyticResPackBehaviorCreator
- rosetta.protocols.filters.Filter(builtins.object)
-
- DiffAtomSasaFilter
- EnzScoreFilter
- EnzdesScorefileFilter
- LigBurialFilter
- LigDSasaFilter
- LigInterfaceEnergyFilter
- RemoveLigandFilter
- RepackWithoutLigandFilter
- ResidueConformerFilter
- rosetta.protocols.filters.FilterCreator(builtins.object)
-
- DiffAtomSasaFilterCreator
- EnzScoreFilterCreator
- EnzdesScorefileFilterCreator
- LigBurialFilterCreator
- LigDSasaFilterCreator
- LigInterfaceEnergyFilterCreator
- RemoveLigandFilterCreator
- RepackWithoutLigandFilterCreator
- ResidueConformerFilterCreator
- rosetta.protocols.jd2.JobInputterCreator(builtins.object)
-
- EnzdesJobInputterCreator
- rosetta.protocols.jd2.JobOutputterCreator(builtins.object)
-
- EnzdesJobOutputterCreator
- rosetta.protocols.jd2.PDBJobInputter(rosetta.protocols.jd2.JobInputter)
-
- EnzdesJobInputter
- rosetta.protocols.jd2.PDBJobOutputter(rosetta.protocols.jd2.FileJobOutputter)
-
- EnzdesJobOutputter
- rosetta.protocols.ligand_docking.LigandBaseProtocol(rosetta.protocols.moves.Mover)
-
- BackboneSampler
- EnzdesBaseProtocol
-
- EnzdesFixBBProtocol
- EnzdesFlexBBProtocol
- SecondaryMatchProtocol
- rosetta.protocols.moves.Mover(builtins.object)
-
- AddOrRemoveMatchCsts
- EnzRepackMinimize
- ModifyStoredRBConfs
-
- ApplyRandomStoredRBConf
- DiversifyStoredRBConfs
- GenerateStoredRBConfs
- MinimizeStoredRBConfs
- PackRotamersMoverPartGreedy
- RepackLigandSiteWithoutLigandMover
- UpdateEnzdesHeaderMover
- rosetta.protocols.moves.MoverCreator(builtins.object)
-
- AddOrRemoveMatchCstsCreator
- BackboneSamplerCreator
- EnzRepackMinimizeCreator
- PackRotamersMoverPartGreedyCreator
- PredesignPerturbMoverCreator
- UpdateEnzdesHeaderMoverCreator
- rosetta.protocols.rigid.RigidBodyPerturbMover(rosetta.protocols.rigid.RigidBodyMover)
-
- PredesignPerturbMover
class AddOrRemoveMatchCsts(rosetta.protocols.moves.Mover) |
| |
A simple wrapper to get the functionality in EnzConstraintIO
into mover format
|
| |
- Method resolution order:
- AddOrRemoveMatchCsts
- 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.enzdes.AddOrRemoveMatchCsts) -> 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.enzdes.AddOrRemoveMatchCsts, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.AddOrRemoveMatchCsts, : rosetta.protocols.enzdes.AddOrRemoveMatchCsts) -> rosetta.protocols.enzdes.AddOrRemoveMatchCsts
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.enzdes.AddOrRemoveMatchCsts) -> rosetta.protocols.moves.Mover
- cstfile(...) from builtins.PyCapsule
- cstfile(self : rosetta.protocols.enzdes.AddOrRemoveMatchCsts, setting : str) -> NoneType
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.enzdes.AddOrRemoveMatchCsts) -> rosetta.protocols.moves.Mover
- get_const_EnzConstraintIO_for_cstfile(...) from builtins.PyCapsule
- get_const_EnzConstraintIO_for_cstfile(*args, **kwargs)
Overloaded function.
1. get_const_EnzConstraintIO_for_cstfile() -> protocols::toolbox::match_enzdes_util::EnzConstraintIO
2. get_const_EnzConstraintIO_for_cstfile(cstfile : str) -> protocols::toolbox::match_enzdes_util::EnzConstraintIO
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.AddOrRemoveMatchCsts) -> str
- set_accept_blocks_missing_header(...) from builtins.PyCapsule
- set_accept_blocks_missing_header(self : rosetta.protocols.enzdes.AddOrRemoveMatchCsts, setting : bool) -> NoneType
- set_cst_action(...) from builtins.PyCapsule
- set_cst_action(self : rosetta.protocols.enzdes.AddOrRemoveMatchCsts, action : rosetta.protocols.enzdes.CstAction) -> NoneType
- set_keep_covalent(...) from builtins.PyCapsule
- set_keep_covalent(self : rosetta.protocols.enzdes.AddOrRemoveMatchCsts, setting : 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
|
class ApplyRandomStoredRBConf(ModifyStoredRBConfs) |
| |
for every ligand that has additional stored rb conformations
in the enzdes cacheable observer, the one currently in the pose gets
exchanged with a random stored one
|
| |
- Method resolution order:
- ApplyRandomStoredRBConf
- ModifyStoredRBConfs
- 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.enzdes.ApplyRandomStoredRBConf) -> 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.enzdes.ApplyRandomStoredRBConf, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.ApplyRandomStoredRBConf, : rosetta.protocols.enzdes.ApplyRandomStoredRBConf) -> rosetta.protocols.enzdes.ApplyRandomStoredRBConf
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.ApplyRandomStoredRBConf) -> str
Methods inherited from ModifyStoredRBConfs:
- closest_orient_atoms_msd(...) from builtins.PyCapsule
- closest_orient_atoms_msd(self : rosetta.protocols.enzdes.ModifyStoredRBConfs, pose : rosetta.core.pose.Pose, confs : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> rosetta.utility.vector1_double
calculates the closest orient atom (i.e. atoms used in rotamer placement
msd between every conf and the confs coming before it in the pose or in the vector
- swap_coordinates_in_pose(...) from builtins.PyCapsule
- swap_coordinates_in_pose(self : rosetta.protocols.enzdes.ModifyStoredRBConfs, pose : rosetta.core.pose.Pose, rescoords : rosetta.core.conformation.Residue) -> NoneType
helper function to exchange coordinates in a pose
this function doesn't actually exchange the residues,
but sets all the coords of pose.residue( rescoords.seqpos() )
to what is in rescoords and vice versa
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
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class BackboneSampler(rosetta.protocols.ligand_docking.LigandBaseProtocol) |
| | |
- Method resolution order:
- BackboneSampler
- rosetta.protocols.ligand_docking.LigandBaseProtocol
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scorefxn : rosetta.core.scoring.ScoreFunction, bb_moves : int, mc_kt : float) -> NoneType
3. __init__(handle, rosetta.protocols.enzdes.BackboneSampler) -> 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.enzdes.BackboneSampler, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.BackboneSampler, : rosetta.protocols.enzdes.BackboneSampler) -> rosetta.protocols.enzdes.BackboneSampler
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.enzdes.BackboneSampler) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.enzdes.BackboneSampler) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.BackboneSampler) -> str
Methods inherited from rosetta.protocols.ligand_docking.LigandBaseProtocol:
- get_ligand_id(...) from builtins.PyCapsule
- get_ligand_id(*args, **kwargs)
Overloaded function.
1. get_ligand_id(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose) -> int
2. get_ligand_id(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, jump_id : int) -> int
- get_ligand_jump_id(...) from builtins.PyCapsule
- get_ligand_jump_id(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose) -> int
- get_non_bb_clashing_rotamers(...) from builtins.PyCapsule
- get_non_bb_clashing_rotamers(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, seqpos : int, scofx : rosetta.core.scoring.ScoreFunction, accepted_rotamers : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
- get_scorefxn(...) from builtins.PyCapsule
- get_scorefxn(*args, **kwargs)
Overloaded function.
1. get_scorefxn(rosetta.protocols.ligand_docking.LigandBaseProtocol) -> rosetta.core.scoring.ScoreFunction
2. get_scorefxn(rosetta.protocols.ligand_docking.LigandBaseProtocol) -> rosetta.core.scoring.ScoreFunction
- reorder_foldtree_around_mobile_regions(...) from builtins.PyCapsule
- reorder_foldtree_around_mobile_regions(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, jump_id : int, mobile_bb : rosetta.utility.vector1_bool, lig_id : int) -> NoneType
- restrain_protein_Calphas(...) from builtins.PyCapsule
- restrain_protein_Calphas(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, is_restrained : rosetta.utility.vector1_bool, restr_func : rosetta.core.scoring.func.Func) -> NoneType
- shared_from_this(...) from builtins.PyCapsule
- shared_from_this(rosetta.protocols.ligand_docking.LigandBaseProtocol) -> rosetta.protocols.ligand_docking.LigandBaseProtocol
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 DetectProteinLigandInterface(rosetta.core.pack.task.operation.TaskOperation) |
| |
Given a set of cut1/cut2/cut3/cut4 distance specifications, alter a
packing task to set residues within alpha carbons within cut1 of a ligand
(or within cut2 with beta carbons facing inwards) to redesign, and within cut3
(or cut4 facing inwards) to repack, and all others to fixed. If a resfile is provided,
only do the detection for those residues set to AUTO in the resfile.
|
| |
- Method resolution order:
- DetectProteinLigandInterface
- 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.enzdes.DetectProteinLigandInterface) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_observer_cache_segments_to_set(...) from builtins.PyCapsule
- add_observer_cache_segments_to_set(pose : rosetta.core.pose.Pose, set : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.enzdes.DetectProteinLigandInterface, pose : rosetta.core.pose.Pose, task : 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.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.DetectProteinLigandInterface, : rosetta.protocols.enzdes.DetectProteinLigandInterface) -> rosetta.protocols.enzdes.DetectProteinLigandInterface
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.enzdes.DetectProteinLigandInterface) -> rosetta.core.pack.task.operation.TaskOperation
- find_design_interface(...) from builtins.PyCapsule
- find_design_interface(self : rosetta.protocols.enzdes.DetectProteinLigandInterface, pose : rosetta.core.pose.Pose, interface_target_res : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, cut1 : float, cut2 : float, cut3 : float, cut4 : float, repack_res : rosetta.utility.vector1_bool, design_res : rosetta.utility.vector1_bool) -> NoneType
- find_design_interface_arg_sweep(...) from builtins.PyCapsule
- find_design_interface_arg_sweep(self : rosetta.protocols.enzdes.DetectProteinLigandInterface, pose : rosetta.core.pose.Pose, interface_target_res : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, cut1 : float, cut2 : float, cut3 : float, cut4 : float, arg_sweep_cutoff : float, repack_res : rosetta.utility.vector1_bool, design_res : rosetta.utility.vector1_bool) -> NoneType
- get_design(...) from builtins.PyCapsule
- get_design(rosetta.protocols.enzdes.DetectProteinLigandInterface) -> bool
- get_no_design_cys(...) from builtins.PyCapsule
- get_no_design_cys(rosetta.protocols.enzdes.DetectProteinLigandInterface) -> bool
- init_from_options(...) from builtins.PyCapsule
- init_from_options(rosetta.protocols.enzdes.DetectProteinLigandInterface) -> NoneType
Initialize the class based on the command line options.
