| | |
- builtins.object
-
- DesignTask
-
- DesignTask_Layer
- DesignTask_Normal
- FilterStructs
-
- FilterStructs_Packstat
- FilterStructs_TotalCharge
- rosetta.core.pack.task.operation.TaskOperation(builtins.object)
-
- CombinedTaskOperation
- LayerDesignOperation
- rosetta.core.pack.task.operation.TaskOperationCreator(builtins.object)
-
- LayerDesignOperationCreator
- rosetta.protocols.moves.Mover(builtins.object)
-
- FlxbbDesign
- InterlockAroma
- rosetta.protocols.moves.MoverCreator(builtins.object)
-
- FlxbbDesignCreator
- InterlockAromaCreator
- rosetta.protocols.simple_moves.PackRotamersMover(rosetta.protocols.moves.Mover)
-
- FlxbbDesignPack
class DesignTask(builtins.object) |
| |
////////////////////////////////////////////////////////////////////////////////////////////////////
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.flxbb.DesignTask) -> NoneType
2. __init__(rosetta.protocols.flxbb.DesignTask, int, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover) -> NoneType
doc
3. __init__(rosetta.protocols.flxbb.DesignTask, int, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, protocols::flxbb::FilterStructs) -> NoneType
doc
4. __init__(rosetta.protocols.flxbb.DesignTask, int, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover, protocols::flxbb::FilterStructs, rosetta.core.pack.task.PackerTask) -> NoneType
doc
5. __init__(self : rosetta.protocols.flxbb.DesignTask, ncycle : int, sfxn : rosetta.core.scoring.ScoreFunction, mover : rosetta.protocols.moves.Mover, filter_structs : protocols::flxbb::FilterStructs, taskf : rosetta.core.pack.task.PackerTask, resfile : str) -> NoneType
6. __init__(rosetta.protocols.flxbb.DesignTask, rosetta.protocols.flxbb.DesignTask) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_task_operation(...) from builtins.PyCapsule
- add_task_operation(self : rosetta.protocols.flxbb.DesignTask, top : rosetta.core.pack.task.operation.TaskOperation) -> NoneType
add task operation
- add_task_operations(...) from builtins.PyCapsule
- add_task_operations(self : rosetta.protocols.flxbb.DesignTask, top : rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) -> NoneType
add task operations
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.flxbb.DesignTask, : rosetta.protocols.flxbb.DesignTask) -> rosetta.protocols.flxbb.DesignTask
- filter_structs(...) from builtins.PyCapsule
- filter_structs(rosetta.protocols.flxbb.DesignTask) -> protocols::flxbb::FilterStructs
filter during fixbb design
- mover(...) from builtins.PyCapsule
- mover(rosetta.protocols.flxbb.DesignTask) -> rosetta.protocols.moves.Mover
mover after fixbb design
- ncycle(...) from builtins.PyCapsule
- ncycle(rosetta.protocols.flxbb.DesignTask) -> int
the number of cycles of fixbb design and mover
- packertask(...) from builtins.PyCapsule
- packertask(rosetta.protocols.flxbb.DesignTask) -> rosetta.core.pack.task.PackerTask
packer task for fixbb design
- resfile(...) from builtins.PyCapsule
- resfile(rosetta.protocols.flxbb.DesignTask) -> str
resfile
- scorefxn(...) from builtins.PyCapsule
- scorefxn(rosetta.protocols.flxbb.DesignTask) -> rosetta.core.scoring.ScoreFunction
scorefxn for fixbb design
- set_filter_structs(...) from builtins.PyCapsule
- set_filter_structs(self : rosetta.protocols.flxbb.DesignTask, value : protocols::flxbb::FilterStructs) -> NoneType
filter during fixbb design
- set_mover(...) from builtins.PyCapsule
- set_mover(self : rosetta.protocols.flxbb.DesignTask, value : rosetta.protocols.moves.Mover) -> NoneType
mover after fixbb design
- set_ncycle(...) from builtins.PyCapsule
- set_ncycle(self : rosetta.protocols.flxbb.DesignTask, ncycle : int) -> NoneType
the number of cycles of design and mover
- set_packertask(...) from builtins.PyCapsule
- set_packertask(self : rosetta.protocols.flxbb.DesignTask, taskf : rosetta.core.pack.task.PackerTask) -> NoneType
packer task
- set_resfile(...) from builtins.PyCapsule
- set_resfile(self : rosetta.protocols.flxbb.DesignTask, resfile : str) -> NoneType
set resfile
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.flxbb.DesignTask, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
scorefxn for fixbb design
- setup(...) from builtins.PyCapsule
- setup(self : rosetta.protocols.flxbb.DesignTask, : rosetta.core.pose.Pose, : rosetta.core.pack.task.PackerTask) -> NoneType
setup packer task
|
class DesignTask_Layer(DesignTask) |
| |
////////////////////////////////////////////////////////////////////////////////////////////////////
|
| |
- Method resolution order:
- DesignTask_Layer
- DesignTask
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, bool, bool, bool, bool, int, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover) -> NoneType
doc
