| | |
- builtins.object
-
- DofUnlock
- EnvClaimBroker
- rosetta.basic.datacache.WriteableCacheableData(rosetta.basic.datacache.CacheableData)
-
- AutoCutData
- rosetta.basic.datacache.WriteableCacheableDataCreator(builtins.object)
-
- AutoCutDataCreator
- rosetta.core.conformation.Conformation(builtins.object)
-
- ProtectedConformation
- rosetta.core.environment.EXCN_Env_Exception(rosetta.utility.excn.EXCN_Msg_Exception)
-
- EXCN_Env_Passport
- EXCN_Env_Security_Exception
- rosetta.core.environment.EnvCore(builtins.object)
-
- Environment
- rosetta.protocols.moves.Mover(builtins.object)
-
- ClientMover
-
- CoMTrackerCM
- ScriptCM
- EnvMover
- rosetta.protocols.moves.MoverCreator(builtins.object)
-
- CoMTrackerCMCreator
- EnvMoverCreator
- ScriptCMCreator
class ClientMover(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- ClientMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.environment.ClientMover) -> NoneType
2. __init__(rosetta.protocols.environment.ClientMover, rosetta.protocols.environment.ClientMover) -> 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.environment.ClientMover, : rosetta.protocols.environment.ClientMover) -> rosetta.protocols.environment.ClientMover
- initialize(...) from builtins.PyCapsule
- initialize(self : rosetta.protocols.environment.ClientMover, conf : rosetta.core.pose.Pose) -> NoneType
this method is called by the broking system in response to a
successful initialization claim by this mover. The passport
will prevent any unauthorized changes.
- yield_claims(...) from builtins.PyCapsule
- yield_claims(self : rosetta.protocols.environment.ClientMover, : rosetta.core.pose.Pose, : rosetta.basic.datacache.WriteableCacheableMap) -> rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_std_allocator_std_shared_ptr_protocols_environment_claims_EnvClaim_t
Returns a list of claims for this mover.
The pose passed as an argument is used for reference informational
purposes only (for example, you want to know the sequence) or access
the pose cache. Any changes to the conformation will get overwritten!
- yield_submovers(...) from builtins.PyCapsule
- yield_submovers(self : rosetta.protocols.environment.ClientMover, : rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_std_less_std_shared_ptr_protocols_environment_ClientMover_std_allocator_std_shared_ptr_protocols_environment_ClientMover_t) -> NoneType
this method is used to make sure any movers contained in this
mover (that want to make claims) also get registered with the
environment.
Methods inherited from rosetta.protocols.moves.Mover:
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.moves.Mover, : rosetta.core.pose.Pose) -> NoneType
- 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_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.moves.Mover) -> str
Each derived class must specify its name. The class name.
- 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 CoMTrackerCM(ClientMover) |
| | |
- Method resolution order:
- CoMTrackerCM
- ClientMover
- 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, mobile_selector : rosetta.core.select.residue_selector.ResidueSelector, stationary_label : str) -> NoneType
3. __init__(self : handle, name : str, mobile_selector : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
4. __init__(handle, rosetta.protocols.environment.CoMTrackerCM) -> 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.environment.CoMTrackerCM, : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.environment.CoMTrackerCM, : rosetta.protocols.environment.CoMTrackerCM) -> rosetta.protocols.environment.CoMTrackerCM
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.environment.CoMTrackerCM) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.environment.CoMTrackerCM) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.environment.CoMTrackerCM) -> str
- initialize(...) from builtins.PyCapsule
- initialize(self : rosetta.protocols.environment.CoMTrackerCM, pose : rosetta.core.pose.Pose) -> NoneType
- name(...) from builtins.PyCapsule
- name(*args, **kwargs)
Overloaded function.
1. name(rosetta.protocols.environment.CoMTrackerCM) -> str
2. name(self : rosetta.protocols.environment.CoMTrackerCM, name : str) -> NoneType
- yield_claims(...) from builtins.PyCapsule
- yield_claims(self : rosetta.protocols.environment.CoMTrackerCM, : rosetta.core.pose.Pose, : rosetta.basic.datacache.WriteableCacheableMap) -> rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_std_allocator_std_shared_ptr_protocols_environment_claims_EnvClaim_t
Methods inherited from ClientMover:
- yield_submovers(...) from builtins.PyCapsule
- yield_submovers(self : rosetta.protocols.environment.ClientMover, : rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_std_less_std_shared_ptr_protocols_environment_ClientMover_std_allocator_std_shared_ptr_protocols_environment_ClientMover_t) -> NoneType
this method is used to make sure any movers contained in this
mover (that want to make claims) also get registered with the
environment.