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.enzdes.DetectProteinLigandInterface, : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- register_options(...) from builtins.PyCapsule
- register_options() -> NoneType
- set_design(...) from builtins.PyCapsule
- set_design(self : rosetta.protocols.enzdes.DetectProteinLigandInterface, design_in : bool) -> NoneType
- set_design_target_res(...) from builtins.PyCapsule
- set_design_target_res(self : rosetta.protocols.enzdes.DetectProteinLigandInterface, target_res : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> NoneType
- set_no_design_cys(...) from builtins.PyCapsule
- set_no_design_cys(self : rosetta.protocols.enzdes.DetectProteinLigandInterface, no_design_cys_in : bool) -> NoneType
|
class DiffAtomSasaFilter(rosetta.protocols.filters.Filter) |
| | |
- Method resolution order:
- DiffAtomSasaFilter
- rosetta.protocols.filters.Filter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, resid1 : int, resid2 : int, atomname1 : str, atomane2 : str, sample_type : str) -> NoneType
3. __init__(handle, rosetta.protocols.enzdes.DiffAtomSasaFilter) -> 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.enzdes.DiffAtomSasaFilter, pose : rosetta.core.pose.Pose) -> bool
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.enzdes.DiffAtomSasaFilter) -> rosetta.protocols.filters.Filter
- compute(...) from builtins.PyCapsule
- compute(self : rosetta.protocols.enzdes.DiffAtomSasaFilter, pose : rosetta.core.pose.Pose) -> bool
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.enzdes.DiffAtomSasaFilter) -> rosetta.protocols.filters.Filter
- report_sm(...) from builtins.PyCapsule
- report_sm(self : rosetta.protocols.enzdes.DiffAtomSasaFilter, pose : rosetta.core.pose.Pose) -> float
Methods inherited from rosetta.protocols.filters.Filter:
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.filters.Filter) -> NoneType
used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.filters.Filter) -> str
- get_user_defined_name(...) from builtins.PyCapsule
- get_user_defined_name(rosetta.protocols.filters.Filter) -> str
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.filters.Filter) -> str
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.filters.Filter, pose : rosetta.core.pose.Pose) -> float
- set_user_defined_name(...) from builtins.PyCapsule
- set_user_defined_name(self : rosetta.protocols.filters.Filter, name : str) -> NoneType
|
class DiversifyStoredRBConfs(ModifyStoredRBConfs) |
| |
uses a docking mover to diversiy the stored confs
until they're all min_rms_ away from each other
note: no scorefunction used here
|
| |
- Method resolution order:
- DiversifyStoredRBConfs
- ModifyStoredRBConfs
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, min_rms : float) -> NoneType
2. __init__(handle, rosetta.protocols.enzdes.DiversifyStoredRBConfs) -> 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.enzdes.DiversifyStoredRBConfs, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.DiversifyStoredRBConfs, : rosetta.protocols.enzdes.DiversifyStoredRBConfs) -> rosetta.protocols.enzdes.DiversifyStoredRBConfs
- diversify_all_confs(...) from builtins.PyCapsule
- diversify_all_confs(self : rosetta.protocols.enzdes.DiversifyStoredRBConfs, pose : rosetta.core.pose.Pose, confs : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.DiversifyStoredRBConfs) -> str
Methods inherited from ModifyStoredRBConfs:
- closest_orient_atoms_msd(...) from builtins.PyCapsule
- closest_orient_atoms_msd(self : rosetta.protocols.enzdes.ModifyStoredRBConfs, pose : rosetta.core.pose.Pose, confs : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> rosetta.utility.vector1_double
calculates the closest orient atom (i.e. atoms used in rotamer placement
msd between every conf and the confs coming before it in the pose or in the vector
- swap_coordinates_in_pose(...) from builtins.PyCapsule
- swap_coordinates_in_pose(self : rosetta.protocols.enzdes.ModifyStoredRBConfs, pose : rosetta.core.pose.Pose, rescoords : rosetta.core.conformation.Residue) -> NoneType
helper function to exchange coordinates in a pose
this function doesn't actually exchange the residues,
but sets all the coords of pose.residue( rescoords.seqpos() )
to what is in rescoords and vice versa
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
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class EnzRepackMinimize(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- EnzRepackMinimize
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, name : str) -> NoneType
3. __init__(handle, rosetta.protocols.enzdes.EnzRepackMinimize) -> 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.enzdes.EnzRepackMinimize, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.EnzRepackMinimize, : rosetta.protocols.enzdes.EnzRepackMinimize) -> rosetta.protocols.enzdes.EnzRepackMinimize
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.enzdes.EnzRepackMinimize) -> rosetta.protocols.moves.Mover
- create_ptask(...) from builtins.PyCapsule
- create_ptask(self : rosetta.protocols.enzdes.EnzRepackMinimize, pose : rosetta.core.pose.Pose) -> rosetta.core.pack.task.PackerTask
- ensure_scofx_cstfication(...) from builtins.PyCapsule
- ensure_scofx_cstfication(self : rosetta.protocols.enzdes.EnzRepackMinimize, pose : rosetta.core.pose.Pose) -> NoneType
turns on constraint score terms in case the pose
has an enzdes cst cache
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.enzdes.EnzRepackMinimize) -> rosetta.protocols.moves.Mover
- get_design(...) from builtins.PyCapsule
- get_design(rosetta.protocols.enzdes.EnzRepackMinimize) -> bool
- get_min_bb(...) from builtins.PyCapsule
- get_min_bb(rosetta.protocols.enzdes.EnzRepackMinimize) -> bool
- get_min_lig(...) from builtins.PyCapsule
- get_min_lig(rosetta.protocols.enzdes.EnzRepackMinimize) -> bool
- get_min_rb(...) from builtins.PyCapsule
- get_min_rb(rosetta.protocols.enzdes.EnzRepackMinimize) -> bool
- get_min_sc(...) from builtins.PyCapsule
- get_min_sc(rosetta.protocols.enzdes.EnzRepackMinimize) -> bool
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.EnzRepackMinimize) -> str
- minimize_in_stages(...) from builtins.PyCapsule
- minimize_in_stages(self : rosetta.protocols.enzdes.EnzRepackMinimize, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, cstopt : bool, min_sc : bool, min_rb : bool, min_lig : bool) -> NoneType
- rb_min_jumps(...) from builtins.PyCapsule
- rb_min_jumps(*args, **kwargs)
Overloaded function.
1. rb_min_jumps(rosetta.protocols.enzdes.EnzRepackMinimize) -> rosetta.utility.vector1_unsigned_long
2. rb_min_jumps(self : rosetta.protocols.enzdes.EnzRepackMinimize, : rosetta.utility.vector1_unsigned_long) -> NoneType
- scorefxn_minimize(...) from builtins.PyCapsule
- scorefxn_minimize(rosetta.protocols.enzdes.EnzRepackMinimize) -> rosetta.core.scoring.ScoreFunction
- scorefxn_repack(...) from builtins.PyCapsule
- scorefxn_repack(rosetta.protocols.enzdes.EnzRepackMinimize) -> rosetta.core.scoring.ScoreFunction
- set_design(...) from builtins.PyCapsule
- set_design(self : rosetta.protocols.enzdes.EnzRepackMinimize, des : bool) -> NoneType
- set_min_bb(...) from builtins.PyCapsule
- set_min_bb(self : rosetta.protocols.enzdes.EnzRepackMinimize, min_bb : bool) -> NoneType
- set_min_lig(...) from builtins.PyCapsule
- set_min_lig(self : rosetta.protocols.enzdes.EnzRepackMinimize, min_lig : bool) -> NoneType
- set_min_rb(...) from builtins.PyCapsule
- set_min_rb(self : rosetta.protocols.enzdes.EnzRepackMinimize, min_rb : bool) -> NoneType
- set_min_sc(...) from builtins.PyCapsule
- set_min_sc(self : rosetta.protocols.enzdes.EnzRepackMinimize, min_sc : bool) -> NoneType
- set_scorefxn_minimize(...) from builtins.PyCapsule
- set_scorefxn_minimize(self : rosetta.protocols.enzdes.EnzRepackMinimize, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- set_scorefxn_repack(...) from builtins.PyCapsule
- set_scorefxn_repack(self : rosetta.protocols.enzdes.EnzRepackMinimize, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- task_factory(...) from builtins.PyCapsule
- task_factory(self : rosetta.protocols.enzdes.EnzRepackMinimize, p : rosetta.core.pack.task.TaskFactory) -> 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
|
class EnzScoreFilter(rosetta.protocols.filters.Filter) |
| | |
- Method resolution order:
- EnzScoreFilter
- rosetta.protocols.filters.Filter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, resnum : int, cstid : str, scorefxn : rosetta.core.scoring.ScoreFunction, score_type : rosetta.core.scoring.ScoreType, threshold : float, whole_pose : bool, is_cstE : bool) -> NoneType
3. __init__(handle, rosetta.protocols.enzdes.EnzScoreFilter) -> 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.enzdes.EnzScoreFilter, pose : rosetta.core.pose.Pose) -> bool
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.enzdes.EnzScoreFilter) -> rosetta.protocols.filters.Filter
- compute(...) from builtins.PyCapsule
- compute(self : rosetta.protocols.enzdes.EnzScoreFilter, pose : rosetta.core.pose.Pose) -> float
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.enzdes.EnzScoreFilter) -> rosetta.protocols.filters.Filter
- report_sm(...) from builtins.PyCapsule
- report_sm(self : rosetta.protocols.enzdes.EnzScoreFilter, pose : rosetta.core.pose.Pose) -> float
Methods inherited from rosetta.protocols.filters.Filter:
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.filters.Filter) -> NoneType
used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.filters.Filter) -> str
- get_user_defined_name(...) from builtins.PyCapsule
- get_user_defined_name(rosetta.protocols.filters.Filter) -> str
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.filters.Filter) -> str
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.filters.Filter, pose : rosetta.core.pose.Pose) -> float
- set_user_defined_name(...) from builtins.PyCapsule
- set_user_defined_name(self : rosetta.protocols.filters.Filter, name : str) -> NoneType
|
class EnzdesBaseProtocol(rosetta.protocols.ligand_docking.LigandBaseProtocol) |
| | |
- Method resolution order:
- EnzdesBaseProtocol
- rosetta.protocols.ligand_docking.LigandBaseProtocol
- 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.enzdes.EnzdesBaseProtocol) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_pregenerated_enzdes_constraints(...) from builtins.PyCapsule
- add_pregenerated_enzdes_constraints(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, : rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.protocols.enzdes.EnzdesBaseProtocol
- catalytic_res(...) from builtins.PyCapsule
- catalytic_res(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long
- create_enzdes_movemap(...) from builtins.PyCapsule
- create_enzdes_movemap(*args, **kwargs)
Overloaded function.
1. create_enzdes_movemap(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> rosetta.core.kinematics.MoveMap
2. create_enzdes_movemap(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, min_all_jumps : bool) -> rosetta.core.kinematics.MoveMap
- create_enzdes_pack_task(...) from builtins.PyCapsule
- create_enzdes_pack_task(*args, **kwargs)
Overloaded function.
1. create_enzdes_pack_task(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> rosetta.core.pack.task.PackerTask
2. create_enzdes_pack_task(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, design : bool) -> rosetta.core.pack.task.PackerTask
- cst_minimize(...) from builtins.PyCapsule
- cst_minimize(*args, **kwargs)
Overloaded function.
1. cst_minimize(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
2. cst_minimize(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, cst_opt : bool) -> NoneType
- design_targets(...) from builtins.PyCapsule
- design_targets(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t
- design_targets_score(...) from builtins.PyCapsule
- design_targets_score(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> float
- enzdes_pack(...) from builtins.PyCapsule
- enzdes_pack(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask, scorefxn : rosetta.core.scoring.ScoreFunction, cycles : int, minimize_after_packing : bool, pack_unconstrained : bool, favor_native : bool) -> NoneType
- generate_explicit_ligand_rotamer_poses(...) from builtins.PyCapsule
- generate_explicit_ligand_rotamer_poses(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, orig_pose : rosetta.core.pose.Pose, ligrot_poses : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, scofx : rosetta.core.scoring.ScoreFunction) -> NoneType
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> str
- is_catalytic_position(...) from builtins.PyCapsule
- is_catalytic_position(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, seqpos : int) -> bool
- rb_min_jumps(...) from builtins.PyCapsule
- rb_min_jumps(*args, **kwargs)
Overloaded function.
1. rb_min_jumps(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.utility.vector1_unsigned_long
2. rb_min_jumps(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, : rosetta.utility.vector1_unsigned_long) -> NoneType
- reduced_scorefxn(...) from builtins.PyCapsule
- reduced_scorefxn(*args, **kwargs)
Overloaded function.