3. __init__(self : handle, dsgn_core : bool, dsgn_boundary : bool, dsgn_surface : bool, use_original_seq : bool, ncycle : int, sfxn : rosetta.core.scoring.ScoreFunction, mover : rosetta.protocols.moves.Mover, filter_structs : protocols::flxbb::FilterStructs) -> NoneType
4. __init__(handle, rosetta.protocols.flxbb.DesignTask_Layer) -> 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.flxbb.DesignTask_Layer, : rosetta.protocols.flxbb.DesignTask_Layer) -> rosetta.protocols.flxbb.DesignTask_Layer
- setup(...) from builtins.PyCapsule
- setup(self : rosetta.protocols.flxbb.DesignTask_Layer, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
Methods inherited from DesignTask:
- add_task_operation(...) from builtins.PyCapsule
- add_task_operation(self : rosetta.protocols.flxbb.DesignTask, top : rosetta.core.pack.task.operation.TaskOperation) -> NoneType
add task operation
- add_task_operations(...) from builtins.PyCapsule
- add_task_operations(self : rosetta.protocols.flxbb.DesignTask, top : rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) -> NoneType
add task operations
- filter_structs(...) from builtins.PyCapsule
- filter_structs(rosetta.protocols.flxbb.DesignTask) -> protocols::flxbb::FilterStructs
filter during fixbb design
- mover(...) from builtins.PyCapsule
- mover(rosetta.protocols.flxbb.DesignTask) -> rosetta.protocols.moves.Mover
mover after fixbb design
- ncycle(...) from builtins.PyCapsule
- ncycle(rosetta.protocols.flxbb.DesignTask) -> int
the number of cycles of fixbb design and mover
- packertask(...) from builtins.PyCapsule
- packertask(rosetta.protocols.flxbb.DesignTask) -> rosetta.core.pack.task.PackerTask
packer task for fixbb design
- resfile(...) from builtins.PyCapsule
- resfile(rosetta.protocols.flxbb.DesignTask) -> str
resfile
- scorefxn(...) from builtins.PyCapsule
- scorefxn(rosetta.protocols.flxbb.DesignTask) -> rosetta.core.scoring.ScoreFunction
scorefxn for fixbb design
- set_filter_structs(...) from builtins.PyCapsule
- set_filter_structs(self : rosetta.protocols.flxbb.DesignTask, value : protocols::flxbb::FilterStructs) -> NoneType
filter during fixbb design
- set_mover(...) from builtins.PyCapsule
- set_mover(self : rosetta.protocols.flxbb.DesignTask, value : rosetta.protocols.moves.Mover) -> NoneType
mover after fixbb design
- set_ncycle(...) from builtins.PyCapsule
- set_ncycle(self : rosetta.protocols.flxbb.DesignTask, ncycle : int) -> NoneType
the number of cycles of design and mover
- set_packertask(...) from builtins.PyCapsule
- set_packertask(self : rosetta.protocols.flxbb.DesignTask, taskf : rosetta.core.pack.task.PackerTask) -> NoneType
packer task
- set_resfile(...) from builtins.PyCapsule
- set_resfile(self : rosetta.protocols.flxbb.DesignTask, resfile : str) -> NoneType
set resfile
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.flxbb.DesignTask, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
scorefxn for fixbb design
|
class DesignTask_Normal(DesignTask) |
| |
////////////////////////////////////////////////////////////////////////////////////////////////////
|
| |
- Method resolution order:
- DesignTask_Normal
- DesignTask
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, int, rosetta.core.scoring.ScoreFunction, rosetta.protocols.moves.Mover) -> NoneType
doc
3. __init__(self : handle, ncycle : int, sfxn : rosetta.core.scoring.ScoreFunction, mover : rosetta.protocols.moves.Mover, filter_structs : protocols::flxbb::FilterStructs) -> NoneType
4. __init__(handle, rosetta.protocols.flxbb.DesignTask_Normal) -> 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.flxbb.DesignTask_Normal, : rosetta.protocols.flxbb.DesignTask_Normal) -> rosetta.protocols.flxbb.DesignTask_Normal
- setup(...) from builtins.PyCapsule
- setup(self : rosetta.protocols.flxbb.DesignTask_Normal, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
Methods inherited from DesignTask:
- add_task_operation(...) from builtins.PyCapsule
- add_task_operation(self : rosetta.protocols.flxbb.DesignTask, top : rosetta.core.pack.task.operation.TaskOperation) -> NoneType
add task operation
- add_task_operations(...) from builtins.PyCapsule
- add_task_operations(self : rosetta.protocols.flxbb.DesignTask, top : rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) -> NoneType
add task operations
- filter_structs(...) from builtins.PyCapsule
- filter_structs(rosetta.protocols.flxbb.DesignTask) -> protocols::flxbb::FilterStructs
filter during fixbb design
- mover(...) from builtins.PyCapsule
- mover(rosetta.protocols.flxbb.DesignTask) -> rosetta.protocols.moves.Mover
mover after fixbb design
- ncycle(...) from builtins.PyCapsule
- ncycle(rosetta.protocols.flxbb.DesignTask) -> int
the number of cycles of fixbb design and mover
- packertask(...) from builtins.PyCapsule
- packertask(rosetta.protocols.flxbb.DesignTask) -> rosetta.core.pack.task.PackerTask