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
- 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 EXCN_Env_Security_Exception(rosetta.core.environment.EXCN_Env_Exception) |
| | |
- Method resolution order:
- EXCN_Env_Security_Exception
- rosetta.core.environment.EXCN_Env_Exception
- rosetta.utility.excn.EXCN_Msg_Exception
- rosetta.utility.excn.EXCN_Exception
- rosetta.utility.excn.EXCN_Base
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, dof : rosetta.core.id.DOF_ID, pass : rosetta.core.environment.DofPassport, mod_type : str, : protocols::environment::ProtectedConformation, mover_name : str, env : rosetta.std.weak_ptr_const_protocols_environment_Environment_t) -> NoneType
2. __init__(self : handle, message : str, mover_name : str, env : rosetta.std.weak_ptr_const_protocols_environment_Environment_t) -> NoneType
3. __init__(handle, rosetta.protocols.environment.EXCN_Env_Security_Exception) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- id(...) from builtins.PyCapsule
- id(rosetta.protocols.environment.EXCN_Env_Security_Exception) -> rosetta.core.id.DOF_ID
- passport(...) from builtins.PyCapsule
- passport(rosetta.protocols.environment.EXCN_Env_Security_Exception) -> rosetta.core.environment.DofPassport
Methods inherited from rosetta.core.environment.EXCN_Env_Exception:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.environment.EXCN_Env_Exception, : rosetta.core.environment.EXCN_Env_Exception) -> rosetta.core.environment.EXCN_Env_Exception
Methods inherited from rosetta.utility.excn.EXCN_Msg_Exception:
- add_msg(...) from builtins.PyCapsule
- add_msg(self : rosetta.utility.excn.EXCN_Msg_Exception, str : str) -> NoneType
- msg(...) from builtins.PyCapsule
- msg(rosetta.utility.excn.EXCN_Msg_Exception) -> str
Methods inherited from rosetta.utility.excn.EXCN_Base:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.utility.excn.EXCN_Base) -> str
|
class EnvMover(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- EnvMover
- 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.environment.EnvMover) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_apply_mover(...) from builtins.PyCapsule
- add_apply_mover(self : rosetta.protocols.environment.EnvMover, : rosetta.protocols.moves.Mover) -> NoneType
- add_registered_mover(...) from builtins.PyCapsule
- add_registered_mover(self : rosetta.protocols.environment.EnvMover, : rosetta.protocols.moves.Mover) -> NoneType
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.environment.EnvMover, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.environment.EnvMover, : rosetta.protocols.environment.EnvMover) -> rosetta.protocols.environment.EnvMover
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.environment.EnvMover) -> rosetta.protocols.moves.Mover
- env(...) from builtins.PyCapsule
- env(rosetta.protocols.environment.EnvMover) -> rosetta.protocols.environment.Environment
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.environment.EnvMover) -> 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
|
class Environment(rosetta.core.environment.EnvCore) |
| | |
- Method resolution order:
- Environment
- rosetta.core.environment.EnvCore
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.environment.Environment, name : str) -> NoneType
2. __init__(self : rosetta.protocols.environment.Environment, : rosetta.protocols.environment.Environment) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- allow_pure_movers(...) from builtins.PyCapsule
- allow_pure_movers(*args, **kwargs)
Overloaded function.
1. allow_pure_movers(rosetta.protocols.environment.Environment) -> bool
2. allow_pure_movers(self : rosetta.protocols.environment.Environment, : bool) -> NoneType
- annotations(...) from builtins.PyCapsule
- annotations(rosetta.protocols.environment.Environment) -> rosetta.core.environment.SequenceAnnotation
- auto_cut(...) from builtins.PyCapsule
- auto_cut(*args, **kwargs)
Overloaded function.
1. auto_cut(rosetta.protocols.environment.Environment) -> bool
2. auto_cut(self : rosetta.protocols.environment.Environment, : bool) -> NoneType
- broker(...) from builtins.PyCapsule
- broker(rosetta.protocols.environment.Environment) -> rosetta.protocols.environment.EnvClaimBroker
- end(...) from builtins.PyCapsule
- end(self : rosetta.protocols.environment.Environment, : rosetta.core.pose.Pose) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.environment.Environment) -> rosetta.protocols.environment.Environment
self pointers
2. get_self_ptr(rosetta.protocols.environment.Environment) -> rosetta.protocols.environment.Environment
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.environment.Environment) -> rosetta.std.weak_ptr_const_protocols_environment_Environment_t
2. get_self_weak_ptr(rosetta.protocols.environment.Environment) -> rosetta.std.weak_ptr_protocols_environment_Environment_t
- inherit_cuts(...) from builtins.PyCapsule
- inherit_cuts(*args, **kwargs)
Overloaded function.
1. inherit_cuts(rosetta.protocols.environment.Environment) -> bool
2. inherit_cuts(self : rosetta.protocols.environment.Environment, : bool) -> NoneType
- is_registered(...) from builtins.PyCapsule
- is_registered(self : rosetta.protocols.environment.Environment, : protocols::environment::ClientMover) -> bool
- pconf_creation(...) from builtins.PyCapsule
- pconf_creation(self : rosetta.protocols.environment.Environment, ptr : rosetta.core.conformation.Conformation) -> NoneType
- pconf_destruction(...) from builtins.PyCapsule
- pconf_destruction(self : rosetta.protocols.environment.Environment, ptr : rosetta.core.conformation.Conformation) -> NoneType
- register_mover(...) from builtins.PyCapsule
- register_mover(self : rosetta.protocols.environment.Environment, : rosetta.protocols.moves.Mover) -> NoneType
- start(...) from builtins.PyCapsule
- start(self : rosetta.protocols.environment.Environment, : rosetta.core.pose.Pose) -> rosetta.core.pose.Pose
- superenv(...) from builtins.PyCapsule
- superenv(rosetta.protocols.environment.Environment) -> rosetta.std.weak_ptr_const_protocols_environment_Environment_t
Methods inherited from rosetta.core.environment.EnvCore:
- id(...) from builtins.PyCapsule
- id(rosetta.core.environment.EnvCore) -> int
- name(...) from builtins.PyCapsule
- name(rosetta.core.environment.EnvCore) -> str
|
class ProtectedConformation(rosetta.core.conformation.Conformation) |
| | |
- Method resolution order:
- ProtectedConformation
- rosetta.core.conformation.Conformation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle, rosetta.protocols.environment.ProtectedConformation) -> NoneType
2. __init__(self : handle, : rosetta.std.weak_ptr_const_protocols_environment_Environment_t, : rosetta.core.conformation.Conformation) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- annotations(...) from builtins.PyCapsule
- annotations(rosetta.protocols.environment.ProtectedConformation) -> rosetta.core.environment.SequenceAnnotation
- append_polymer_residue_after_seqpos(...) from builtins.PyCapsule
- append_polymer_residue_after_seqpos(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.core.conformation.Residue, : int, : bool) -> NoneType
- append_residue_by_jump(...) from builtins.PyCapsule
- append_residue_by_jump(*args, **kwargs)
Overloaded function.