1. reduced_scorefxn(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.core.scoring.ScoreFunction
2. reduced_scorefxn(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.core.scoring.ScoreFunction
- 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
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, smap : rosetta.core.id.SequenceMapping) -> NoneType
- remove_enzdes_constraints(...) from builtins.PyCapsule
- remove_enzdes_constraints(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, keep_covalent : bool) -> NoneType
- restype_set(...) from builtins.PyCapsule
- restype_set(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t
- set_all_jumps_minimizable(...) from builtins.PyCapsule
- set_all_jumps_minimizable(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, setting : bool) -> NoneType
- set_fix_cataa(...) from builtins.PyCapsule
- set_fix_cataa(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, setting : bool) -> NoneType
- set_minimize_options(...) from builtins.PyCapsule
- set_minimize_options(*args, **kwargs)
Overloaded function.
1. set_minimize_options(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, min_sc : bool, min_bb : bool, min_rb : bool, min_lig : bool) -> NoneType
2. set_minimize_options(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, min_sc : bool, min_bb : bool, min_rb : bool, min_lig : bool, backrub : bool) -> NoneType
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- setup_bbmin_ft_and_csts(...) from builtins.PyCapsule
- setup_bbmin_ft_and_csts(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, allow_move_bb : rosetta.utility.vector1_bool, jump_id : int) -> NoneType
- setup_sequence_recovery_cache(...) from builtins.PyCapsule
- setup_sequence_recovery_cache(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
Methods inherited from rosetta.protocols.ligand_docking.LigandBaseProtocol:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose) -> NoneType
- get_ligand_id(...) from builtins.PyCapsule
- get_ligand_id(*args, **kwargs)
Overloaded function.
1. get_ligand_id(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose) -> int
2. get_ligand_id(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, jump_id : int) -> int
- get_ligand_jump_id(...) from builtins.PyCapsule
- get_ligand_jump_id(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose) -> int
- get_non_bb_clashing_rotamers(...) from builtins.PyCapsule
- get_non_bb_clashing_rotamers(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, seqpos : int, scofx : rosetta.core.scoring.ScoreFunction, accepted_rotamers : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
- get_scorefxn(...) from builtins.PyCapsule
- get_scorefxn(*args, **kwargs)
Overloaded function.
1. get_scorefxn(rosetta.protocols.ligand_docking.LigandBaseProtocol) -> rosetta.core.scoring.ScoreFunction
2. get_scorefxn(rosetta.protocols.ligand_docking.LigandBaseProtocol) -> rosetta.core.scoring.ScoreFunction
- reorder_foldtree_around_mobile_regions(...) from builtins.PyCapsule
- reorder_foldtree_around_mobile_regions(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, jump_id : int, mobile_bb : rosetta.utility.vector1_bool, lig_id : int) -> NoneType
- restrain_protein_Calphas(...) from builtins.PyCapsule
- restrain_protein_Calphas(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, is_restrained : rosetta.utility.vector1_bool, restr_func : rosetta.core.scoring.func.Func) -> NoneType
- shared_from_this(...) from builtins.PyCapsule
- shared_from_this(rosetta.protocols.ligand_docking.LigandBaseProtocol) -> rosetta.protocols.ligand_docking.LigandBaseProtocol
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
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- 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 EnzdesFixBBProtocol(EnzdesBaseProtocol) |
| | |
- Method resolution order:
- EnzdesFixBBProtocol
- EnzdesBaseProtocol
- rosetta.protocols.ligand_docking.LigandBaseProtocol
- 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.enzdes.EnzdesFixBBProtocol) -> 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.enzdes.EnzdesFixBBProtocol, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.EnzdesFixBBProtocol, : rosetta.protocols.enzdes.EnzdesFixBBProtocol) -> rosetta.protocols.enzdes.EnzdesFixBBProtocol
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.EnzdesFixBBProtocol) -> 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
Methods inherited from EnzdesBaseProtocol:
- add_pregenerated_enzdes_constraints(...) from builtins.PyCapsule
- add_pregenerated_enzdes_constraints(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> NoneType
- catalytic_res(...) from builtins.PyCapsule
- catalytic_res(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long
- create_enzdes_movemap(...) from builtins.PyCapsule
- create_enzdes_movemap(*args, **kwargs)
Overloaded function.
1. create_enzdes_movemap(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> rosetta.core.kinematics.MoveMap
2. create_enzdes_movemap(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, min_all_jumps : bool) -> rosetta.core.kinematics.MoveMap
- create_enzdes_pack_task(...) from builtins.PyCapsule
- create_enzdes_pack_task(*args, **kwargs)
Overloaded function.
1. create_enzdes_pack_task(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> rosetta.core.pack.task.PackerTask
2. create_enzdes_pack_task(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, design : bool) -> rosetta.core.pack.task.PackerTask
- cst_minimize(...) from builtins.PyCapsule
- cst_minimize(*args, **kwargs)
Overloaded function.
1. cst_minimize(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
2. cst_minimize(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, cst_opt : bool) -> NoneType
- design_targets(...) from builtins.PyCapsule
- design_targets(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t
- design_targets_score(...) from builtins.PyCapsule
- design_targets_score(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> float
- enzdes_pack(...) from builtins.PyCapsule
- enzdes_pack(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask, scorefxn : rosetta.core.scoring.ScoreFunction, cycles : int, minimize_after_packing : bool, pack_unconstrained : bool, favor_native : bool) -> NoneType
- generate_explicit_ligand_rotamer_poses(...) from builtins.PyCapsule
- generate_explicit_ligand_rotamer_poses(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, orig_pose : rosetta.core.pose.Pose, ligrot_poses : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, scofx : rosetta.core.scoring.ScoreFunction) -> NoneType
- is_catalytic_position(...) from builtins.PyCapsule
- is_catalytic_position(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, seqpos : int) -> bool
- rb_min_jumps(...) from builtins.PyCapsule
- rb_min_jumps(*args, **kwargs)
Overloaded function.
1. rb_min_jumps(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.utility.vector1_unsigned_long
2. rb_min_jumps(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, : rosetta.utility.vector1_unsigned_long) -> NoneType
- reduced_scorefxn(...) from builtins.PyCapsule
- reduced_scorefxn(*args, **kwargs)
Overloaded function.
1. reduced_scorefxn(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.core.scoring.ScoreFunction
2. reduced_scorefxn(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.core.scoring.ScoreFunction
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, smap : rosetta.core.id.SequenceMapping) -> NoneType
- remove_enzdes_constraints(...) from builtins.PyCapsule
- remove_enzdes_constraints(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, keep_covalent : bool) -> NoneType
- restype_set(...) from builtins.PyCapsule
- restype_set(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t
- set_all_jumps_minimizable(...) from builtins.PyCapsule
- set_all_jumps_minimizable(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, setting : bool) -> NoneType
- set_fix_cataa(...) from builtins.PyCapsule
- set_fix_cataa(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, setting : bool) -> NoneType
- set_minimize_options(...) from builtins.PyCapsule
- set_minimize_options(*args, **kwargs)
Overloaded function.
1. set_minimize_options(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, min_sc : bool, min_bb : bool, min_rb : bool, min_lig : bool) -> NoneType
2. set_minimize_options(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, min_sc : bool, min_bb : bool, min_rb : bool, min_lig : bool, backrub : bool) -> NoneType
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- setup_bbmin_ft_and_csts(...) from builtins.PyCapsule
- setup_bbmin_ft_and_csts(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, allow_move_bb : rosetta.utility.vector1_bool, jump_id : int) -> NoneType
- setup_sequence_recovery_cache(...) from builtins.PyCapsule
- setup_sequence_recovery_cache(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
Methods inherited from rosetta.protocols.ligand_docking.LigandBaseProtocol:
- get_ligand_id(...) from builtins.PyCapsule
- get_ligand_id(*args, **kwargs)
Overloaded function.
1. get_ligand_id(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose) -> int
2. get_ligand_id(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, jump_id : int) -> int
- get_ligand_jump_id(...) from builtins.PyCapsule
- get_ligand_jump_id(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose) -> int
- get_non_bb_clashing_rotamers(...) from builtins.PyCapsule
- get_non_bb_clashing_rotamers(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, seqpos : int, scofx : rosetta.core.scoring.ScoreFunction, accepted_rotamers : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
- get_scorefxn(...) from builtins.PyCapsule
- get_scorefxn(*args, **kwargs)
Overloaded function.
1. get_scorefxn(rosetta.protocols.ligand_docking.LigandBaseProtocol) -> rosetta.core.scoring.ScoreFunction
2. get_scorefxn(rosetta.protocols.ligand_docking.LigandBaseProtocol) -> rosetta.core.scoring.ScoreFunction
- reorder_foldtree_around_mobile_regions(...) from builtins.PyCapsule
- reorder_foldtree_around_mobile_regions(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, jump_id : int, mobile_bb : rosetta.utility.vector1_bool, lig_id : int) -> NoneType
- restrain_protein_Calphas(...) from builtins.PyCapsule
- restrain_protein_Calphas(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, is_restrained : rosetta.utility.vector1_bool, restr_func : rosetta.core.scoring.func.Func) -> NoneType
- shared_from_this(...) from builtins.PyCapsule
- shared_from_this(rosetta.protocols.ligand_docking.LigandBaseProtocol) -> rosetta.protocols.ligand_docking.LigandBaseProtocol
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
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- 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 EnzdesFlexBBProtocol(EnzdesBaseProtocol) |
| | |
- Method resolution order:
- EnzdesFlexBBProtocol
- EnzdesBaseProtocol
- rosetta.protocols.ligand_docking.LigandBaseProtocol
- 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.enzdes.EnzdesFlexBBProtocol) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_flexible_region(...) from builtins.PyCapsule
- add_flexible_region(self : rosetta.protocols.enzdes.EnzdesFlexBBProtocol, start : int, end : int, pose : rosetta.core.pose.Pose, clear_existing : bool) -> NoneType
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.EnzdesFlexBBProtocol, : rosetta.protocols.enzdes.EnzdesFlexBBProtocol) -> rosetta.protocols.enzdes.EnzdesFlexBBProtocol
- determine_flexible_regions(...) from builtins.PyCapsule
- determine_flexible_regions(self : rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
- enz_flexible_region(...) from builtins.PyCapsule
- enz_flexible_region(self : rosetta.protocols.enzdes.EnzdesFlexBBProtocol, region : int) -> protocols::enzdes::EnzdesFlexibleRegion
- enz_loops_file(...) from builtins.PyCapsule
- enz_loops_file(rosetta.protocols.enzdes.EnzdesFlexBBProtocol) -> rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile
- generate_alc_ensemble_for_region(...) from builtins.PyCapsule
- generate_alc_ensemble_for_region(self : rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose : rosetta.core.pose.Pose, region : int) -> NoneType
- generate_backrub_ensemble_for_region(...) from builtins.PyCapsule
- generate_backrub_ensemble_for_region(self : rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose : rosetta.core.pose.Pose, region : int) -> NoneType
- generate_ensemble_for_region(...) from builtins.PyCapsule
- generate_ensemble_for_region(self : rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose : rosetta.core.pose.Pose, region : int) -> NoneType
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.EnzdesFlexBBProtocol) -> str
- get_tenA_neighbor_residues(...) from builtins.PyCapsule
- get_tenA_neighbor_residues(self : rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose : rosetta.core.pose.Pose, residue_positions : rosetta.utility.vector1_bool) -> NoneType
- is_flexible(...) from builtins.PyCapsule
- is_flexible(self : rosetta.protocols.enzdes.EnzdesFlexBBProtocol, seqpos : int) -> bool
- is_remodelable(...) from builtins.PyCapsule
- is_remodelable(self : rosetta.protocols.enzdes.EnzdesFlexBBProtocol, seqpos : int) -> bool
- minimize_flexible_region(...) from builtins.PyCapsule
- minimize_flexible_region(self : rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose : rosetta.core.pose.Pose, region : int, scorefxn : rosetta.core.scoring.ScoreFunction, chi_to_move : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, including_CA_angles : bool, min_tolerance : float) -> bool
- modified_task(...) from builtins.PyCapsule
- modified_task(self : rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose : rosetta.core.pose.Pose, orig_task : rosetta.core.pack.task.PackerTask) -> rosetta.core.pack.task.PackerTask
- 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
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose : rosetta.core.pose.Pose, smap : rosetta.core.id.SequenceMapping) -> NoneType
- test_flexbb_rotamer_sets(...) from builtins.PyCapsule
- test_flexbb_rotamer_sets(self : rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
Methods inherited from EnzdesBaseProtocol:
- add_pregenerated_enzdes_constraints(...) from builtins.PyCapsule
- add_pregenerated_enzdes_constraints(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> NoneType
- catalytic_res(...) from builtins.PyCapsule
- catalytic_res(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long
- create_enzdes_movemap(...) from builtins.PyCapsule
- create_enzdes_movemap(*args, **kwargs)
Overloaded function.