packer task for fixbb design
- resfile(...) from builtins.PyCapsule
- resfile(rosetta.protocols.flxbb.DesignTask) -> str
resfile
- scorefxn(...) from builtins.PyCapsule
- scorefxn(rosetta.protocols.flxbb.DesignTask) -> rosetta.core.scoring.ScoreFunction
scorefxn for fixbb design
- set_filter_structs(...) from builtins.PyCapsule
- set_filter_structs(self : rosetta.protocols.flxbb.DesignTask, value : protocols::flxbb::FilterStructs) -> NoneType
filter during fixbb design
- set_mover(...) from builtins.PyCapsule
- set_mover(self : rosetta.protocols.flxbb.DesignTask, value : rosetta.protocols.moves.Mover) -> NoneType
mover after fixbb design
- set_ncycle(...) from builtins.PyCapsule
- set_ncycle(self : rosetta.protocols.flxbb.DesignTask, ncycle : int) -> NoneType
the number of cycles of design and mover
- set_packertask(...) from builtins.PyCapsule
- set_packertask(self : rosetta.protocols.flxbb.DesignTask, taskf : rosetta.core.pack.task.PackerTask) -> NoneType
packer task
- set_resfile(...) from builtins.PyCapsule
- set_resfile(self : rosetta.protocols.flxbb.DesignTask, resfile : str) -> NoneType
set resfile
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.flxbb.DesignTask, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
scorefxn for fixbb design
|
class FilterStructs(builtins.object) |
| |
/////////////////////////////////////////////////////////////////////////////////////
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.flxbb.FilterStructs) -> NoneType
2. __init__(self : rosetta.protocols.flxbb.FilterStructs, name : str) -> NoneType
3. __init__(self : rosetta.protocols.flxbb.FilterStructs, name : str, ntrial : int) -> NoneType
4. __init__(self : rosetta.protocols.flxbb.FilterStructs, name : str, pose : rosetta.core.pose.Pose, ntrial : int) -> NoneType
5. __init__(rosetta.protocols.flxbb.FilterStructs, rosetta.protocols.flxbb.FilterStructs) -> 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.flxbb.FilterStructs, : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.flxbb.FilterStructs, : rosetta.protocols.flxbb.FilterStructs) -> rosetta.protocols.flxbb.FilterStructs
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.flxbb.FilterStructs) -> rosetta.protocols.flxbb.FilterStructs
- current_trial(...) from builtins.PyCapsule
- current_trial(rosetta.protocols.flxbb.FilterStructs) -> int
- filter_on(...) from builtins.PyCapsule
- filter_on(rosetta.protocols.flxbb.FilterStructs) -> bool
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.flxbb.FilterStructs) -> rosetta.protocols.flxbb.FilterStructs
- get_bestpose(...) from builtins.PyCapsule
- get_bestpose(rosetta.protocols.flxbb.FilterStructs) -> rosetta.core.pose.Pose
- name(...) from builtins.PyCapsule
- name(*args, **kwargs)
Overloaded function.
1. name(rosetta.protocols.flxbb.FilterStructs) -> str
2. name(self : rosetta.protocols.flxbb.FilterStructs, name : str) -> NoneType
- reset(...) from builtins.PyCapsule
- reset(self : rosetta.protocols.flxbb.FilterStructs, : rosetta.core.pose.Pose) -> NoneType
- set_ntrial(...) from builtins.PyCapsule
- set_ntrial(self : rosetta.protocols.flxbb.FilterStructs, ntrial : int) -> NoneType
|
class FilterStructs_Packstat(FilterStructs) |
| |
/////////////////////////////////////////////////////////////////////////////////////
|
| |
- Method resolution order:
- FilterStructs_Packstat
- FilterStructs
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
doc
2. __init__(self : handle, ntrial : int) -> NoneType
3. __init__(handle, rosetta.core.pose.Pose) -> NoneType
doc
4. __init__(self : handle, pose : rosetta.core.pose.Pose, ntrial : int) -> NoneType
5. __init__(handle, rosetta.protocols.flxbb.FilterStructs_Packstat) -> 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.flxbb.FilterStructs_Packstat, : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.flxbb.FilterStructs_Packstat, : rosetta.protocols.flxbb.FilterStructs_Packstat) -> rosetta.protocols.flxbb.FilterStructs_Packstat
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.flxbb.FilterStructs_Packstat) -> rosetta.protocols.flxbb.FilterStructs
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.flxbb.FilterStructs_Packstat) -> rosetta.protocols.flxbb.FilterStructs
- reset(...) from builtins.PyCapsule
- reset(self : rosetta.protocols.flxbb.FilterStructs_Packstat, : rosetta.core.pose.Pose) -> NoneType
Methods inherited from FilterStructs:
- current_trial(...) from builtins.PyCapsule
- current_trial(rosetta.protocols.flxbb.FilterStructs) -> int
- filter_on(...) from builtins.PyCapsule
- filter_on(rosetta.protocols.flxbb.FilterStructs) -> bool
- get_bestpose(...) from builtins.PyCapsule
- get_bestpose(rosetta.protocols.flxbb.FilterStructs) -> rosetta.core.pose.Pose
- name(...) from builtins.PyCapsule
- name(*args, **kwargs)
Overloaded function.
