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- builtins.object
-
- RNA_AtrRepChecker
- RNA_BaseCentroidChecker
- RNA_ChainClosableGeometryChecker
- RNA_VDW_BinChecker
- rosetta.basic.datacache.CacheableData(builtins.object)
-
- VDW_CachedRepScreenInfo
- rosetta.core.scoring.methods.EnergyMethodCreator(builtins.object)
-
- VDWGridEnergyCreator
- rosetta.core.scoring.methods.WholeStructureEnergy(rosetta.core.scoring.methods.EnergyMethod)
-
- VDWGridEnergy
- rosetta.protocols.moves.Mover(builtins.object)
-
- RNA_ChainClosureChecker
class RNA_AtrRepChecker(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker, rosetta.core.pose.Pose, protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> NoneType
doc
2. __init__(rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker, rosetta.core.pose.Pose, protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, bool) -> NoneType
doc
3. __init__(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker, pose : rosetta.core.pose.Pose, working_parameters : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, loose_rep_cutoff : bool, energy_method_options : rosetta.core.scoring.methods.EnergyMethodOptions) -> NoneType
4. __init__(rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker, rosetta.core.pose.Pose, int, int, int) -> NoneType
doc
5. __init__(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker, pose : rosetta.core.pose.Pose, moving_res : int, reference_res : int, gap_size : int, energy_method_options : rosetta.core.scoring.methods.EnergyMethodOptions) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- base_atr_score(...) from builtins.PyCapsule
- base_atr_score(rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker) -> float
- base_rep_score(...) from builtins.PyCapsule
- base_rep_score(rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker) -> float
- check_screen(...) from builtins.PyCapsule
- check_screen(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker, current_pose_screen : rosetta.core.pose.Pose) -> bool
- count_data(...) from builtins.PyCapsule
- count_data(rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker) -> rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct
- delta_atr_score(...) from builtins.PyCapsule
- delta_atr_score(rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker) -> float
- delta_rep_score(...) from builtins.PyCapsule
- delta_rep_score(rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker) -> float
- set_extra_loose_rep_cutoff(...) from builtins.PyCapsule
- set_extra_loose_rep_cutoff(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker, setting : bool) -> NoneType
- set_loose_rep_cutoff(...) from builtins.PyCapsule
- set_loose_rep_cutoff(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker, setting : bool) -> NoneType
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class RNA_BaseCentroidChecker(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, rosetta.core.pose.Pose, protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> NoneType
doc
2. __init__(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, pose : rosetta.core.pose.Pose, working_parameters : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters, tether_jump : bool) -> NoneType
3. __init__(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, : rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- allow_base_pair_only_screen(...) from builtins.PyCapsule
- allow_base_pair_only_screen(rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker) -> bool
- check_centroid_interaction(...) from builtins.PyCapsule
- check_centroid_interaction(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, moving_res_base_stub : rosetta.core.kinematics.Stub, count_data : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct) -> bool
- check_that_terminal_res_are_unstacked(...) from builtins.PyCapsule
- check_that_terminal_res_are_unstacked(*args, **kwargs)
Overloaded function.
1. check_that_terminal_res_are_unstacked(rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker) -> bool
2. check_that_terminal_res_are_unstacked(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, verbose : bool) -> bool
- found_centroid_interaction(...) from builtins.PyCapsule
- found_centroid_interaction(rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker) -> bool
- set_allow_base_pair_only_screen(...) from builtins.PyCapsule
- set_allow_base_pair_only_screen(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, setting : bool) -> NoneType
- set_floating_base(...) from builtins.PyCapsule
- set_floating_base(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, setting : bool) -> NoneType
- update_base_stub_list_and_check_centroid_interaction(...) from builtins.PyCapsule
- update_base_stub_list_and_check_centroid_interaction(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, pose : rosetta.core.pose.Pose, count_data : rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct) -> bool
- update_base_stub_list_and_check_that_terminal_res_are_unstacked(...) from builtins.PyCapsule
- update_base_stub_list_and_check_that_terminal_res_are_unstacked(*args, **kwargs)
Overloaded function.
1. update_base_stub_list_and_check_that_terminal_res_are_unstacked(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, pose : rosetta.core.pose.Pose) -> bool
2. update_base_stub_list_and_check_that_terminal_res_are_unstacked(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, pose : rosetta.core.pose.Pose, reinitialize : bool) -> bool
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class RNA_ChainClosableGeometryChecker(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, five_prime_chain_break_res : int, gap_size : int) -> NoneType
2. __init__(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, five_prime_chain_break_res : int, three_prime_chain_break_res : int, gap_size : int) -> NoneType
3. __init__(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- check_chain_closable_geometry(...) from builtins.PyCapsule
- check_chain_closable_geometry(*args, **kwargs)
Overloaded function.