1. create_enzdes_movemap(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> rosetta.core.kinematics.MoveMap
2. create_enzdes_movemap(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, min_all_jumps : bool) -> rosetta.core.kinematics.MoveMap
- create_enzdes_pack_task(...) from builtins.PyCapsule
- create_enzdes_pack_task(*args, **kwargs)
Overloaded function.
1. create_enzdes_pack_task(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> rosetta.core.pack.task.PackerTask
2. create_enzdes_pack_task(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, design : bool) -> rosetta.core.pack.task.PackerTask
- cst_minimize(...) from builtins.PyCapsule
- cst_minimize(*args, **kwargs)
Overloaded function.
1. cst_minimize(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
2. cst_minimize(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, cst_opt : bool) -> NoneType
- design_targets(...) from builtins.PyCapsule
- design_targets(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t
- design_targets_score(...) from builtins.PyCapsule
- design_targets_score(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> float
- enzdes_pack(...) from builtins.PyCapsule
- enzdes_pack(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask, scorefxn : rosetta.core.scoring.ScoreFunction, cycles : int, minimize_after_packing : bool, pack_unconstrained : bool, favor_native : bool) -> NoneType
- generate_explicit_ligand_rotamer_poses(...) from builtins.PyCapsule
- generate_explicit_ligand_rotamer_poses(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, orig_pose : rosetta.core.pose.Pose, ligrot_poses : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, scofx : rosetta.core.scoring.ScoreFunction) -> NoneType
- is_catalytic_position(...) from builtins.PyCapsule
- is_catalytic_position(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, seqpos : int) -> bool
- rb_min_jumps(...) from builtins.PyCapsule
- rb_min_jumps(*args, **kwargs)
Overloaded function.
1. rb_min_jumps(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.utility.vector1_unsigned_long
2. rb_min_jumps(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, : rosetta.utility.vector1_unsigned_long) -> NoneType
- reduced_scorefxn(...) from builtins.PyCapsule
- reduced_scorefxn(*args, **kwargs)
Overloaded function.
1. reduced_scorefxn(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.core.scoring.ScoreFunction
2. reduced_scorefxn(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.core.scoring.ScoreFunction
- remove_enzdes_constraints(...) from builtins.PyCapsule
- remove_enzdes_constraints(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, keep_covalent : bool) -> NoneType
- restype_set(...) from builtins.PyCapsule
- restype_set(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t
- set_all_jumps_minimizable(...) from builtins.PyCapsule
- set_all_jumps_minimizable(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, setting : bool) -> NoneType
- set_fix_cataa(...) from builtins.PyCapsule
- set_fix_cataa(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, setting : bool) -> NoneType
- set_minimize_options(...) from builtins.PyCapsule
- set_minimize_options(*args, **kwargs)
Overloaded function.
1. set_minimize_options(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, min_sc : bool, min_bb : bool, min_rb : bool, min_lig : bool) -> NoneType
2. set_minimize_options(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, min_sc : bool, min_bb : bool, min_rb : bool, min_lig : bool, backrub : bool) -> NoneType
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- setup_bbmin_ft_and_csts(...) from builtins.PyCapsule
- setup_bbmin_ft_and_csts(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, allow_move_bb : rosetta.utility.vector1_bool, jump_id : int) -> NoneType
- setup_sequence_recovery_cache(...) from builtins.PyCapsule
- setup_sequence_recovery_cache(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
Methods inherited from rosetta.protocols.ligand_docking.LigandBaseProtocol:
- get_ligand_id(...) from builtins.PyCapsule
- get_ligand_id(*args, **kwargs)
Overloaded function.
1. get_ligand_id(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose) -> int
2. get_ligand_id(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, jump_id : int) -> int
- get_ligand_jump_id(...) from builtins.PyCapsule
- get_ligand_jump_id(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose) -> int
- get_non_bb_clashing_rotamers(...) from builtins.PyCapsule
- get_non_bb_clashing_rotamers(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, seqpos : int, scofx : rosetta.core.scoring.ScoreFunction, accepted_rotamers : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
- get_scorefxn(...) from builtins.PyCapsule
- get_scorefxn(*args, **kwargs)
Overloaded function.
1. get_scorefxn(rosetta.protocols.ligand_docking.LigandBaseProtocol) -> rosetta.core.scoring.ScoreFunction
2. get_scorefxn(rosetta.protocols.ligand_docking.LigandBaseProtocol) -> rosetta.core.scoring.ScoreFunction
- reorder_foldtree_around_mobile_regions(...) from builtins.PyCapsule
- reorder_foldtree_around_mobile_regions(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, jump_id : int, mobile_bb : rosetta.utility.vector1_bool, lig_id : int) -> NoneType
- restrain_protein_Calphas(...) from builtins.PyCapsule
- restrain_protein_Calphas(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, is_restrained : rosetta.utility.vector1_bool, restr_func : rosetta.core.scoring.func.Func) -> NoneType
- shared_from_this(...) from builtins.PyCapsule
- shared_from_this(rosetta.protocols.ligand_docking.LigandBaseProtocol) -> rosetta.protocols.ligand_docking.LigandBaseProtocol
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
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- 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 EnzdesFlexibleRegion(rosetta.core.fragment.Frame) |
| | |
- Method resolution order:
- EnzdesFlexibleRegion
- rosetta.core.fragment.Frame
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, index_in : int, start : int, end : int, nr_res : int, pose : rosetta.core.pose.Pose, enz_prot : rosetta.std.weak_ptr_const_protocols_enzdes_EnzdesFlexBBProtocol_t) -> NoneType
2. __init__(handle, rosetta.protocols.enzdes.EnzdesFlexibleRegion) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- apply_ranked_fragment(...) from builtins.PyCapsule
- apply_ranked_fragment(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose : rosetta.core.pose.Pose, frag_rank : int) -> NoneType
- assemble_enzdes_fragdata(...) from builtins.PyCapsule
- assemble_enzdes_fragdata(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose : rosetta.core.pose.Pose) -> rosetta.core.fragment.FragData
- calculate_rotamer_set_design_targets_partition_sum(...) from builtins.PyCapsule
- calculate_rotamer_set_design_targets_partition_sum(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask) -> float
- compare_SizeRealPairs(...) from builtins.PyCapsule
- compare_SizeRealPairs(first : (int, float), second : (int, float)) -> bool
- contains_catalytic_res(...) from builtins.PyCapsule
- contains_catalytic_res(rosetta.protocols.enzdes.EnzdesFlexibleRegion) -> bool
- declare_remodelable(...) from builtins.PyCapsule
- declare_remodelable(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, min_length : int, max_length : int) -> NoneType
- deltaE_best(...) from builtins.PyCapsule
- deltaE_best(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, frag_rank : int) -> float
- enz_loop_info(...) from builtins.PyCapsule
- enz_loop_info(rosetta.protocols.enzdes.EnzdesFlexibleRegion) -> rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo
- examine_new_loopconf(...) from builtins.PyCapsule
- examine_new_loopconf(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose : rosetta.core.pose.Pose, template_pose : rosetta.core.pose.Pose, compare_poses : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, rmsd_to_native : rosetta.utility.vector1_double) -> bool
- extract_lig_designability_score(...) from builtins.PyCapsule
- extract_lig_designability_score(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, backgroundE : float) -> float
- get_10A_neighbors(...) from builtins.PyCapsule
- get_10A_neighbors(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose : rosetta.core.pose.Pose) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t
- get_region_mm_bend_score(...) from builtins.PyCapsule
- get_region_mm_bend_score(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose : rosetta.core.pose.Pose) -> float
- get_region_total_score(...) from builtins.PyCapsule
- get_region_total_score(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose : rosetta.core.pose.Pose) -> float
- hack_fillup_frag_designabilities(...) from builtins.PyCapsule
- hack_fillup_frag_designabilities(rosetta.protocols.enzdes.EnzdesFlexibleRegion) -> NoneType
- index(...) from builtins.PyCapsule
- index(rosetta.protocols.enzdes.EnzdesFlexibleRegion) -> int
- minimize_region(...) from builtins.PyCapsule
- minimize_region(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, chi_to_move : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, including_CA_angles : bool, min_tolerance : float) -> bool
- no_ranked_frags(...) from builtins.PyCapsule
- no_ranked_frags(rosetta.protocols.enzdes.EnzdesFlexibleRegion) -> int
- positions(...) from builtins.PyCapsule
- positions(rosetta.protocols.enzdes.EnzdesFlexibleRegion) -> rosetta.utility.vector1_unsigned_long
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose : rosetta.core.pose.Pose, smap : rosetta.core.id.SequenceMapping) -> bool
- remodel_max_length(...) from builtins.PyCapsule
- remodel_max_length(rosetta.protocols.enzdes.EnzdesFlexibleRegion) -> int
- remodel_min_length(...) from builtins.PyCapsule
- remodel_min_length(rosetta.protocols.enzdes.EnzdesFlexibleRegion) -> int
- remodelable(...) from builtins.PyCapsule
- remodelable(rosetta.protocols.enzdes.EnzdesFlexibleRegion) -> bool
- scale_target_proximity_to_other_conformations(...) from builtins.PyCapsule
- scale_target_proximity_to_other_conformations(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, factor : float) -> NoneType
- scale_target_proximity_to_starting_conformation(...) from builtins.PyCapsule
- scale_target_proximity_to_starting_conformation(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, factor : float) -> NoneType
- set_target_proximity_to_starting_conformation(...) from builtins.PyCapsule
- set_target_proximity_to_starting_conformation(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, proximity : float) -> NoneType
- sort_ensemble_by_designability(...) from builtins.PyCapsule
- sort_ensemble_by_designability(self : rosetta.protocols.enzdes.EnzdesFlexibleRegion, ref_pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask) -> NoneType
Methods inherited from rosetta.core.fragment.Frame:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.fragment.Frame) -> str
- add_fragment(...) from builtins.PyCapsule
- add_fragment(*args, **kwargs)
Overloaded function.
1. add_fragment(self : rosetta.core.fragment.Frame, new_frag : core::fragment::FragData) -> int
add a fragment .. return new frag_nr
2. add_fragment(self : rosetta.core.fragment.Frame, new_frags : rosetta.utility.vector1_std_shared_ptr_const_core_fragment_FragData_t) -> bool
add all fragments in list
- align(...) from builtins.PyCapsule
- align(self : rosetta.core.fragment.Frame, map : rosetta.core.id.SequenceMapping) -> bool
change frames residue numbers accoriding to map
- apply(...) from builtins.PyCapsule
- apply(*args, **kwargs)
Overloaded function.