1. name(rosetta.protocols.flxbb.FilterStructs) -> str
2. name(self : rosetta.protocols.flxbb.FilterStructs, name : str) -> NoneType
- set_ntrial(...) from builtins.PyCapsule
- set_ntrial(self : rosetta.protocols.flxbb.FilterStructs, ntrial : int) -> NoneType
|
class FilterStructs_TotalCharge(FilterStructs) |
| |
/////////////////////////////////////////////////////////////////////////////////////
|
| |
- Method resolution order:
- FilterStructs_TotalCharge
- FilterStructs
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
doc
2. __init__(self : handle, ntrial : int) -> NoneType
3. __init__(handle, rosetta.core.pose.Pose) -> NoneType
doc
4. __init__(self : handle, pose : rosetta.core.pose.Pose, ntrial : int) -> NoneType
5. __init__(handle, rosetta.protocols.flxbb.FilterStructs_TotalCharge) -> 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.flxbb.FilterStructs_TotalCharge, : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.flxbb.FilterStructs_TotalCharge, : rosetta.protocols.flxbb.FilterStructs_TotalCharge) -> rosetta.protocols.flxbb.FilterStructs_TotalCharge
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.flxbb.FilterStructs_TotalCharge) -> rosetta.protocols.flxbb.FilterStructs
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.flxbb.FilterStructs_TotalCharge) -> rosetta.protocols.flxbb.FilterStructs
- reset(...) from builtins.PyCapsule
- reset(self : rosetta.protocols.flxbb.FilterStructs_TotalCharge, : rosetta.core.pose.Pose) -> NoneType
Methods inherited from FilterStructs:
- current_trial(...) from builtins.PyCapsule
- current_trial(rosetta.protocols.flxbb.FilterStructs) -> int
- filter_on(...) from builtins.PyCapsule
- filter_on(rosetta.protocols.flxbb.FilterStructs) -> bool
- get_bestpose(...) from builtins.PyCapsule
- get_bestpose(rosetta.protocols.flxbb.FilterStructs) -> rosetta.core.pose.Pose
- name(...) from builtins.PyCapsule
- name(*args, **kwargs)
Overloaded function.
1. name(rosetta.protocols.flxbb.FilterStructs) -> str
2. name(self : rosetta.protocols.flxbb.FilterStructs, name : str) -> NoneType
- set_ntrial(...) from builtins.PyCapsule
- set_ntrial(self : rosetta.protocols.flxbb.FilterStructs, ntrial : int) -> NoneType
|
class FlxbbDesign(rosetta.protocols.moves.Mover) |
| |
////////////////////////////////////////////////////////////////////////////////////////////////////
|
| |
- Method resolution order:
- FlxbbDesign
- 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.core.scoring.ScoreFunction, rosetta.core.scoring.ScoreFunction) -> NoneType
doc
3. __init__(handle, rosetta.core.scoring.ScoreFunction, rosetta.core.scoring.ScoreFunction, int) -> NoneType
doc
4. __init__(handle, rosetta.core.scoring.ScoreFunction, rosetta.core.scoring.ScoreFunction, int, str) -> NoneType
doc
5. __init__(handle, rosetta.core.scoring.ScoreFunction, rosetta.core.scoring.ScoreFunction, int, str, bool) -> NoneType
doc
6. __init__(self : handle, sfxnd : rosetta.core.scoring.ScoreFunction, sfxnr : rosetta.core.scoring.ScoreFunction, ncycle : int, layer_mode : str, use_origseq_for_not_dsgned_layer : bool, no_relax : bool) -> NoneType
7. __init__(handle, rosetta.protocols.flxbb.FlxbbDesign) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_design_task(...) from builtins.PyCapsule
- add_design_task(self : rosetta.protocols.flxbb.FlxbbDesign, design_task : rosetta.protocols.flxbb.DesignTask) -> NoneType
add the design task which cotrols the iteration of fixbb design and relax
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.flxbb.FlxbbDesign, pose : rosetta.core.pose.Pose) -> NoneType
mover apply
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.flxbb.FlxbbDesign, : rosetta.protocols.flxbb.FlxbbDesign) -> rosetta.protocols.flxbb.FlxbbDesign
- clear_design_taskset(...) from builtins.PyCapsule
- clear_design_taskset(rosetta.protocols.flxbb.FlxbbDesign) -> NoneType
clear DesignTaskSet
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.flxbb.FlxbbDesign) -> rosetta.protocols.moves.Mover
clone this object
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.flxbb.FlxbbDesign) -> rosetta.protocols.moves.Mover
create this type of object
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.flxbb.FlxbbDesign) -> str
- initialize_filter(...) from builtins.PyCapsule
- initialize_filter(self : rosetta.protocols.flxbb.FlxbbDesign, filter_trial : int, filter_type : str) -> NoneType
initialize filter parameters
- movemap_from_blueprint(...) from builtins.PyCapsule
- movemap_from_blueprint(self : rosetta.protocols.flxbb.FlxbbDesign, value : bool) -> NoneType
set movemap for relax
- no_design(...) from builtins.PyCapsule
- no_design(self : rosetta.protocols.flxbb.FlxbbDesign, no_design : bool) -> NoneType