1. append_residue_by_jump(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.core.conformation.Residue, : int) -> NoneType
2. append_residue_by_jump(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.core.conformation.Residue, : int, : str) -> NoneType
3. append_residue_by_jump(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.core.conformation.Residue, : int, : str, : str) -> NoneType
4. append_residue_by_jump(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.core.conformation.Residue, : int, : str, : str, _ : bool) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(*args, **kwargs)
Overloaded function.
1. assign(self : rosetta.protocols.environment.ProtectedConformation, src : rosetta.core.conformation.Conformation) -> rosetta.core.conformation.Conformation
2. assign(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.protocols.environment.ProtectedConformation) -> rosetta.protocols.environment.ProtectedConformation
- batch_set_xyz(...) from builtins.PyCapsule
- batch_set_xyz(self : rosetta.protocols.environment.ProtectedConformation, id : rosetta.utility.vector1_core_id_AtomID, position : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType
- chain_endings(...) from builtins.PyCapsule
- chain_endings(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.utility.vector1_unsigned_long) -> NoneType
- chains_from_termini(...) from builtins.PyCapsule
- chains_from_termini(rosetta.protocols.environment.ProtectedConformation) -> NoneType
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.environment.ProtectedConformation) -> NoneType
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.environment.ProtectedConformation) -> rosetta.core.conformation.Conformation
- declare_chemical_bond(...) from builtins.PyCapsule
- declare_chemical_bond(self : rosetta.protocols.environment.ProtectedConformation, : int, : str, : int, : str) -> NoneType
- delete_chain_ending(...) from builtins.PyCapsule
- delete_chain_ending(self : rosetta.protocols.environment.ProtectedConformation, : int) -> NoneType
- delete_polymer_residue(...) from builtins.PyCapsule
- delete_polymer_residue(self : rosetta.protocols.environment.ProtectedConformation, : int) -> NoneType
- delete_residue_range_slow(...) from builtins.PyCapsule
- delete_residue_range_slow(self : rosetta.protocols.environment.ProtectedConformation, range_begin : int, range_end : int) -> NoneType
- delete_residue_slow(...) from builtins.PyCapsule
- delete_residue_slow(self : rosetta.protocols.environment.ProtectedConformation, : int) -> NoneType
- env_destruction(...) from builtins.PyCapsule
- env_destruction(rosetta.protocols.environment.ProtectedConformation) -> NoneType
- environment(...) from builtins.PyCapsule
- environment(rosetta.protocols.environment.ProtectedConformation) -> rosetta.std.weak_ptr_const_protocols_environment_Environment_t
- fill_missing_atoms(...) from builtins.PyCapsule
- fill_missing_atoms(self : rosetta.protocols.environment.ProtectedConformation, missing : rosetta.core.id.AtomID_Map_bool_t) -> NoneType
- fix_disulfides(...) from builtins.PyCapsule
- fix_disulfides(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> NoneType
- fold_tree(...) from builtins.PyCapsule
- fold_tree(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.core.kinematics.FoldTree) -> NoneType
- insert_chain_ending(...) from builtins.PyCapsule
- insert_chain_ending(self : rosetta.protocols.environment.ProtectedConformation, : int) -> NoneType
- insert_conformation_by_jump(...) from builtins.PyCapsule
- insert_conformation_by_jump(*args, **kwargs)
Overloaded function.
1. insert_conformation_by_jump(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.core.conformation.Conformation, : int, : int, : int, : int) -> NoneType
2. insert_conformation_by_jump(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.core.conformation.Conformation, : int, : int, : int, : int, : str) -> NoneType
3. insert_conformation_by_jump(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.core.conformation.Conformation, : int, : int, : int, : int, : str, : str) -> NoneType
- insert_ideal_geometry_at_polymer_bond(...) from builtins.PyCapsule
- insert_ideal_geometry_at_polymer_bond(self : rosetta.protocols.environment.ProtectedConformation, seqpos : int) -> NoneType
- insert_ideal_geometry_at_residue_connection(...) from builtins.PyCapsule
- insert_ideal_geometry_at_residue_connection(self : rosetta.protocols.environment.ProtectedConformation, pos1 : int, connid1 : int) -> NoneType
- is_protected(...) from builtins.PyCapsule
- is_protected(rosetta.protocols.environment.ProtectedConformation) -> bool
- match_variants(...) from builtins.PyCapsule
- match_variants(self : rosetta.protocols.environment.ProtectedConformation, seqpos : int, in_rsd : rosetta.core.conformation.Residue) -> rosetta.core.conformation.Residue
- prepend_polymer_residue_before_seqpos(...) from builtins.PyCapsule
- prepend_polymer_residue_before_seqpos(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.core.conformation.Residue, : int, : bool) -> NoneType
- rebuild_polymer_bond_dependent_atoms(...) from builtins.PyCapsule
- rebuild_polymer_bond_dependent_atoms(self : rosetta.protocols.environment.ProtectedConformation, : int) -> NoneType
- replace_residue(...) from builtins.PyCapsule
- replace_residue(*args, **kwargs)
Overloaded function.