1. apply(self : rosetta.core.fragment.Frame, : core::kinematics::MoveMap, frag_num : int, pose : core::pose::Pose) -> int
insert fragment frag_num into pose
2. apply(self : rosetta.core.fragment.Frame, frag_num : int, pose : core::pose::Pose) -> int
insert fragment frag_num into pose --- ignore movemap
- apply_ss(...) from builtins.PyCapsule
- apply_ss(self : rosetta.core.fragment.Frame, : core::kinematics::MoveMap, frag_num : int, ss : str) -> int
change ss-string according to sec-struct info in fragments
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.fragment.Frame, : rosetta.core.fragment.Frame) -> rosetta.core.fragment.Frame
- cache(...) from builtins.PyCapsule
- cache(self : rosetta.core.fragment.Frame, tag : str, new_cache : rosetta.core.fragment.BaseCacheUnit) -> rosetta.core.fragment.BaseCacheUnit
return handle to cached data stored under "tag"
shouldn't be called directly
- clear(...) from builtins.PyCapsule
- clear(rosetta.core.fragment.Frame) -> NoneType
remove all valid fragments, a template fragment will be left over
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.fragment.Frame) -> rosetta.core.fragment.Frame
clone method, new frame with same alignment position, fragments are not copied!
- clone_cache_data(...) from builtins.PyCapsule
- clone_cache_data(self : rosetta.core.fragment.Frame, source : rosetta.core.fragment.Frame, sid : int, nid : int) -> NoneType
copies all entries in the Frame-Cache for fragment "sid" of Frame "source" to fragment "nid" of "this" frame
- clone_with_frags(...) from builtins.PyCapsule
- clone_with_frags(rosetta.core.fragment.Frame) -> rosetta.core.fragment.Frame
clone method, new frame with same alignment position, fragments are not copied!
- clone_with_template(...) from builtins.PyCapsule
- clone_with_template(rosetta.core.fragment.Frame) -> rosetta.core.fragment.Frame
clone method, new frame with same alignment position, one fragments is copied as template ( valid() == false )
- contains_seqpos(...) from builtins.PyCapsule
- contains_seqpos(self : rosetta.core.fragment.Frame, seqpos : int) -> bool
whether this fragment contains a certain position
- end(...) from builtins.PyCapsule
- end(rosetta.core.fragment.Frame) -> int
last sequence position affected by this frame
- frag_id(...) from builtins.PyCapsule
- frag_id(self : rosetta.core.fragment.Frame, frag_num : int) -> int
a unique id for every fragment in the list.
his is silly, but would enable later on to avoid cache_clearence on deletion of FragData entries
in this case, we would require that the ID of a certain fragment never changes, even if the position in FragList changes
- fragment(...) from builtins.PyCapsule
- fragment(self : rosetta.core.fragment.Frame, frag_num : int) -> core::fragment::FragData
accesors for underlying FragData
- fragment_as_pose(...) from builtins.PyCapsule
- fragment_as_pose(self : rosetta.core.fragment.Frame, frag_num : int, pose : core::pose::Pose, restype_set : rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t) -> NoneType
returns a (small) pose with fragment ( continous from seqpos 1 ... nr_res_affected() )
- fragment_ptr(...) from builtins.PyCapsule
- fragment_ptr(self : rosetta.core.fragment.Frame, frag_num : int) -> core::fragment::FragData
accessor for underlying FragData as owning ptr
- generate_sub_frame(...) from builtins.PyCapsule
- generate_sub_frame(*args, **kwargs)
Overloaded function.
1. generate_sub_frame(self : rosetta.core.fragment.Frame, length : int) -> rosetta.core.fragment.Frame
generate_sub_frame of length from start ( internal numbers )
2. generate_sub_frame(self : rosetta.core.fragment.Frame, length : int, start : int) -> rosetta.core.fragment.Frame
generate_sub_frame of length from start ( internal numbers )
- is_applicable(...) from builtins.PyCapsule
- is_applicable(self : rosetta.core.fragment.Frame, : core::kinematics::MoveMap) -> int
is the Frame applicable to the pose with the given movemap?
- is_continuous(...) from builtins.PyCapsule
- is_continuous(rosetta.core.fragment.Frame) -> bool
true if frame is continuous (always true for base class)
- is_mergeable(...) from builtins.PyCapsule
- is_mergeable(self : rosetta.core.fragment.Frame, other : rosetta.core.fragment.Frame) -> bool
- is_valid(...) from builtins.PyCapsule
- is_valid(rosetta.core.fragment.Frame) -> bool
a frame is considered valid if at least one fragment is contained and this fragment is also valid
(not an empty template fragment)
- length(...) from builtins.PyCapsule
- length(rosetta.core.fragment.Frame) -> int
number of residues in this frame ( for continuous frames it is the same as end()-start() + 1 )
- merge(...) from builtins.PyCapsule
- merge(self : rosetta.core.fragment.Frame, other : rosetta.core.fragment.Frame) -> bool
- moves_residue(...) from builtins.PyCapsule
- moves_residue(self : rosetta.core.fragment.Frame, pos : int) -> bool
- nr_frags(...) from builtins.PyCapsule
- nr_frags(rosetta.core.fragment.Frame) -> int
number of fragments attached to this frame
- nr_res_affected(...) from builtins.PyCapsule
- nr_res_affected(self : rosetta.core.fragment.Frame, mm : core::kinematics::MoveMap) -> int
number of residues affected by this frame
- seqpos(...) from builtins.PyCapsule
- seqpos(self : rosetta.core.fragment.Frame, intra_pos : int) -> int
translate intra-frame position into sequence position. (trivial for base-class)
- shift_by(...) from builtins.PyCapsule
- shift_by(self : rosetta.core.fragment.Frame, offset : int) -> NoneType
shift frame by offset relative to current start position ( change end accordingly )
- shift_to(...) from builtins.PyCapsule
- shift_to(self : rosetta.core.fragment.Frame, setting : int) -> NoneType
shift to new start position ( change end accordingly )
- start(...) from builtins.PyCapsule
- start(rosetta.core.fragment.Frame) -> int
first seqpos of this frame
- steal(...) from builtins.PyCapsule
- steal(self : rosetta.core.fragment.Frame, pose : core::pose::Pose) -> bool
obtain fragment from pose at frame position
- stop(...) from builtins.PyCapsule
- stop(rosetta.core.fragment.Frame) -> int
last sequence position affected by this frame
- type(...) from builtins.PyCapsule
- type(rosetta.core.fragment.Frame) -> str
type() is specifying the output name of the Frame in FragmentIO ("FRAME", "JUMPFRAME", etc)
|
class EnzdesJobInputter(rosetta.protocols.jd2.PDBJobInputter) |
| | |
- Method resolution order:
- EnzdesJobInputter
- rosetta.protocols.jd2.PDBJobInputter
- rosetta.protocols.jd2.JobInputter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.enzdes.EnzdesJobInputter) -> 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.enzdes.EnzdesJobInputter, : rosetta.protocols.enzdes.EnzdesJobInputter) -> rosetta.protocols.enzdes.EnzdesJobInputter
- pose_from_job(...) from builtins.PyCapsule
- pose_from_job(self : rosetta.protocols.enzdes.EnzdesJobInputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType
this function is responsible for filling the pose reference with the pose
indicated by the job. The Job object (within its InnerJob) contains a PoseCOP.
This function needs to either fill the pose reference from the InnerJob or, on
first demand of a pose from that InnerJob, instantiate the pose, hand off a COP
to the InnerJob, and fill the reference. This implementation uses pose_from_pdb
Methods inherited from rosetta.protocols.jd2.PDBJobInputter:
- fill_jobs(...) from builtins.PyCapsule
- fill_jobs(self : rosetta.protocols.jd2.PDBJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType
this function determines what jobs exist from -s/-l
- input_source(...) from builtins.PyCapsule
- input_source(rosetta.protocols.jd2.PDBJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum
Return the type of input source that the PDBJobInputter is currently
using.
Always PDB_FILE.
Methods inherited from rosetta.protocols.jd2.JobInputter:
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter
Get self const owning pointers.
2. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter
Get self owning pointers.
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_const_protocols_jd2_JobInputter_t
Get self const weak pointers.
2. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_protocols_jd2_JobInputter_t
Get self weak pointers.
- job_inputter_input_source_to_string(...) from builtins.PyCapsule
- job_inputter_input_source_to_string(source : rosetta.protocols.jd2.JobInputterInputSource.Enum) -> str
call this with input_source() to get the input source of a
particular job inputter
- update_jobs_list(...) from builtins.PyCapsule
- update_jobs_list(self : rosetta.protocols.jd2.JobInputter, jobs : protocols::jd2::JobsContainer) -> NoneType
This function is only called by certain JobInputters to update the jobs list after it has already been created.
An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back.
- updates_jobs_list(...) from builtins.PyCapsule
- updates_jobs_list(rosetta.protocols.jd2.JobInputter) -> bool
Does this type of JobInputter update the jobs list?
False by default. Override this function in derived classes to make it true.
|
class EnzdesJobOutputter(rosetta.protocols.jd2.PDBJobOutputter) |
| |
for now this class only writes a different scorefile
than the default one written by the FileJobOutputter. the structure
output format is pdb
|
| |
- Method resolution order:
- EnzdesJobOutputter
- rosetta.protocols.jd2.PDBJobOutputter
- rosetta.protocols.jd2.FileJobOutputter
- rosetta.protocols.jd2.JobOutputter
- 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.
- final_pose(...) from builtins.PyCapsule
- final_pose(self : rosetta.protocols.enzdes.EnzdesJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType
- job_has_completed(...) from builtins.PyCapsule
- job_has_completed(self : rosetta.protocols.enzdes.EnzdesJobOutputter, job : rosetta.protocols.jd2.Job) -> bool
Methods inherited from rosetta.protocols.jd2.PDBJobOutputter:
- other_pose(...) from builtins.PyCapsule
- other_pose(*args, **kwargs)
Overloaded function.
1. other_pose(self : rosetta.protocols.jd2.PDBJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str) -> NoneType
this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. This implementation will write a PDB file (plus scores).
2. other_pose(self : rosetta.protocols.jd2.PDBJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int) -> NoneType
this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. This implementation will write a PDB file (plus scores).
3. other_pose(self : rosetta.protocols.jd2.PDBJobOutputter, job : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose, tag : str, copy_count : int, score_only : bool) -> NoneType
this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. This implementation will write a PDB file (plus scores).
- output_name(...) from builtins.PyCapsule
- output_name(self : rosetta.protocols.jd2.PDBJobOutputter, job : rosetta.protocols.jd2.Job) -> str
this is the master function for determining the unique output identifier for a job
Methods inherited from rosetta.protocols.jd2.FileJobOutputter:
- file(...) from builtins.PyCapsule
- file(self : rosetta.protocols.jd2.FileJobOutputter, job : rosetta.protocols.jd2.Job, data : str) -> NoneType
this function takes a string and writes it to disk (separately from Tracer output).
- scorefile_name(...) from builtins.PyCapsule
- scorefile_name(rosetta.protocols.jd2.FileJobOutputter) -> rosetta.utility.file.FileName
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.jd2.FileJobOutputter) -> NoneType
- write_scorefile(...) from builtins.PyCapsule
- write_scorefile(rosetta.protocols.jd2.FileJobOutputter) -> bool
Methods inherited from rosetta.protocols.jd2.JobOutputter:
- add_evaluation(...) from builtins.PyCapsule
- add_evaluation(self : rosetta.protocols.jd2.JobOutputter, : rosetta.protocols.evaluation.PoseEvaluator) -> NoneType
////////////////////////////// evaluator interface ////////////////////////////////////////////
- call_output_observers(...) from builtins.PyCapsule
- call_output_observers(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType
call all output_observers
- clear_evaluators(...) from builtins.PyCapsule
- clear_evaluators(rosetta.protocols.jd2.JobOutputter) -> NoneType
- evaluate(...) from builtins.PyCapsule
- evaluate(self : rosetta.protocols.jd2.JobOutputter, pose : rosetta.core.pose.Pose, tag : str, pss : rosetta.core.io.silent.SilentStruct) -> NoneType
- evaluators(...) from builtins.PyCapsule
- evaluators(rosetta.protocols.jd2.JobOutputter) -> rosetta.protocols.evaluation.MetaPoseEvaluator
- filename(...) from builtins.PyCapsule
- filename(self : rosetta.protocols.jd2.JobOutputter, : rosetta.protocols.jd2.Job) -> str
- flush(...) from builtins.PyCapsule
- flush(rosetta.protocols.jd2.JobOutputter) -> NoneType
this function is meant to be redefined in child classes to allow for flushing of memory buffers.