1. check_chain_closable_geometry(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, xyz_1 : rosetta.numeric.xyzVector_double_t, xyz_2 : rosetta.numeric.xyzVector_double_t) -> bool
2. check_chain_closable_geometry(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, five_prime_residue : rosetta.core.conformation.Residue, three_prime_residue : rosetta.core.conformation.Residue) -> bool
- check_screen(...) from builtins.PyCapsule
- check_screen(*args, **kwargs)
Overloaded function.
1. check_screen(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, pose : rosetta.core.pose.Pose) -> bool
2. check_screen(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, pose : rosetta.core.pose.Pose, strict : bool) -> bool
3. check_screen(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, moving_pose : rosetta.core.pose.Pose, reference_pose : rosetta.core.pose.Pose, is_prepend : bool) -> bool
4. check_screen(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, moving_pose : rosetta.core.pose.Pose, reference_pose : rosetta.core.pose.Pose, is_prepend : bool, strict : bool) -> bool
5. check_screen(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, pose : rosetta.core.pose.Pose, rsd_at_origin_list : rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, moving_res_base_stub : rosetta.core.kinematics.Stub, reference_res : int) -> bool
6. check_screen(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, pose_data_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, rsd_at_origin_list : rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, moving_res_base_stub : rosetta.core.kinematics.Stub, reference_res : int) -> bool
- dist_squared(...) from builtins.PyCapsule
- dist_squared(rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker) -> float
- five_prime_chain_break_res(...) from builtins.PyCapsule
- five_prime_chain_break_res(rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker) -> int
- max_dist_squared(...) from builtins.PyCapsule
- max_dist_squared(rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker) -> float
- three_prime_chain_break_res(...) from builtins.PyCapsule
- three_prime_chain_break_res(rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker) -> int
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class RNA_ChainClosureChecker(rosetta.protocols.moves.Mover) |
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- Method resolution order:
- RNA_ChainClosureChecker
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, pose : rosetta.core.pose.Pose, five_prime_res : int) -> NoneType
2. __init__(handle, rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker) -> 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.stepwise.modeler.rna.checker.RNA_ChainClosureChecker, pose : rosetta.core.pose.Pose) -> NoneType
- chain_break_screening_general(...) from builtins.PyCapsule
- chain_break_screening_general(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker, chain_break_screening_pose : rosetta.core.pose.Pose, chainbreak_scorefxn : rosetta.core.scoring.ScoreFunction, five_ : int) -> bool
- check_loop_closed(...) from builtins.PyCapsule
- check_loop_closed(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker, pose : rosetta.core.pose.Pose) -> bool
- check_screen(...) from builtins.PyCapsule
- check_screen(*args, **kwargs)
Overloaded function.
1. check_screen(rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker) -> bool
2. check_screen(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker, pose : rosetta.core.pose.Pose) -> bool
- copy_CCD_torsions(...) from builtins.PyCapsule
- copy_CCD_torsions(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker, pose : rosetta.core.pose.Pose) -> NoneType
- copy_CCD_torsions_general(...) from builtins.PyCapsule
- copy_CCD_torsions_general(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker, pose : rosetta.core.pose.Pose, five_prime_res : int, three_prime_res : int) -> NoneType
- five_prime_res(...) from builtins.PyCapsule
- five_prime_res(rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker) -> int
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker) -> str
- pose(...) from builtins.PyCapsule
- pose(rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker) -> rosetta.core.pose.Pose
- set_reinitialize_CCD_torsions(...) from builtins.PyCapsule
- set_reinitialize_CCD_torsions(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker, setting : bool) -> NoneType
Methods inherited from rosetta.protocols.moves.Mover:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.moves.Mover, other : rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
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class RNA_VDW_BinChecker(builtins.object) |
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Methods defined here:
- FARFAR_setup_using_user_input_VDW_pose(...) from builtins.PyCapsule
- FARFAR_setup_using_user_input_VDW_pose(*args, **kwargs)
Overloaded function.
1. FARFAR_setup_using_user_input_VDW_pose(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, VDW_rep_screen_pose_info : rosetta.utility.vector1_std_string, const_working_pose : rosetta.core.pose.Pose) -> NoneType
2. FARFAR_setup_using_user_input_VDW_pose(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, All_VDW_rep_screen_pose_info : rosetta.utility.vector1_std_string, const_working_pose : rosetta.core.pose.Pose, include_side_chains : bool) -> NoneType
- VDW_rep_screen(...) from builtins.PyCapsule
- VDW_rep_screen(*args, **kwargs)
Overloaded function.