1. replace_residue(self : rosetta.protocols.environment.ProtectedConformation, seqpos : int, new_rsd : rosetta.core.conformation.Residue, atom_pairs : rosetta.utility.vector1_std_pair_std_string_std_string_t) -> NoneType
2. replace_residue(self : rosetta.protocols.environment.ProtectedConformation, seqpos : int, new_rsd : rosetta.core.conformation.Residue, orient_backbone : bool) -> NoneType
- reset_chain_endings(...) from builtins.PyCapsule
- reset_chain_endings(rosetta.protocols.environment.ProtectedConformation) -> NoneType
- reset_move_data(...) from builtins.PyCapsule
- reset_move_data(rosetta.protocols.environment.ProtectedConformation) -> NoneType
- resolver(...) from builtins.PyCapsule
- resolver(rosetta.protocols.environment.ProtectedConformation) -> rosetta.core.environment.SequenceAnnotation
- safely_append_polymer_residue_after_seqpos(...) from builtins.PyCapsule
- safely_append_polymer_residue_after_seqpos(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.core.conformation.Residue, : int, : bool) -> NoneType
- safely_prepend_polymer_residue_before_seqpos(...) from builtins.PyCapsule
- safely_prepend_polymer_residue_before_seqpos(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.core.conformation.Residue, : int, : bool) -> NoneType
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(self : rosetta.protocols.environment.ProtectedConformation, other : rosetta.core.conformation.Conformation, recurse : bool) -> bool
- set_bond_angle(...) from builtins.PyCapsule
- set_bond_angle(self : rosetta.protocols.environment.ProtectedConformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, setting : float) -> NoneType
- set_bond_length(...) from builtins.PyCapsule
- set_bond_length(self : rosetta.protocols.environment.ProtectedConformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, setting : float) -> NoneType
- set_dof(...) from builtins.PyCapsule
- set_dof(self : rosetta.protocols.environment.ProtectedConformation, id : rosetta.core.id.DOF_ID, setting : float) -> NoneType
- set_jump(...) from builtins.PyCapsule
- set_jump(*args, **kwargs)
Overloaded function.
1. set_jump(self : rosetta.protocols.environment.ProtectedConformation, : rosetta.core.id.AtomID, : rosetta.core.kinematics.Jump) -> NoneType
2. set_jump(self : rosetta.protocols.environment.ProtectedConformation, : int, : rosetta.core.kinematics.Jump) -> NoneType
- set_polymeric_connection(...) from builtins.PyCapsule
- set_polymeric_connection(self : rosetta.protocols.environment.ProtectedConformation, : int, : int) -> NoneType
- set_secstruct(...) from builtins.PyCapsule
- set_secstruct(self : rosetta.protocols.environment.ProtectedConformation, seqpos : int, setting : str) -> NoneType
- set_stub_transform(...) from builtins.PyCapsule
- set_stub_transform(self : rosetta.protocols.environment.ProtectedConformation, stub_id1 : rosetta.core.id.StubID, stub_id2 : rosetta.core.id.StubID, target_rt : rosetta.core.kinematics.RT) -> NoneType
- set_torsion(...) from builtins.PyCapsule
- set_torsion(self : rosetta.protocols.environment.ProtectedConformation, id : rosetta.core.id.TorsionID, setting : float) -> NoneType
- set_torsion_angle(...) from builtins.PyCapsule
- set_torsion_angle(*args, **kwargs)
Overloaded function.
1. set_torsion_angle(self : rosetta.protocols.environment.ProtectedConformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, atom4 : rosetta.core.id.AtomID, setting : float) -> NoneType
2. set_torsion_angle(self : rosetta.protocols.environment.ProtectedConformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, atom4 : rosetta.core.id.AtomID, setting : float, quiet : bool) -> NoneType
- set_xyz(...) from builtins.PyCapsule
- set_xyz(self : rosetta.protocols.environment.ProtectedConformation, id : rosetta.core.id.AtomID, position : rosetta.numeric.xyzVector_double_t) -> NoneType
Methods inherited from rosetta.core.conformation.Conformation:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.conformation.Conformation) -> str
- aa(...) from builtins.PyCapsule
- aa(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.chemical.AA
Returns the AA enum for position <seqpos>
- add_parameters_set(...) from builtins.PyCapsule
- add_parameters_set(self : rosetta.core.conformation.Conformation, newset : rosetta.core.conformation.parametric.ParametersSet) -> NoneType
Add a (predefined) ParametersSet object (via its owning pointer)
to the current Conformation object.
Vikram K. Mulligan (vmullig.edu)
- annotated_sequence(...) from builtins.PyCapsule
- annotated_sequence(self : rosetta.core.conformation.Conformation, show_all_variants : bool) -> str
Returns the variant-tagged string representing the
residue types that make up a conformation; e.g.
M[MET:N-Terminus-Variant]CDH[HIS_D]LLR[ARG:C-Terminus-Variant]
- append_residue_by_bond(...) from builtins.PyCapsule
- append_residue_by_bond(*args, **kwargs)
Overloaded function.
1. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue) -> NoneType
Append a new residue by a bond.
2. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool) -> NoneType
Append a new residue by a bond.
3. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int) -> NoneType
Append a new residue by a bond.
4. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int) -> NoneType
Append a new residue by a bond.
5. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int, anchor_connection_index : int) -> NoneType
Append a new residue by a bond.
6. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int, anchor_connection_index : int, start_new_chain : bool) -> NoneType
Append a new residue by a bond.
7. append_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection_index : int, anchor_residue : int, anchor_connection_index : int, start_new_chain : bool, lookup_bond_length : bool) -> NoneType
Append a new residue by a bond.