Here's the long version: The SilentFileJobOutputter wanted to buffer output, but needed to guaruntee that
the output would be flushed at end of runtime. The original implementation was to A) bend over backward to ensure
that the destructor was run (JobOutputter lives inside static JobDistributor, which was previously not destructed
because it's static) and B) flush the buffers in the destructor. This caused a problem because the buffer-flushing
tried to use the Tracers, which had already been destructed...boom crash.
New solution: re-forbid use of destructors within the static JobDistributor system, and create a flush
function to force this stuff out. So here it is:
- set_evaluators(...) from builtins.PyCapsule
- set_evaluators(self : rosetta.protocols.jd2.JobOutputter, : rosetta.protocols.evaluation.MetaPoseEvaluator) -> NoneType
- starting_pose(...) from builtins.PyCapsule
- starting_pose(self : rosetta.protocols.jd2.JobOutputter, : rosetta.core.pose.Pose) -> NoneType
optionally pass a starting (reference) pose to a JobOutputter for later comparison
purposes and/or as interface for initializing evaluators
|
class GenerateStoredRBConfs(ModifyStoredRBConfs) |
| |
generates random rbconfs until a total of num_total_rbconfs_
are present in the cacheable observer. The diversifier is used to
ensure that all newly generated confs are different.
note: no scorefunction used
|
| |
- Method resolution order:
- GenerateStoredRBConfs
- ModifyStoredRBConfs
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, num_total_rbconfs : int, include_metals : bool) -> NoneType
2. __init__(handle, rosetta.protocols.enzdes.GenerateStoredRBConfs) -> 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.enzdes.GenerateStoredRBConfs, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.GenerateStoredRBConfs, : rosetta.protocols.enzdes.GenerateStoredRBConfs) -> rosetta.protocols.enzdes.GenerateStoredRBConfs
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.GenerateStoredRBConfs) -> str
Methods inherited from ModifyStoredRBConfs:
- closest_orient_atoms_msd(...) from builtins.PyCapsule
- closest_orient_atoms_msd(self : rosetta.protocols.enzdes.ModifyStoredRBConfs, pose : rosetta.core.pose.Pose, confs : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> rosetta.utility.vector1_double
calculates the closest orient atom (i.e. atoms used in rotamer placement
msd between every conf and the confs coming before it in the pose or in the vector
- swap_coordinates_in_pose(...) from builtins.PyCapsule
- swap_coordinates_in_pose(self : rosetta.protocols.enzdes.ModifyStoredRBConfs, pose : rosetta.core.pose.Pose, rescoords : rosetta.core.conformation.Residue) -> NoneType
helper function to exchange coordinates in a pose
this function doesn't actually exchange the residues,
but sets all the coords of pose.residue( rescoords.seqpos() )
to what is in rescoords and vice versa
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
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class LigBurialFilter(rosetta.protocols.filters.Filter) |
| | |
- Method resolution order:
- LigBurialFilter
- rosetta.protocols.filters.Filter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, lig_id : int, numneighbors : int, distance_threshold : float) -> NoneType
3. __init__(handle, rosetta.protocols.enzdes.LigBurialFilter) -> 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.enzdes.LigBurialFilter, pose : rosetta.core.pose.Pose) -> bool
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.enzdes.LigBurialFilter) -> rosetta.protocols.filters.Filter
- compute(...) from builtins.PyCapsule
- compute(self : rosetta.protocols.enzdes.LigBurialFilter, pose : rosetta.core.pose.Pose) -> int
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.enzdes.LigBurialFilter) -> rosetta.protocols.filters.Filter
- report_sm(...) from builtins.PyCapsule
- report_sm(self : rosetta.protocols.enzdes.LigBurialFilter, pose : rosetta.core.pose.Pose) -> float
Methods inherited from rosetta.protocols.filters.Filter:
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.filters.Filter) -> NoneType
used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.filters.Filter) -> str
- get_user_defined_name(...) from builtins.PyCapsule
- get_user_defined_name(rosetta.protocols.filters.Filter) -> str
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.filters.Filter) -> str
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.filters.Filter, pose : rosetta.core.pose.Pose) -> float
- set_user_defined_name(...) from builtins.PyCapsule
- set_user_defined_name(self : rosetta.protocols.filters.Filter, name : str) -> NoneType
|
class LigDSasaFilter(rosetta.protocols.filters.Filter) |
| | |
- Method resolution order:
- LigDSasaFilter
- rosetta.protocols.filters.Filter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, lower_threshold : float, upper_threshold : float) -> NoneType
3. __init__(handle, rosetta.protocols.enzdes.LigDSasaFilter) -> 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.enzdes.LigDSasaFilter, pose : rosetta.core.pose.Pose) -> bool
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.enzdes.LigDSasaFilter) -> rosetta.protocols.filters.Filter
- compute(...) from builtins.PyCapsule
- compute(self : rosetta.protocols.enzdes.LigDSasaFilter, pose : rosetta.core.pose.Pose) -> float
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.enzdes.LigDSasaFilter) -> rosetta.protocols.filters.Filter
- report_sm(...) from builtins.PyCapsule
- report_sm(self : rosetta.protocols.enzdes.LigDSasaFilter, pose : rosetta.core.pose.Pose) -> float
Methods inherited from rosetta.protocols.filters.Filter:
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.filters.Filter) -> NoneType
used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.filters.Filter) -> str
- get_user_defined_name(...) from builtins.PyCapsule
- get_user_defined_name(rosetta.protocols.filters.Filter) -> str
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.filters.Filter) -> str
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.filters.Filter, pose : rosetta.core.pose.Pose) -> float
- set_user_defined_name(...) from builtins.PyCapsule
- set_user_defined_name(self : rosetta.protocols.filters.Filter, name : str) -> NoneType
|
class LigInterfaceEnergyFilter(rosetta.protocols.filters.Filter) |
| | |
- Method resolution order:
- LigInterfaceEnergyFilter
- rosetta.protocols.filters.Filter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.scoring.ScoreFunction, float) -> NoneType
doc
3. __init__(handle, rosetta.core.scoring.ScoreFunction, float, bool) -> NoneType
doc
4. __init__(handle, rosetta.core.scoring.ScoreFunction, float, bool, int) -> NoneType
doc
5. __init__(self : handle, scorefxn : rosetta.core.scoring.ScoreFunction, threshold : float, include_cstE : bool, rb_jump : int, interface_distance_cutoff : float) -> NoneType
6. __init__(handle, rosetta.protocols.enzdes.LigInterfaceEnergyFilter) -> 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.enzdes.LigInterfaceEnergyFilter, pose : rosetta.core.pose.Pose) -> bool
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.enzdes.LigInterfaceEnergyFilter) -> rosetta.protocols.filters.Filter
- compute(...) from builtins.PyCapsule
- compute(self : rosetta.protocols.enzdes.LigInterfaceEnergyFilter, pose : rosetta.core.pose.Pose) -> float
- constraint_energy(...) from builtins.PyCapsule
- constraint_energy(self : rosetta.protocols.enzdes.LigInterfaceEnergyFilter, pose : rosetta.core.pose.Pose, which_res : int) -> float
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.enzdes.LigInterfaceEnergyFilter) -> rosetta.protocols.filters.Filter
- report_sm(...) from builtins.PyCapsule
- report_sm(self : rosetta.protocols.enzdes.LigInterfaceEnergyFilter, pose : rosetta.core.pose.Pose) -> float
Methods inherited from rosetta.protocols.filters.Filter:
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.filters.Filter) -> NoneType
used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.filters.Filter) -> str
- get_user_defined_name(...) from builtins.PyCapsule
- get_user_defined_name(rosetta.protocols.filters.Filter) -> str
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.filters.Filter) -> str
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.filters.Filter, pose : rosetta.core.pose.Pose) -> float
- set_user_defined_name(...) from builtins.PyCapsule
- set_user_defined_name(self : rosetta.protocols.filters.Filter, name : str) -> NoneType
|
class MinimizeStoredRBConfs(ModifyStoredRBConfs) |
| |
rotamer trials/minimizes each of the ligand conformations stored in the enzdes
cacheable observer and overwrites them with the minimized position.
if the new, minimized position is too close to one that already exists,
a random small perturbation is applied to ensure diversity
note: only jump minimization
|
| |
- Method resolution order:
- MinimizeStoredRBConfs
- ModifyStoredRBConfs
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
2. __init__(handle, rosetta.protocols.enzdes.MinimizeStoredRBConfs) -> 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.enzdes.MinimizeStoredRBConfs, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.MinimizeStoredRBConfs, : rosetta.protocols.enzdes.MinimizeStoredRBConfs) -> rosetta.protocols.enzdes.MinimizeStoredRBConfs
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.MinimizeStoredRBConfs) -> str
- rb_minimize_all_confs(...) from builtins.PyCapsule
- rb_minimize_all_confs(self : rosetta.protocols.enzdes.MinimizeStoredRBConfs, pose : rosetta.core.pose.Pose, confs : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
Methods inherited from ModifyStoredRBConfs:
- closest_orient_atoms_msd(...) from builtins.PyCapsule
- closest_orient_atoms_msd(self : rosetta.protocols.enzdes.ModifyStoredRBConfs, pose : rosetta.core.pose.Pose, confs : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> rosetta.utility.vector1_double
calculates the closest orient atom (i.e. atoms used in rotamer placement
msd between every conf and the confs coming before it in the pose or in the vector
- swap_coordinates_in_pose(...) from builtins.PyCapsule
- swap_coordinates_in_pose(self : rosetta.protocols.enzdes.ModifyStoredRBConfs, pose : rosetta.core.pose.Pose, rescoords : rosetta.core.conformation.Residue) -> NoneType
helper function to exchange coordinates in a pose
this function doesn't actually exchange the residues,
but sets all the coords of pose.residue( rescoords.seqpos() )
to what is in rescoords and vice versa
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
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class ModifyStoredRBConfs(rosetta.protocols.moves.Mover) |
| |
virtual base class that has some common functionality
|
| |
- Method resolution order:
- ModifyStoredRBConfs
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.enzdes.ModifyStoredRBConfs, name : str) -> NoneType
2. __init__(rosetta.protocols.enzdes.ModifyStoredRBConfs, rosetta.protocols.enzdes.ModifyStoredRBConfs) -> 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.enzdes.ModifyStoredRBConfs, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.ModifyStoredRBConfs, : rosetta.protocols.enzdes.ModifyStoredRBConfs) -> rosetta.protocols.enzdes.ModifyStoredRBConfs
- closest_orient_atoms_msd(...) from builtins.PyCapsule
- closest_orient_atoms_msd(self : rosetta.protocols.enzdes.ModifyStoredRBConfs, pose : rosetta.core.pose.Pose, confs : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> rosetta.utility.vector1_double
calculates the closest orient atom (i.e. atoms used in rotamer placement
msd between every conf and the confs coming before it in the pose or in the vector
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.ModifyStoredRBConfs) -> str
- swap_coordinates_in_pose(...) from builtins.PyCapsule
- swap_coordinates_in_pose(self : rosetta.protocols.enzdes.ModifyStoredRBConfs, pose : rosetta.core.pose.Pose, rescoords : rosetta.core.conformation.Residue) -> NoneType
helper function to exchange coordinates in a pose
this function doesn't actually exchange the residues,
but sets all the coords of pose.residue( rescoords.seqpos() )
to what is in rescoords and vice versa
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
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class PackRotamersMoverPartGreedy(rosetta.protocols.moves.Mover) |
| |
a mover that packs the side-chains around a given set of target residues in a greedy fashion, and then packs the rest using the sim annealer.