design protocol will not be performed (default false)
- no_relax(...) from builtins.PyCapsule
- no_relax(self : rosetta.protocols.flxbb.FlxbbDesign, no_relax : bool) -> NoneType
relax is not performed after design (default false)
- read_options(...) from builtins.PyCapsule
- read_options(rosetta.protocols.flxbb.FlxbbDesign) -> NoneType
read parameters
- 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
- set_blueprint(...) from builtins.PyCapsule
- set_blueprint(self : rosetta.protocols.flxbb.FlxbbDesign, blueprint : protocols::jd2::parser::BluePrint) -> NoneType
set BluePrintOP
- set_design_taskset(...) from builtins.PyCapsule
- set_design_taskset(self : rosetta.protocols.flxbb.FlxbbDesign, design_taskset : rosetta.utility.vector1_std_shared_ptr_protocols_flxbb_DesignTask_t) -> NoneType
set DesignTaskSet
Once you set DesignTaskSet, this controls almost every setups of this class
- set_filter_during_design(...) from builtins.PyCapsule
- set_filter_during_design(self : rosetta.protocols.flxbb.FlxbbDesign, filter_during_design : rosetta.protocols.flxbb.FilterStructs) -> NoneType
filtering during design
- set_layer_mode(...) from builtins.PyCapsule
- set_layer_mode(self : rosetta.protocols.flxbb.FlxbbDesign, layer_mode : str) -> NoneType
set layer mode
- set_movemap(...) from builtins.PyCapsule
- set_movemap(self : rosetta.protocols.flxbb.FlxbbDesign, movemap : rosetta.core.kinematics.MoveMap) -> NoneType
set movemap for relax
- set_ncycles(...) from builtins.PyCapsule
- set_ncycles(self : rosetta.protocols.flxbb.FlxbbDesign, ncycles : int) -> NoneType
the number of cycles of fixbb and relax
- set_scorefxn_design(...) from builtins.PyCapsule
- set_scorefxn_design(self : rosetta.protocols.flxbb.FlxbbDesign, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
set the score function for fixbb design
- set_scorefxn_relax(...) from builtins.PyCapsule
- set_scorefxn_relax(self : rosetta.protocols.flxbb.FlxbbDesign, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
set the score function for relax
- set_weight_constraints_NtoC(...) from builtins.PyCapsule
- set_weight_constraints_NtoC(self : rosetta.protocols.flxbb.FlxbbDesign, value : float) -> NoneType
set weight of constraints_NtoC which constrain between Ca atoms of C- and N-terminal
if this weight > 0.0, the constraints is applied ( default = -1.0 )
- set_weight_constraints_sheet(...) from builtins.PyCapsule
- set_weight_constraints_sheet(self : rosetta.protocols.flxbb.FlxbbDesign, value : float) -> NoneType
set weight of constraints_sheet which constrains between Ca atoms in beta-sheets
if this weight > 0.0, the constraints is applied ( default = -1.0 )
- use_origseq_for_not_dsgned_layer(...) from builtins.PyCapsule
- use_origseq_for_not_dsgned_layer(self : rosetta.protocols.flxbb.FlxbbDesign, use : bool) -> NoneType
use original sequence for not designed region in layer_mode,
otherwise the residues of the region turned into Ala ( default true )
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
- 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 FlxbbDesignPack(rosetta.protocols.simple_moves.PackRotamersMover) |
| |
////////////////////////////////////////////////////////////////////////////////////////////////////
|
| |
- Method resolution order:
- FlxbbDesignPack
- rosetta.protocols.simple_moves.PackRotamersMover
- 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.core.scoring.ScoreFunction, rosetta.core.pack.task.PackerTask) -> NoneType
doc
3. __init__(self : handle, scorefxn : rosetta.core.scoring.ScoreFunction, task : rosetta.core.pack.task.PackerTask, filter : rosetta.protocols.flxbb.FilterStructs) -> NoneType
4. __init__(handle, rosetta.protocols.flxbb.FlxbbDesignPack) -> 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.flxbb.FlxbbDesignPack, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.flxbb.FlxbbDesignPack, : rosetta.protocols.flxbb.FlxbbDesignPack) -> rosetta.protocols.flxbb.FlxbbDesignPack
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.flxbb.FlxbbDesignPack) -> str
Methods inherited from rosetta.protocols.simple_moves.PackRotamersMover:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.simple_moves.PackRotamersMover) -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.protocols.moves.Mover
required in the context of the parser/scripting scheme
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.protocols.moves.Mover
required in the context of the parser/scripting scheme
- ig(...) from builtins.PyCapsule
- ig(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.interaction_graph.AnnealableGraphBase
- nloop(...) from builtins.PyCapsule
- nloop(*args, **kwargs)
Overloaded function.