- apply_transform_Rx_plus_v(...) from builtins.PyCapsule
- apply_transform_Rx_plus_v(self : rosetta.core.conformation.Conformation, R : rosetta.numeric.xyzMatrix_double_t, v : rosetta.numeric.xyzVector_double_t) -> NoneType
- atom_is_backbone_norefold(...) from builtins.PyCapsule
- atom_is_backbone_norefold(self : rosetta.core.conformation.Conformation, pos : int, atomno : int) -> bool
returns true if atom is part of backbone.
- atom_tree(...) from builtins.PyCapsule
- atom_tree(rosetta.core.conformation.Conformation) -> core::kinematics::AtomTree
Returns the conformation's AtomTree
- batch_get_xyz(...) from builtins.PyCapsule
- batch_get_xyz(self : rosetta.core.conformation.Conformation, id : rosetta.utility.vector1_core_id_AtomID, position : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType
- block_signals(...) from builtins.PyCapsule
- block_signals(rosetta.core.conformation.Conformation) -> NoneType
block signals from being sent
- blocking_signals(...) from builtins.PyCapsule
- blocking_signals(rosetta.core.conformation.Conformation) -> bool
are signals being blocked?
- bond_angle(...) from builtins.PyCapsule
- bond_angle(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID) -> float
Returns the bond angle defined by <atom[1-3]> through the AtomTree
- bond_length(...) from builtins.PyCapsule
- bond_length(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID) -> float
Returns the bond length between <atom1> and <atom2> through the AtomTree
- bonded_neighbor_all_res(...) from builtins.PyCapsule
- bonded_neighbor_all_res(*args, **kwargs)
Overloaded function.
1. bonded_neighbor_all_res(self : rosetta.core.conformation.Conformation, atomid : rosetta.core.id.AtomID) -> rosetta.utility.vector1_core_id_AtomID
get all atoms bonded to another
2. bonded_neighbor_all_res(self : rosetta.core.conformation.Conformation, atomid : rosetta.core.id.AtomID, virt : bool) -> rosetta.utility.vector1_core_id_AtomID
get all atoms bonded to another
- buffer_signals(...) from builtins.PyCapsule
- buffer_signals(rosetta.core.conformation.Conformation) -> NoneType
block signals from being sent and buffer them to be sent after unblocking
- buffering_signals(...) from builtins.PyCapsule
- buffering_signals(rosetta.core.conformation.Conformation) -> bool
are signals being blocked and buffered?
- chain_begin(...) from builtins.PyCapsule
- chain_begin(self : rosetta.core.conformation.Conformation, chain : int) -> int
Returns the position number of the first residue in <chain>
- chain_end(...) from builtins.PyCapsule
- chain_end(self : rosetta.core.conformation.Conformation, chain : int) -> int
Returns the position number of the last residue in <chain>
- check_valid_membrane(...) from builtins.PyCapsule
- check_valid_membrane(rosetta.core.conformation.Conformation) -> NoneType
Check that a new membrane position is valid
Given a new membrane normal/center pair, check that the newly constructed stub represents
an orthogonal coordinate frame
- clear_observers(...) from builtins.PyCapsule
- clear_observers(rosetta.core.conformation.Conformation) -> NoneType
clear all observers
- clear_parameters_set_list(...) from builtins.PyCapsule
- clear_parameters_set_list(rosetta.core.conformation.Conformation) -> NoneType
Delete the list of ParametersSetOP objects.
Vikram K. Mulligan (vmullig.edu)
- const_residues(...) from builtins.PyCapsule
- const_residues(rosetta.core.conformation.Conformation) -> rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t
Inefficient -- constructs copy of residues_
- contains_carbohydrate_residues(...) from builtins.PyCapsule
- contains_carbohydrate_residues(*args, **kwargs)
Overloaded function.
1. contains_carbohydrate_residues(rosetta.core.conformation.Conformation) -> bool
Return true if this conformation contains any carbohydrate residues.
2. contains_carbohydrate_residues(self : rosetta.core.conformation.Conformation, setting : bool) -> NoneType
Set whether this conformation contains any carbohydrate residues.
- copy_segment(...) from builtins.PyCapsule
- copy_segment(self : rosetta.core.conformation.Conformation, size : int, src : rosetta.core.conformation.Conformation, begin : int, src_begin : int) -> NoneType
copy a stretch of coordinates/torsions from another Conformation
- create_new_parameters_set(...) from builtins.PyCapsule
- create_new_parameters_set(rosetta.core.conformation.Conformation) -> NoneType
Create a new (empty) ParametersSet object and add its owning pointer
to the current Conformation object.
Vikram K. Mulligan (vmullig.edu)
- debug_pause(...) from builtins.PyCapsule
- debug_pause(*args, **kwargs)
Overloaded function.
1. debug_pause(self : rosetta.core.conformation.Conformation, flag : bool) -> NoneType
wait for stdin after sending a GeneralEvent signal
2. debug_pause(rosetta.core.conformation.Conformation) -> bool
waiting for stdin after sending a GeneralEvent signal?
- debug_residue_torsions(...) from builtins.PyCapsule
- debug_residue_torsions(*args, **kwargs)
Overloaded function.
1. debug_residue_torsions(rosetta.core.conformation.Conformation) -> NoneType
debugging
2. debug_residue_torsions(self : rosetta.core.conformation.Conformation, verbose : bool) -> NoneType
debugging
- detached_copy(...) from builtins.PyCapsule
- detached_copy(self : rosetta.core.conformation.Conformation, src : rosetta.core.conformation.Conformation) -> NoneType
copy the other conformation into this, but make sure that the two
share no possibly-non-bitwise-const data nor do they refer to each other
(as the AtomTree does with its topological observer system).