|
| |
- Method resolution order:
- PackRotamersMoverPartGreedy
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, scorefxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, target_residues : rosetta.utility.vector1_unsigned_long) -> NoneType
2. __init__(handle) -> NoneType
3. __init__(handle, rosetta.protocols.enzdes.PackRotamersMoverPartGreedy) -> 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.enzdes.PackRotamersMoverPartGreedy, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.PackRotamersMoverPartGreedy, : rosetta.protocols.enzdes.PackRotamersMoverPartGreedy) -> rosetta.protocols.enzdes.PackRotamersMoverPartGreedy
- choose_n_best(...) from builtins.PyCapsule
- choose_n_best(self : rosetta.protocols.enzdes.PackRotamersMoverPartGreedy, pose : rosetta.core.pose.Pose, n_best : int) -> rosetta.utility.vector1_unsigned_long
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.enzdes.PackRotamersMoverPartGreedy) -> rosetta.protocols.moves.Mover
- compute_designable_neighbors(...) from builtins.PyCapsule
- compute_designable_neighbors(self : rosetta.protocols.enzdes.PackRotamersMoverPartGreedy, position : int, task : rosetta.core.pack.task.PackerTask, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.enzdes.PackRotamersMoverPartGreedy) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.PackRotamersMoverPartGreedy) -> str
- greedy_around(...) from builtins.PyCapsule
- greedy_around(self : rosetta.protocols.enzdes.PackRotamersMoverPartGreedy, pose : rosetta.core.pose.Pose, target_res : rosetta.utility.vector1_unsigned_long, task : rosetta.core.pack.task.PackerTask, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- target_residues(...) from builtins.PyCapsule
- target_residues(self : rosetta.protocols.enzdes.PackRotamersMoverPartGreedy, trg_res : rosetta.utility.vector1_unsigned_long) -> NoneType
- task(...) from builtins.PyCapsule
- task(self : rosetta.protocols.enzdes.PackRotamersMoverPartGreedy, task : rosetta.core.pack.task.PackerTask) -> NoneType
- task_factory(...) from builtins.PyCapsule
- task_factory(self : rosetta.protocols.enzdes.PackRotamersMoverPartGreedy, p : rosetta.core.pack.task.TaskFactory) -> NoneType
- update_task_and_neighbors(...) from builtins.PyCapsule
- update_task_and_neighbors(self : rosetta.protocols.enzdes.PackRotamersMoverPartGreedy, best_neigh : int, task : rosetta.core.pack.task.PackerTask, current_neighbors : rosetta.utility.vector1_unsigned_long) -> 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
|
class PredesignPerturbMover(rosetta.protocols.rigid.RigidBodyPerturbMover) |
| | |
- Method resolution order:
- PredesignPerturbMover
- rosetta.protocols.rigid.RigidBodyPerturbMover
- rosetta.protocols.rigid.RigidBodyMover
- rosetta.protocols.canonical_sampling.ThermodynamicMover
- 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.enzdes.PredesignPerturbMover) -> 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.enzdes.PredesignPerturbMover, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.PredesignPerturbMover, : rosetta.protocols.enzdes.PredesignPerturbMover) -> rosetta.protocols.enzdes.PredesignPerturbMover
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.enzdes.PredesignPerturbMover) -> rosetta.protocols.moves.Mover
- find_constraints_to_ligand(...) from builtins.PyCapsule
- find_constraints_to_ligand(self : rosetta.protocols.enzdes.PredesignPerturbMover, pose : rosetta.core.pose.Pose) -> NoneType
- find_geometric_center_for_constrained_lig_atoms(...) from builtins.PyCapsule
- find_geometric_center_for_constrained_lig_atoms(self : rosetta.protocols.enzdes.PredesignPerturbMover, pose : rosetta.core.pose.Pose) -> rosetta.numeric.xyzVector_double_t
- find_rotation_center(...) from builtins.PyCapsule
- find_rotation_center(self : rosetta.protocols.enzdes.PredesignPerturbMover, pose : rosetta.core.pose.Pose) -> rosetta.numeric.xyzVector_double_t
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.enzdes.PredesignPerturbMover) -> rosetta.protocols.moves.Mover
- get_constrained_lig_atoms(...) from builtins.PyCapsule
- get_constrained_lig_atoms(rosetta.protocols.enzdes.PredesignPerturbMover) -> rosetta.utility.vector1_unsigned_long
Allow an outside interpretter to the set of atoms for which there are AtomPair constraints to
the ligand.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.PredesignPerturbMover) -> str
- reinstate_pose(...) from builtins.PyCapsule
- reinstate_pose(self : rosetta.protocols.enzdes.PredesignPerturbMover, pose : rosetta.core.pose.Pose, old_Pose : rosetta.core.pose.Pose) -> NoneType
- set_docking_pose(...) from builtins.PyCapsule
- set_docking_pose(self : rosetta.protocols.enzdes.PredesignPerturbMover, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
- set_ligand(...) from builtins.PyCapsule
- set_ligand(self : rosetta.protocols.enzdes.PredesignPerturbMover, res_no : int) -> NoneType
Methods inherited from rosetta.protocols.rigid.RigidBodyPerturbMover:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.rigid.RigidBodyPerturbMover) -> str
- get_rot_mag(...) from builtins.PyCapsule
- get_rot_mag(rosetta.protocols.rigid.RigidBodyPerturbMover) -> float
- get_trans_mag(...) from builtins.PyCapsule
- get_trans_mag(rosetta.protocols.rigid.RigidBodyPerturbMover) -> float
- rot_center(...) from builtins.PyCapsule
- rot_center(self : rosetta.protocols.rigid.RigidBodyPerturbMover, : rosetta.numeric.xyzVector_double_t) -> NoneType
Manual override of rotation center.
- rot_magnitude(...) from builtins.PyCapsule
- rot_magnitude(self : rosetta.protocols.rigid.RigidBodyPerturbMover, magnitude : float) -> NoneType
- trans_magnitude(...) from builtins.PyCapsule
- trans_magnitude(self : rosetta.protocols.rigid.RigidBodyPerturbMover, magnitude : float) -> NoneType
Methods inherited from rosetta.protocols.rigid.RigidBodyMover:
- freeze(...) from builtins.PyCapsule
- freeze(rosetta.protocols.rigid.RigidBodyMover) -> NoneType
- preserve_detailed_balance(...) from builtins.PyCapsule
- preserve_detailed_balance(rosetta.protocols.rigid.RigidBodyMover) -> bool
- rb_jump(...) from builtins.PyCapsule
- rb_jump(*args, **kwargs)
Overloaded function.
1. rb_jump(rosetta.protocols.rigid.RigidBodyMover) -> int
2. rb_jump(self : rosetta.protocols.rigid.RigidBodyMover, jump_id : int) -> NoneType
- set_preserve_detailed_balance(...) from builtins.PyCapsule
- set_preserve_detailed_balance(self : rosetta.protocols.rigid.RigidBodyMover, : bool) -> NoneType
set whether detailed balance is preserved (i.e. no branch angle optimization during moves)
- torsion_id_ranges(...) from builtins.PyCapsule
- torsion_id_ranges(self : rosetta.protocols.rigid.RigidBodyMover, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_core_id_TorsionID_Range
get the TorsionIDs perturbed by the mover during moves, along with their ranges
- unfreeze(...) from builtins.PyCapsule
- unfreeze(rosetta.protocols.rigid.RigidBodyMover) -> NoneType
Methods inherited from rosetta.protocols.canonical_sampling.ThermodynamicMover:
- finalize_simulation(...) from builtins.PyCapsule
- finalize_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicMover, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
Callback executed after all Monte Carlo trials are completed.
- initialize_simulation(...) from builtins.PyCapsule
- initialize_simulation(self : rosetta.protocols.canonical_sampling.ThermodynamicMover, pose : rosetta.core.pose.Pose, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover, cycle : int) -> NoneType
Callback executed before any Monte Carlo trials are attempted.
- is_multi_trial(...) from builtins.PyCapsule
- is_multi_trial(rosetta.protocols.canonical_sampling.ThermodynamicMover) -> bool
Return true if the move performs multiple trials on each apply.
last_inner_score_delta_over_temperature()
metropolis_hastings_mover()
set_metropolis_hastings_mover()
- last_inner_score_delta_over_temperature(...) from builtins.PyCapsule
- last_inner_score_delta_over_temperature(rosetta.protocols.canonical_sampling.ThermodynamicMover) -> float
If this is a multi-trial move, return the change in internal
score/temperature caused by the last call to apply().
is_multi_trial()
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.canonical_sampling.ThermodynamicMover) -> float
Return the proposal density ratio for last apply method.
- metropolis_hastings_mover(...) from builtins.PyCapsule
- metropolis_hastings_mover(rosetta.protocols.canonical_sampling.ThermodynamicMover) -> rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t
If this is a multi-trial move, return the MetropolisHastingsMover
being used internally.
is_multi_trial()
- observe_after_metropolis(...) from builtins.PyCapsule
- observe_after_metropolis(self : rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover : protocols::canonical_sampling::MetropolisHastingsMover) -> NoneType
Callback executed after the Metropolis criterion is evaluated.
- set_metropolis_hastings_mover(...) from builtins.PyCapsule
- set_metropolis_hastings_mover(self : rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover : rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) -> NoneType
If this is a multi-trial move, set the MetropolisHastingsMover to
be used internally.
is_multi_trial()
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
- 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 RepackLigandSiteWithoutLigandMover(rosetta.protocols.moves.Mover) |
| |
class that will identify the region around the ligand,
remove it, and then do a repack. It can also calculate the following
parameters: E diff after the repack, (in essence a crude delta G calc)
rmsd of the repacked site after the repack and rmsd of catalytic residues
|
| |
- Method resolution order:
- RepackLigandSiteWithoutLigandMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, sfxn : rosetta.core.scoring.ScoreFunction, calculate_silent_Es : bool) -> NoneType
3. __init__(handle, rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover) -> 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.enzdes.RepackLigandSiteWithoutLigandMover, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover, : rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover) -> rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover) -> str
- get_ptask(...) from builtins.PyCapsule
- get_ptask(rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover) -> rosetta.core.pack.task.PackerTask
- set_calculate_silent_Es(...) from builtins.PyCapsule
- set_calculate_silent_Es(self : rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover, calculate : bool) -> NoneType
- set_cstio(...) from builtins.PyCapsule
- set_cstio(self : rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover, enzcst_io : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> NoneType
- set_separate_prt_ligand(...) from builtins.PyCapsule
- set_separate_prt_ligand(self : rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover, separate_prt_ligand : bool) -> NoneType
- set_sfxn(...) from builtins.PyCapsule
- set_sfxn(self : rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- silent_Es(...) from builtins.PyCapsule
- silent_Es(rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover) -> rosetta.utility.vector1_core_io_silent_SilentEnergy
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
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class RepackWithoutLigandFilter(rosetta.protocols.filters.Filter) |
| | |
- Method resolution order:
- RepackWithoutLigandFilter
- rosetta.protocols.filters.Filter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, scorefxn : rosetta.core.scoring.ScoreFunction, rms_thresh : float, energy_thresh : float, rms_target_res : rosetta.utility.vector1_unsigned_long) -> NoneType
3. __init__(handle, rosetta.protocols.enzdes.RepackWithoutLigandFilter) -> 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.enzdes.RepackWithoutLigandFilter, pose : rosetta.core.pose.Pose) -> bool
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.enzdes.RepackWithoutLigandFilter) -> rosetta.protocols.filters.Filter
- compute(...) from builtins.PyCapsule
- compute(self : rosetta.protocols.enzdes.RepackWithoutLigandFilter, pose : rosetta.core.pose.Pose) -> float
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.enzdes.RepackWithoutLigandFilter) -> rosetta.protocols.filters.Filter
- report_sm(...) from builtins.PyCapsule
- report_sm(self : rosetta.protocols.enzdes.RepackWithoutLigandFilter, pose : rosetta.core.pose.Pose) -> float
- set_cstid_list(...) from builtins.PyCapsule
- set_cstid_list(self : rosetta.protocols.enzdes.RepackWithoutLigandFilter, setting : str) -> NoneType
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.enzdes.RepackWithoutLigandFilter, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
Methods inherited from rosetta.protocols.filters.Filter:
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.filters.Filter) -> NoneType
used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.filters.Filter) -> str
- get_user_defined_name(...) from builtins.PyCapsule
- get_user_defined_name(rosetta.protocols.filters.Filter) -> str
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.filters.Filter) -> str
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.filters.Filter, pose : rosetta.core.pose.Pose) -> float
- set_user_defined_name(...) from builtins.PyCapsule
- set_user_defined_name(self : rosetta.protocols.filters.Filter, name : str) -> NoneType
|
class ResidueConformerFilter(rosetta.protocols.filters.Filter) |
| |
filter that figures out which rotamer of a given
rotamer lib is in the pose at apply time, and can be used
to filter on it. supposed to be used for ligands,
and for now only tested for them, but
should also work with any other residue.