1. nloop(self : rosetta.protocols.simple_moves.PackRotamersMover, nloop_in : int) -> NoneType
2. nloop(rosetta.protocols.simple_moves.PackRotamersMover) -> int
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- rotamer_sets(...) from builtins.PyCapsule
- rotamer_sets(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.rotamer_set.RotamerSets
- score_function(...) from builtins.PyCapsule
- score_function(*args, **kwargs)
Overloaded function.
1. score_function(self : rosetta.protocols.simple_moves.PackRotamersMover, sf : rosetta.core.scoring.ScoreFunction) -> NoneType
Sets the ScoreFunction to <sf>
example(s):
packmover.score_function(scorefxn)
See Also:
PackRotamersMover
PackRotamersMover.task
2. score_function(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.scoring.ScoreFunction
Returns the ScoreFunction
example(s):
packmover.score_function()
See Also:
PackRotamersMover
PackRotamersMover.task
- task(...) from builtins.PyCapsule
- task(*args, **kwargs)
Overloaded function.
1. task(self : rosetta.protocols.simple_moves.PackRotamersMover, t : rosetta.core.pack.task.PackerTask) -> NoneType
Sets the PackerTask to <t>
example(s):
packmover.task(task_pack)
See Also:
PackRotamersMover
PackRotamersMover.task_factory
2. task(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.task.PackerTask
Returns the PackerTask
example(s):
packmover.task()
See Also:
PackRotamersMover
PackRotamersMover.task_factory
- task_factory(...) from builtins.PyCapsule
- task_factory(*args, **kwargs)
Overloaded function.
1. task_factory(self : rosetta.protocols.simple_moves.PackRotamersMover, tf : rosetta.core.pack.task.TaskFactory) -> NoneType
Sets the TaskFactory to <tf>
example(s):
packmover.task_factory(task_design)
See Also:
PackRotamersMover
PackRotamersMover.task
2. task_factory(rosetta.protocols.simple_moves.PackRotamersMover) -> rosetta.core.pack.task.TaskFactory
Returns the TaskFactory
example(s):
packmover.task_factory()
See Also:
PackRotamersMover
PackRotamersMover.task
- task_is_valid(...) from builtins.PyCapsule
- task_is_valid(self : rosetta.protocols.simple_moves.PackRotamersMover, pose : rosetta.core.pose.Pose) -> bool
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 InterlockAroma(rosetta.protocols.moves.Mover) |
| |
////////////////////////////////////////////////////////////////////////////////////////////////////
|
| |
- Method resolution order:
- InterlockAroma
- 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.flxbb.InterlockAroma) -> 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.flxbb.InterlockAroma, pose : rosetta.core.pose.Pose) -> NoneType
mover apply
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.flxbb.InterlockAroma, : rosetta.protocols.flxbb.InterlockAroma) -> rosetta.protocols.flxbb.InterlockAroma
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.flxbb.InterlockAroma) -> rosetta.protocols.moves.Mover
clone this object
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.flxbb.InterlockAroma) -> rosetta.protocols.moves.Mover
create this type of object
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.flxbb.InterlockAroma) -> str
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
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class LayerDesignOperation(rosetta.core.pack.task.operation.TaskOperation) |
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- Method resolution order:
- LayerDesignOperation
- rosetta.core.pack.task.operation.TaskOperation
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, dsgn_core : bool, dsgn_boundary : bool, dsgn_surface : bool) -> NoneType
3. __init__(self : handle, dsgn_core : bool, dsgn_boundary : bool, dsgn_surface : bool, Nt : bool, Ct : bool, core_score : float, surf_score : float, coreAA : str, boundaryAA : str, surfaceAA : str) -> NoneType
4. __init__(handle, rosetta.protocols.flxbb.LayerDesignOperation) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_layer(...) from builtins.PyCapsule
- add_layer(self : rosetta.protocols.flxbb.LayerDesignOperation, layer_name : str, task : rosetta.core.pack.task.operation.TaskOperation, operation : rosetta.protocols.flxbb.LayerOperationType, specification : rosetta.protocols.flxbb.LayerSpecificationType) -> NoneType