- detect_bonds(...) from builtins.PyCapsule
- detect_bonds(rosetta.core.conformation.Conformation) -> NoneType
- detect_disulfides(...) from builtins.PyCapsule
- detect_disulfides(*args, **kwargs)
Overloaded function.
1. detect_disulfides(rosetta.core.conformation.Conformation) -> NoneType
2. detect_disulfides(self : rosetta.core.conformation.Conformation, disulf_one : rosetta.utility.vector1_unsigned_long) -> NoneType
3. detect_disulfides(self : rosetta.core.conformation.Conformation, disulf_one : rosetta.utility.vector1_unsigned_long, disulf_two : rosetta.utility.vector1_unsigned_long) -> NoneType
- detect_pseudobonds(...) from builtins.PyCapsule
- detect_pseudobonds(rosetta.core.conformation.Conformation) -> NoneType
- dof(...) from builtins.PyCapsule
- dof(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.DOF_ID) -> float
Returns the AtomTree degree of freedom (DOF) <id>
- dof_id_from_torsion_id(...) from builtins.PyCapsule
- dof_id_from_torsion_id(self : rosetta.core.conformation.Conformation, id : core::id::TorsionID) -> rosetta.core.id.DOF_ID
- downstream_jump_stub(...) from builtins.PyCapsule
- downstream_jump_stub(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.kinematics.Stub
The upstream and downstream Stubs are the coordinate frames between which this jump is transforming
- empty(...) from builtins.PyCapsule
- empty(rosetta.core.conformation.Conformation) -> bool
Returns true if this conformation does not have any residues
- get_jump_atom_ids(...) from builtins.PyCapsule
- get_jump_atom_ids(self : rosetta.core.conformation.Conformation, jump_number : int, upstream_id : rosetta.core.id.AtomID, downstream_id : rosetta.core.id.AtomID) -> bool
get two atoms connect by jump
- get_residue_mask(...) from builtins.PyCapsule
- get_residue_mask(rosetta.core.conformation.Conformation) -> rosetta.utility.vector1_bool
returns a mask of residues to be used in scoring
- get_residue_weight(...) from builtins.PyCapsule
- get_residue_weight(self : rosetta.core.conformation.Conformation, : int, : int) -> float
returns a residue-pair weight
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.core.conformation.Conformation) -> rosetta.core.conformation.Conformation
self pointers
2. get_self_ptr(rosetta.core.conformation.Conformation) -> rosetta.core.conformation.Conformation
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.core.conformation.Conformation) -> rosetta.std.weak_ptr_const_core_conformation_Conformation_t
2. get_self_weak_ptr(rosetta.core.conformation.Conformation) -> rosetta.std.weak_ptr_core_conformation_Conformation_t
- get_stub_transform(...) from builtins.PyCapsule
- get_stub_transform(self : rosetta.core.conformation.Conformation, stub_id1 : rosetta.core.id.StubID, stub_id2 : rosetta.core.id.StubID) -> rosetta.core.kinematics.RT
get the transform between two stubs
- get_torsion_angle_atom_ids(...) from builtins.PyCapsule
- get_torsion_angle_atom_ids(self : rosetta.core.conformation.Conformation, tor_id : core::id::TorsionID, id1 : rosetta.core.id.AtomID, id2 : rosetta.core.id.AtomID, id3 : rosetta.core.id.AtomID, id4 : rosetta.core.id.AtomID) -> bool
get four atoms which defined this torsion
- has_passport(...) from builtins.PyCapsule
- has_passport(rosetta.core.conformation.Conformation) -> bool
- insert_residue_by_bond(...) from builtins.PyCapsule
- insert_residue_by_bond(*args, **kwargs)
Overloaded function.
1. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
2. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
3. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
4. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str, root_atom : str) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
5. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str, root_atom : str, new_chain : bool) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
6. insert_residue_by_bond(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str, root_atom : str, new_chain : bool, lookup_bond_length : bool) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
- insert_residue_by_jump(...) from builtins.PyCapsule
- insert_residue_by_jump(*args, **kwargs)
Overloaded function.
1. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
2. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, anchor_atom : str) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
3. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, anchor_atom : str, root_atom : str) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
4. insert_residue_by_jump(self : rosetta.core.conformation.Conformation, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, anchor_atom : str, root_atom : str, new_chain : bool) -> NoneType
Insert a new residue by jump. If new_chain is "true", then seqpos must be the last
residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )
- inter_residue_connection_partner(...) from builtins.PyCapsule
- inter_residue_connection_partner(self : rosetta.core.conformation.Conformation, seqpos : int, connection_index : int) -> rosetta.core.id.AtomID
This returns the AtomID of the atom in the other residue to which the "connection_index"-th
connection of residue seqpos is connected to.
- is_centroid(...) from builtins.PyCapsule
- is_centroid(rosetta.core.conformation.Conformation) -> bool
convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos )
- is_fullatom(...) from builtins.PyCapsule
- is_fullatom(rosetta.core.conformation.Conformation) -> bool
convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos )
- is_membrane(...) from builtins.PyCapsule
- is_membrane(rosetta.core.conformation.Conformation) -> bool
convenience test for if the conformation contains information for a membrane protein
- is_residue_typeset(...) from builtins.PyCapsule
- is_residue_typeset(self : rosetta.core.conformation.Conformation, tag : str) -> bool
convenience test for residue_type_set ( based on two middle residue -- to avoid hitting on ligands or pseudos )
- jump(...) from builtins.PyCapsule
- jump(*args, **kwargs)
Overloaded function.