can be used for example in specificity redesign, if one
wants to divide up a bunch of designs according to the
orientation in which they bind the ligand
|
| |
- Method resolution order:
- ResidueConformerFilter
- rosetta.protocols.filters.Filter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.enzdes.ResidueConformerFilter) -> 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.enzdes.ResidueConformerFilter, pose : rosetta.core.pose.Pose) -> bool
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.enzdes.ResidueConformerFilter) -> rosetta.protocols.filters.Filter
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.enzdes.ResidueConformerFilter) -> rosetta.protocols.filters.Filter
- get_current_conformer(...) from builtins.PyCapsule
- get_current_conformer(self : rosetta.protocols.enzdes.ResidueConformerFilter, pose : rosetta.core.pose.Pose) -> int
- report_sm(...) from builtins.PyCapsule
- report_sm(self : rosetta.protocols.enzdes.ResidueConformerFilter, pose : rosetta.core.pose.Pose) -> float
Methods inherited from rosetta.protocols.filters.Filter:
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.filters.Filter) -> NoneType
used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.filters.Filter) -> str
- get_user_defined_name(...) from builtins.PyCapsule
- get_user_defined_name(rosetta.protocols.filters.Filter) -> str
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.filters.Filter) -> str
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.filters.Filter, pose : rosetta.core.pose.Pose) -> float
- set_user_defined_name(...) from builtins.PyCapsule
- set_user_defined_name(self : rosetta.protocols.filters.Filter, name : str) -> NoneType
|
class SecondaryMatchProtocol(EnzdesBaseProtocol) |
| | |
- Method resolution order:
- SecondaryMatchProtocol
- EnzdesBaseProtocol
- rosetta.protocols.ligand_docking.LigandBaseProtocol
- 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.enzdes.SecondaryMatchProtocol) -> 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.enzdes.SecondaryMatchProtocol, start_pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.SecondaryMatchProtocol, : rosetta.protocols.enzdes.SecondaryMatchProtocol) -> rosetta.protocols.enzdes.SecondaryMatchProtocol
- do_matching(...) from builtins.PyCapsule
- do_matching(self : rosetta.protocols.enzdes.SecondaryMatchProtocol, start_pose : rosetta.core.pose.Pose) -> bool
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.SecondaryMatchProtocol) -> str
- residues_compatible(...) from builtins.PyCapsule
- residues_compatible(self : rosetta.protocols.enzdes.SecondaryMatchProtocol, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue) -> int
- set_trial_positions(...) from builtins.PyCapsule
- set_trial_positions(self : rosetta.protocols.enzdes.SecondaryMatchProtocol, trial_pos : rosetta.utility.vector1_unsigned_long) -> NoneType
Methods inherited from EnzdesBaseProtocol:
- add_pregenerated_enzdes_constraints(...) from builtins.PyCapsule
- add_pregenerated_enzdes_constraints(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> NoneType
- catalytic_res(...) from builtins.PyCapsule
- catalytic_res(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long
- create_enzdes_movemap(...) from builtins.PyCapsule
- create_enzdes_movemap(*args, **kwargs)
Overloaded function.
1. create_enzdes_movemap(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> rosetta.core.kinematics.MoveMap
2. create_enzdes_movemap(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, min_all_jumps : bool) -> rosetta.core.kinematics.MoveMap
- create_enzdes_pack_task(...) from builtins.PyCapsule
- create_enzdes_pack_task(*args, **kwargs)
Overloaded function.
1. create_enzdes_pack_task(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> rosetta.core.pack.task.PackerTask
2. create_enzdes_pack_task(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, design : bool) -> rosetta.core.pack.task.PackerTask
- cst_minimize(...) from builtins.PyCapsule
- cst_minimize(*args, **kwargs)
Overloaded function.
1. cst_minimize(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
2. cst_minimize(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, cst_opt : bool) -> NoneType
- design_targets(...) from builtins.PyCapsule
- design_targets(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t
- design_targets_score(...) from builtins.PyCapsule
- design_targets_score(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose) -> float
- enzdes_pack(...) from builtins.PyCapsule
- enzdes_pack(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask, scorefxn : rosetta.core.scoring.ScoreFunction, cycles : int, minimize_after_packing : bool, pack_unconstrained : bool, favor_native : bool) -> NoneType
- generate_explicit_ligand_rotamer_poses(...) from builtins.PyCapsule
- generate_explicit_ligand_rotamer_poses(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, orig_pose : rosetta.core.pose.Pose, ligrot_poses : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, scofx : rosetta.core.scoring.ScoreFunction) -> NoneType
- is_catalytic_position(...) from builtins.PyCapsule
- is_catalytic_position(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, seqpos : int) -> bool
- rb_min_jumps(...) from builtins.PyCapsule
- rb_min_jumps(*args, **kwargs)
Overloaded function.
1. rb_min_jumps(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.utility.vector1_unsigned_long
2. rb_min_jumps(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, : rosetta.utility.vector1_unsigned_long) -> NoneType
- reduced_scorefxn(...) from builtins.PyCapsule
- reduced_scorefxn(*args, **kwargs)
Overloaded function.
1. reduced_scorefxn(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.core.scoring.ScoreFunction
2. reduced_scorefxn(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.core.scoring.ScoreFunction
- 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
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, smap : rosetta.core.id.SequenceMapping) -> NoneType
- remove_enzdes_constraints(...) from builtins.PyCapsule
- remove_enzdes_constraints(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, keep_covalent : bool) -> NoneType
- restype_set(...) from builtins.PyCapsule
- restype_set(rosetta.protocols.enzdes.EnzdesBaseProtocol) -> rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t
- set_all_jumps_minimizable(...) from builtins.PyCapsule
- set_all_jumps_minimizable(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, setting : bool) -> NoneType
- set_fix_cataa(...) from builtins.PyCapsule
- set_fix_cataa(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, setting : bool) -> NoneType
- set_minimize_options(...) from builtins.PyCapsule
- set_minimize_options(*args, **kwargs)
Overloaded function.
1. set_minimize_options(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, min_sc : bool, min_bb : bool, min_rb : bool, min_lig : bool) -> NoneType
2. set_minimize_options(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, min_sc : bool, min_bb : bool, min_rb : bool, min_lig : bool, backrub : bool) -> NoneType
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
- setup_bbmin_ft_and_csts(...) from builtins.PyCapsule
- setup_bbmin_ft_and_csts(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, allow_move_bb : rosetta.utility.vector1_bool, jump_id : int) -> NoneType
- setup_sequence_recovery_cache(...) from builtins.PyCapsule
- setup_sequence_recovery_cache(self : rosetta.protocols.enzdes.EnzdesBaseProtocol, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
Methods inherited from rosetta.protocols.ligand_docking.LigandBaseProtocol:
- get_ligand_id(...) from builtins.PyCapsule
- get_ligand_id(*args, **kwargs)
Overloaded function.
1. get_ligand_id(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose) -> int
2. get_ligand_id(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, jump_id : int) -> int
- get_ligand_jump_id(...) from builtins.PyCapsule
- get_ligand_jump_id(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose) -> int
- get_non_bb_clashing_rotamers(...) from builtins.PyCapsule
- get_non_bb_clashing_rotamers(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, seqpos : int, scofx : rosetta.core.scoring.ScoreFunction, accepted_rotamers : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
- get_scorefxn(...) from builtins.PyCapsule
- get_scorefxn(*args, **kwargs)
Overloaded function.
1. get_scorefxn(rosetta.protocols.ligand_docking.LigandBaseProtocol) -> rosetta.core.scoring.ScoreFunction
2. get_scorefxn(rosetta.protocols.ligand_docking.LigandBaseProtocol) -> rosetta.core.scoring.ScoreFunction
- reorder_foldtree_around_mobile_regions(...) from builtins.PyCapsule
- reorder_foldtree_around_mobile_regions(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, jump_id : int, mobile_bb : rosetta.utility.vector1_bool, lig_id : int) -> NoneType
- restrain_protein_Calphas(...) from builtins.PyCapsule
- restrain_protein_Calphas(self : rosetta.protocols.ligand_docking.LigandBaseProtocol, pose : rosetta.core.pose.Pose, is_restrained : rosetta.utility.vector1_bool, restr_func : rosetta.core.scoring.func.Func) -> NoneType
- shared_from_this(...) from builtins.PyCapsule
- shared_from_this(rosetta.protocols.ligand_docking.LigandBaseProtocol) -> rosetta.protocols.ligand_docking.LigandBaseProtocol
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
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- 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 SetCatalyticResPackBehavior(rosetta.core.pack.task.operation.TaskOperation) |
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queries the pose cst cache for the catalytic residues,
and sets the behavior for them as specified in the cstfile
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- Method resolution order:
- SetCatalyticResPackBehavior
- 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.enzdes.SetCatalyticResPackBehavior) -> 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.enzdes.SetCatalyticResPackBehavior, pose : rosetta.core.pose.Pose, task : 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.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.SetCatalyticResPackBehavior, : rosetta.protocols.enzdes.SetCatalyticResPackBehavior) -> rosetta.protocols.enzdes.SetCatalyticResPackBehavior
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.enzdes.SetCatalyticResPackBehavior) -> rosetta.core.pack.task.operation.TaskOperation
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.enzdes.SetCatalyticResPackBehavior, 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_fix_catalytic_aa(...) from builtins.PyCapsule
- set_fix_catalytic_aa(self : rosetta.protocols.enzdes.SetCatalyticResPackBehavior, setting : bool) -> NoneType
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class UpdateEnzdesHeaderMover(rosetta.protocols.moves.Mover) |
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mover that updates the enzdes pdb header, for use in cases where catalytic residues may be designed
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- Method resolution order:
- UpdateEnzdesHeaderMover
- 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.enzdes.UpdateEnzdesHeaderMover) -> 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.enzdes.UpdateEnzdesHeaderMover, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.enzdes.UpdateEnzdesHeaderMover, : rosetta.protocols.enzdes.UpdateEnzdesHeaderMover) -> rosetta.protocols.enzdes.UpdateEnzdesHeaderMover
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.enzdes.UpdateEnzdesHeaderMover) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.enzdes.UpdateEnzdesHeaderMover) -> 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
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
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class ValueEvaluator(builtins.object) |
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tiny helper struct for EnzdesScoreFileFilter
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : rosetta.protocols.enzdes.ValueEvaluator, mode : protocols::enzdes::ValueEvaluator::CompareMode, cutoff : float) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- value_passes(...) from builtins.PyCapsule
- value_passes(self : rosetta.protocols.enzdes.ValueEvaluator, value : float) -> bool
Data descriptors defined here:
- cutoff_
- mode_
Data and other attributes defined here:
- CompareMode = <class 'rosetta.protocols.enzdes.ValueEvaluator.CompareMode'>
- EQUALS = CompareMode.EQUALS
- LARGER = CompareMode.LARGER
- SMALLER = CompareMode.SMALLER
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