add a new layer which will be created based on a task operation
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.flxbb.LayerDesignOperation, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
apply
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.flxbb.LayerDesignOperation, : rosetta.protocols.flxbb.LayerDesignOperation) -> rosetta.protocols.flxbb.LayerDesignOperation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.flxbb.LayerDesignOperation) -> rosetta.core.pack.task.operation.TaskOperation
make clone
- copy_layer_residues(...) from builtins.PyCapsule
- copy_layer_residues(self : rosetta.protocols.flxbb.LayerDesignOperation, src_layer : str, dest_layer : str) -> NoneType
copies residues allowed from src to dest
- design_layer(...) from builtins.PyCapsule
- design_layer(self : rosetta.protocols.flxbb.LayerDesignOperation, dsgn_core : bool, dsgn_boundary : bool, dsgn_surface : bool) -> NoneType
layer to be designed in internal SRBL object
- ignore_pikaa_natro(...) from builtins.PyCapsule
- ignore_pikaa_natro(rosetta.protocols.flxbb.LayerDesignOperation) -> bool
Returns whether residues set with PIKAA and NATRO in previously-applied resfiles are ignored.
Default behaviour is now FALSE to preserve commutativity.
- keyname(...) from builtins.PyCapsule
- keyname() -> str
- layer_nc_residues(...) from builtins.PyCapsule
- layer_nc_residues(self : rosetta.protocols.flxbb.LayerDesignOperation, layer_name : str, ss_name : str) -> rosetta.utility.vector1_std_string
gets the residues allowed for a given secondary structure in a given layer
- layer_residues(...) from builtins.PyCapsule
- layer_residues(self : rosetta.protocols.flxbb.LayerDesignOperation, layer_name : str, ss_name : str) -> str
gets the residues allowed for a given secondary structure in a given layer
- make_pymol_script(...) from builtins.PyCapsule
- make_pymol_script(self : rosetta.protocols.flxbb.LayerDesignOperation, value : bool) -> NoneType
make pymol scripts showing the different layers
- parse_layer_secstruct_tag(...) from builtins.PyCapsule
- parse_layer_secstruct_tag(self : rosetta.protocols.flxbb.LayerDesignOperation, secstruct_tag : rosetta.utility.tag.Tag, datamap : rosetta.basic.datacache.DataMap, layer_name : str) -> NoneType
- parse_layer_tag(...) from builtins.PyCapsule
- parse_layer_tag(self : rosetta.protocols.flxbb.LayerDesignOperation, layer_tag : rosetta.utility.tag.Tag, datamap : rosetta.basic.datacache.DataMap) -> NoneType
- parse_tag(...) from builtins.PyCapsule
- parse_tag(self : rosetta.protocols.flxbb.LayerDesignOperation, tag : rosetta.utility.tag.Tag, : rosetta.basic.datacache.DataMap) -> NoneType
- pore_radius(...) from builtins.PyCapsule
- pore_radius(self : rosetta.protocols.flxbb.LayerDesignOperation, ps : float) -> NoneType
set pore radius for colculating asa
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : rosetta.utility.tag.XMLSchemaDefinition) -> NoneType
- sasa_core(...) from builtins.PyCapsule
- sasa_core(*args, **kwargs)
Overloaded function.
1. sasa_core(self : rosetta.protocols.flxbb.LayerDesignOperation, r : float) -> NoneType
accessible surface for evaluating residues are in core or not
2. sasa_core(self : rosetta.protocols.flxbb.LayerDesignOperation, r : float, ss : str) -> NoneType
accessible surface for evaluating residues are in core or not
- sasa_surface(...) from builtins.PyCapsule
- sasa_surface(*args, **kwargs)
Overloaded function.
1. sasa_surface(self : rosetta.protocols.flxbb.LayerDesignOperation, r : float) -> NoneType
accessible surface for evaluating residues are in surface or not
2. sasa_surface(self : rosetta.protocols.flxbb.LayerDesignOperation, r : float, ss : str) -> NoneType
accessible surface for evaluating residues are in surface or not
- set_design_layers(...) from builtins.PyCapsule
- set_design_layers(self : rosetta.protocols.flxbb.LayerDesignOperation, layers : rosetta.utility.vector1_std_string) -> NoneType
sets names of layers to design
- set_ignore_pikaa_natro(...) from builtins.PyCapsule
- set_ignore_pikaa_natro(self : rosetta.protocols.flxbb.LayerDesignOperation, val : bool) -> NoneType
Sets whether residues set with PIKAA and NATRO in previously-applied resfiles are ignored.