1. jump(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.kinematics.Jump
Returns the Jump with jump number <jump_number>
2. jump(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.AtomID) -> rosetta.core.kinematics.Jump
access a jump
- jump_atom_id(...) from builtins.PyCapsule
- jump_atom_id(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.id.AtomID
- membrane_info(...) from builtins.PyCapsule
- membrane_info(rosetta.core.conformation.Conformation) -> core::conformation::membrane::MembraneInfo
Returns the const MembraneInfo object in conformation
Membrane Info contains information describing location of the
membrane virtual residue in the pose sequence, membrane spanning region definitions
and lipid exposure/burial data
- n_parameters_sets(...) from builtins.PyCapsule
- n_parameters_sets(rosetta.core.conformation.Conformation) -> int
Get the number of parameters sets defined for this Conformation.
Vikram K. Mulligan (vmullig.edu)
- num_chains(...) from builtins.PyCapsule
- num_chains(rosetta.core.conformation.Conformation) -> int
Returns the number of chains
- parameters_set(...) from builtins.PyCapsule
- parameters_set(*args, **kwargs)
Overloaded function.
1. parameters_set(self : rosetta.core.conformation.Conformation, index : int) -> rosetta.core.conformation.parametric.ParametersSet
Access one of the ParametersSets objects linked to this Conformation.
Vikram K. Mulligan (vmullig.edu)
2. parameters_set(self : rosetta.core.conformation.Conformation, index : int) -> rosetta.core.conformation.parametric.ParametersSet
Const access to one of the ParametersSets objects linked to this Conformation.
Vikram K. Mulligan (vmullig.edu)
- pop_passport(...) from builtins.PyCapsule
- pop_passport(rosetta.core.conformation.Conformation) -> core::environment::DofPassport
- push_passport(...) from builtins.PyCapsule
- push_passport(self : rosetta.core.conformation.Conformation, : core::environment::DofPassport) -> NoneType
- rebuild_polymer_bond_dependent_atoms_this_residue_only(...) from builtins.PyCapsule
- rebuild_polymer_bond_dependent_atoms_this_residue_only(self : rosetta.core.conformation.Conformation, seqpos : int) -> NoneType
Rebuilds the atoms that are depenent on polymer bonds for the specified residue only.
Vikram K. Mulligan (vmullig.edu)
- rebuild_residue_connection_dependent_atoms(...) from builtins.PyCapsule
- rebuild_residue_connection_dependent_atoms(self : rosetta.core.conformation.Conformation, seqpos : int, connid : int) -> NoneType
- receive_observers_from(...) from builtins.PyCapsule
- receive_observers_from(self : rosetta.core.conformation.Conformation, src : rosetta.core.conformation.Conformation) -> NoneType
fire a ConnectionEvent::TRANSFER to transfer observers from some source Conformation
- reset_structure_moved(...) from builtins.PyCapsule
- reset_structure_moved(rosetta.core.conformation.Conformation) -> NoneType
reset the structure_moved_ bool
- residue(...) from builtins.PyCapsule
- residue(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.conformation.Residue
access one of the residues
this access is inlined, since otherwise it
shows up in the profiler. This will call non-inlined refold methods if necessary.
update coordinates and torsions for this and all other residues before
allowing read access
- residue_cop(...) from builtins.PyCapsule
- residue_cop(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.conformation.Residue
access one of the residues, using COP
- residue_op(...) from builtins.PyCapsule
- residue_op(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.conformation.Residue
Access one of the residues, using OP
Non-const access.
- residue_type(...) from builtins.PyCapsule
- residue_type(self : rosetta.core.conformation.Conformation, seqpos : int) -> rosetta.core.chemical.ResidueType
access one of the residue's types -- avoids coord/torsion update
- secstruct(...) from builtins.PyCapsule
- secstruct(self : rosetta.core.conformation.Conformation, seqpos : int) -> str
Returns the secondary structure the position <seqpos>
character representing secondary structure; returns 'L' if the
requested sequence position is larger than the length in the
secondary structure array
- sequence_matches(...) from builtins.PyCapsule
- sequence_matches(self : rosetta.core.conformation.Conformation, other : rosetta.core.conformation.Conformation) -> bool
do the names of all residues in this and src match?
- set_jump_atom_stub_id(...) from builtins.PyCapsule
- set_jump_atom_stub_id(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.StubID) -> NoneType
- set_membrane_info(...) from builtins.PyCapsule
- set_membrane_info(self : rosetta.core.conformation.Conformation, mem_info : core::conformation::membrane::MembraneInfo) -> NoneType
Setup a Membrane Info object in Conformation - pos & topology
Add a MembraneInfo object - describes the position of the
membrane virtual residue, information on membrane spanning regions,
lipid exposure/burial of residues in the pose, and fullatom steepness
and thickness parameters. At construction, specify membrane position
and list of spanning topology objects by chain.
- set_noncanonical_connection(...) from builtins.PyCapsule
- set_noncanonical_connection(self : rosetta.core.conformation.Conformation, res_id_lower : int, lr_conn_id : int, res_id_upper : int, ur_conn_id : int) -> NoneType
Create an arbitrary covalent connection between two residues.
- show_residue_connections(...) from builtins.PyCapsule
- show_residue_connections(rosetta.core.conformation.Conformation) -> NoneType
Show residue connections for debugging purposes.