Default behaviour is now FALSE to preserve commutativity.
- set_layer_operation(...) from builtins.PyCapsule
- set_layer_operation(self : rosetta.protocols.flxbb.LayerDesignOperation, layer_name : str, operation : rosetta.protocols.flxbb.LayerOperationType) -> NoneType
sets layer operation
- set_layer_residues(...) from builtins.PyCapsule
- set_layer_residues(self : rosetta.protocols.flxbb.LayerDesignOperation, layer_name : str, ss_name : str, residues : str) -> NoneType
sets residues allowed for a particular secondary structure in the given layer
- set_layer_specification(...) from builtins.PyCapsule
- set_layer_specification(self : rosetta.protocols.flxbb.LayerDesignOperation, layer_name : str, specification : rosetta.protocols.flxbb.LayerSpecificationType) -> NoneType
sets layer specification
- set_nc_layer_residues(...) from builtins.PyCapsule
- set_nc_layer_residues(*args, **kwargs)
Overloaded function.
1. set_nc_layer_residues(self : rosetta.protocols.flxbb.LayerDesignOperation, layer_name : str, ss_name : str, residues : str) -> NoneType
sets nc residues allowed for a particular secondary structure in the given layer
2. set_nc_layer_residues(self : rosetta.protocols.flxbb.LayerDesignOperation, layer_name : str, ss_name : str, residues : rosetta.utility.vector1_std_string) -> NoneType
- set_restrict_restypes(...) from builtins.PyCapsule
- set_restrict_restypes(self : rosetta.protocols.flxbb.LayerDesignOperation, b : bool) -> NoneType
set restrict_restypes
- set_sc_neighbor_angle_exponent(...) from builtins.PyCapsule
- set_sc_neighbor_angle_exponent(self : rosetta.protocols.flxbb.LayerDesignOperation, value : float) -> NoneType
Set another parameter (the angle exponent) in the calculation that the sidechain neighbors algorithm uses.
See core::select::util::SelectResiduesByLayer class for details.
- set_sc_neighbor_angle_shift_factor(...) from builtins.PyCapsule
- set_sc_neighbor_angle_shift_factor(self : rosetta.protocols.flxbb.LayerDesignOperation, value : float) -> NoneType
Set a parameter in the calculation that the sidechain neighbors algorithm uses.
See core::select::util::SelectResiduesByLayer class for details.
- set_sc_neighbor_denominator(...) from builtins.PyCapsule
- set_sc_neighbor_denominator(self : rosetta.protocols.flxbb.LayerDesignOperation, value : float) -> NoneType
Set the factor by which neighbor counts are divided when using the sidechain neighbors method.
- set_sc_neighbor_dist_exponent(...) from builtins.PyCapsule
- set_sc_neighbor_dist_exponent(self : rosetta.protocols.flxbb.LayerDesignOperation, value : float) -> NoneType
Set another parameter (the distance exponent) in the calculation that the sidechain neighbors algorithm uses.
See core::select::util::SelectResiduesByLayer class for details.
- set_sc_neighbor_dist_midpoint(...) from builtins.PyCapsule
- set_sc_neighbor_dist_midpoint(self : rosetta.protocols.flxbb.LayerDesignOperation, value : float) -> NoneType
Set the midpoint of the sigmoidal distance falloff for the sidechain neighbors method.
- set_use_sidechain_neighbors(...) from builtins.PyCapsule
- set_use_sidechain_neighbors(self : rosetta.protocols.flxbb.LayerDesignOperation, value : bool) -> NoneType
Set whether to use sidechain neighbors to determine core/boundary/surface (default=false)
- set_verbose(...) from builtins.PyCapsule
- set_verbose(self : rosetta.protocols.flxbb.LayerDesignOperation, b : bool) -> NoneType
set verbose
- use_original_seq(...) from builtins.PyCapsule
- use_original_seq(rosetta.protocols.flxbb.LayerDesignOperation) -> NoneType
use original sequence for not designed layer
Data and other attributes defined here:
- DESIGN = LayerOperationType.DESIGN
- DESIGNABLE = LayerSpecificationType.DESIGNABLE
- FIXED = LayerSpecificationType.FIXED
- LayerOperationType = <class 'rosetta.protocols.flxbb.LayerDesignOperation.LayerOperationType'>
- LayerSpecificationType = <class 'rosetta.protocols.flxbb.LayerDesignOperation.LayerSpecificationType'>
- NO_DESIGN = LayerOperationType.NO_DESIGN
- OMIT = LayerOperationType.OMIT
- PACKABLE = LayerSpecificationType.PACKABLE
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