- size(...) from builtins.PyCapsule
- size(rosetta.core.conformation.Conformation) -> int
Returns the number of residues in the Conformation
- structure_moved(...) from builtins.PyCapsule
- structure_moved(rosetta.core.conformation.Conformation) -> bool
has the structure moved since the last call to reset_move_data or reset_structure_moved
- stub_from_id(...) from builtins.PyCapsule
- stub_from_id(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.StubID) -> rosetta.core.kinematics.Stub
- torsion(...) from builtins.PyCapsule
- torsion(self : rosetta.core.conformation.Conformation, id : core::id::TorsionID) -> float
Return the torsion angle OR rigid-body offset for <id>
- torsion_angle(...) from builtins.PyCapsule
- torsion_angle(self : rosetta.core.conformation.Conformation, atom1 : rosetta.core.id.AtomID, atom2 : rosetta.core.id.AtomID, atom3 : rosetta.core.id.AtomID, atom4 : rosetta.core.id.AtomID) -> float
Returns the torsion angle defined by <atom[1-4]>
- unblock_signals(...) from builtins.PyCapsule
- unblock_signals(rosetta.core.conformation.Conformation) -> NoneType
allow signals to be sent
- update_actcoord(...) from builtins.PyCapsule
- update_actcoord(self : rosetta.core.conformation.Conformation, resid : int) -> NoneType
- update_actcoords(...) from builtins.PyCapsule
- update_actcoords(rosetta.core.conformation.Conformation) -> NoneType
- update_domain_map(...) from builtins.PyCapsule
- update_domain_map(self : rosetta.core.conformation.Conformation, domain_map : ObjexxFCL::FArray1D<int>) -> NoneType
Generate a domain_map from the current dof/xyz moved data
- update_membrane_position(...) from builtins.PyCapsule
- update_membrane_position(self : rosetta.core.conformation.Conformation, center : rosetta.numeric.xyzVector_double_t, normal : rosetta.numeric.xyzVector_double_t) -> NoneType
Update Normal, Center in the Membrane
Sets the center and normal coordinates to the appropriate
parameters and checks for a valid stub prior to returning.
- update_noncanonical_connection(...) from builtins.PyCapsule
- update_noncanonical_connection(self : rosetta.core.conformation.Conformation, lower_seqpos : int, lr_conn_id : int, upper_seqpos : int, ur_conn_id : int) -> NoneType
Update the connection status between the lower_seqpos residue's lr_conn_id connection ID and
the upper_seqpos residue's ur_conn_id connection ID.
- update_orbital_coords(...) from builtins.PyCapsule
- update_orbital_coords(*args, **kwargs)
Overloaded function.
1. update_orbital_coords(self : rosetta.core.conformation.Conformation, rsd : rosetta.core.conformation.Residue) -> NoneType
2. update_orbital_coords(self : rosetta.core.conformation.Conformation, resid : int) -> NoneType
- update_polymeric_connection(...) from builtins.PyCapsule
- update_polymeric_connection(*args, **kwargs)
Overloaded function.
1. update_polymeric_connection(self : rosetta.core.conformation.Conformation, lower_seqpos : int) -> NoneType
Update the polymer connection status between lower_seqpos and lower_seqpos+1
based on chainID's and termini. If update_connection_dep_atoms is true, positions of
atoms dependent on the polymer connection are updated.
2. update_polymeric_connection(self : rosetta.core.conformation.Conformation, lower_seqpos : int, update_connection_dep_atoms : bool) -> NoneType
Update the polymer connection status between lower_seqpos and lower_seqpos+1
based on chainID's and termini. If update_connection_dep_atoms is true, positions of
atoms dependent on the polymer connection are updated.
- upstream_jump_stub(...) from builtins.PyCapsule
- upstream_jump_stub(self : rosetta.core.conformation.Conformation, jump_number : int) -> rosetta.core.kinematics.Stub
The upstream and downstream Stubs are the coordinate frames between which this jump is transforming
- xyz(...) from builtins.PyCapsule
- xyz(self : rosetta.core.conformation.Conformation, id : rosetta.core.id.AtomID) -> rosetta.numeric.xyzVector_double_t
access xyz coordinates of an atom
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class ScriptCM(ClientMover) |
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- Method resolution order:
- ScriptCM
- ClientMover
- 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.environment.ScriptCM) -> 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.environment.ScriptCM, : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.environment.ScriptCM, : rosetta.protocols.environment.ScriptCM) -> rosetta.protocols.environment.ScriptCM
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.environment.ScriptCM) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.environment.ScriptCM) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.environment.ScriptCM) -> str
- initialize(...) from builtins.PyCapsule
- initialize(self : rosetta.protocols.environment.ScriptCM, pose : rosetta.core.pose.Pose) -> NoneType
- name(...) from builtins.PyCapsule
- name(*args, **kwargs)
Overloaded function.
1. name(rosetta.protocols.environment.ScriptCM) -> str
2. name(self : rosetta.protocols.environment.ScriptCM, name : str) -> NoneType
- yield_claims(...) from builtins.PyCapsule
- yield_claims(self : rosetta.protocols.environment.ScriptCM, : rosetta.core.pose.Pose, : rosetta.basic.datacache.WriteableCacheableMap) -> rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_std_allocator_std_shared_ptr_protocols_environment_claims_EnvClaim_t
Methods inherited from ClientMover:
- yield_submovers(...) from builtins.PyCapsule
- yield_submovers(self : rosetta.protocols.environment.ClientMover, : rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_std_less_std_shared_ptr_protocols_environment_ClientMover_std_allocator_std_shared_ptr_protocols_environment_ClientMover_t) -> NoneType
this method is used to make sure any movers contained in this
mover (that want to make claims) also get registered with the
environment.
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
- 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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