1. VDW_rep_screen(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, screening_pose : rosetta.core.pose.Pose, moving_res : int, rsd_at_origin : rosetta.core.conformation.Residue, moving_res_base_stub : rosetta.core.kinematics.Stub) -> bool
2. VDW_rep_screen(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, screening_pose : rosetta.core.pose.Pose, moving_res : int) -> bool
- VDW_rep_screen_with_act_pose(...) from builtins.PyCapsule
- VDW_rep_screen_with_act_pose(*args, **kwargs)
Overloaded function.
1. VDW_rep_screen_with_act_pose(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, screening_pose : rosetta.core.pose.Pose, moving_res_list : rosetta.utility.vector1_unsigned_long) -> bool
2. VDW_rep_screen_with_act_pose(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, screening_pose : rosetta.core.pose.Pose, moving_res_list : rosetta.utility.vector1_unsigned_long, local_verbose : bool) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, pose : rosetta.core.pose.Pose) -> NoneType
2. __init__(rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- align_working_pose(...) from builtins.PyCapsule
- align_working_pose(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, working_pose : rosetta.core.pose.Pose) -> NoneType
- create_VDW_screen_bin(...) from builtins.PyCapsule
- create_VDW_screen_bin(*args, **kwargs)
Overloaded function.
1. create_VDW_screen_bin(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, pose : rosetta.core.pose.Pose, ignore_res_list : rosetta.utility.vector1_unsigned_long, is_prepend : bool, reference_xyz : rosetta.numeric.xyzVector_double_t) -> NoneType
2. create_VDW_screen_bin(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, pose : rosetta.core.pose.Pose, ignore_res_list : rosetta.utility.vector1_unsigned_long, is_prepend : bool, reference_xyz : rosetta.numeric.xyzVector_double_t, verbose : bool) -> NoneType
3. create_VDW_screen_bin(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, VDW_rep_screen_info_list : rosetta.utility.vector1_core_pose_rna_VDW_RepScreenInfo, reference_xyz : rosetta.numeric.xyzVector_double_t, verbose : bool) -> NoneType
4. create_VDW_screen_bin(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, pose_list : rosetta.utility.vector1_core_pose_Pose, list_of_ignore_res_list : rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t, list_of_is_prepend : rosetta.utility.vector1_bool, reference_xyz : rosetta.numeric.xyzVector_double_t, verbose : bool) -> NoneType
- get_VDW_align_res(...) from builtins.PyCapsule
- get_VDW_align_res(rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker) -> rosetta.utility.vector1_unsigned_long
- reference_xyz_consistency_check(...) from builtins.PyCapsule
- reference_xyz_consistency_check(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, inputted_reference_xyz : rosetta.numeric.xyzVector_double_t) -> NoneType
- set_VDW_rep_alignment_RMSD_CUTOFF(...) from builtins.PyCapsule
- set_VDW_rep_alignment_RMSD_CUTOFF(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, setting : float) -> NoneType
- set_VDW_rep_delete_matching_res(...) from builtins.PyCapsule
- set_VDW_rep_delete_matching_res(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, setting : rosetta.utility.vector1_std_string) -> NoneType
- set_num_clash_atom_cutoff(...) from builtins.PyCapsule
- set_num_clash_atom_cutoff(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, setting : int) -> NoneType
- set_output_pdb(...) from builtins.PyCapsule
- set_output_pdb(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, setting : bool) -> NoneType
- set_physical_pose_clash_dist_cutoff(...) from builtins.PyCapsule
- set_physical_pose_clash_dist_cutoff(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, setting : float) -> NoneType
- setup_using_user_input_VDW_pose(...) from builtins.PyCapsule
- setup_using_user_input_VDW_pose(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, All_VDW_rep_screen_pose_info : rosetta.utility.vector1_std_string, const_working_pose : rosetta.core.pose.Pose, working_parameters : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> NoneType
- setup_using_working_pose(...) from builtins.PyCapsule
- setup_using_working_pose(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, const_working_pose : rosetta.core.pose.Pose, working_parameters : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) -> NoneType
- setup_working_alignment(...) from builtins.PyCapsule
- setup_working_alignment(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, working_pose : rosetta.core.pose.Pose) -> NoneType
- update_VDW_screen_bin(...) from builtins.PyCapsule
- update_VDW_screen_bin(self : rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, pose : rosetta.core.pose.Pose, ignore_res_list : rosetta.utility.vector1_unsigned_long, is_prepend : bool, outfile_act : rosetta.std.basic_ofstream_char_std_char_traits_char_t) -> NoneType
- user_inputted_VDW_screen_pose(...) from builtins.PyCapsule
- user_inputted_VDW_screen_pose(rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker) -> bool
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class VDWGridEnergy(rosetta.core.scoring.methods.WholeStructureEnergy) |
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- Method resolution order:
- VDWGridEnergy
- rosetta.core.scoring.methods.WholeStructureEnergy
- rosetta.core.scoring.methods.EnergyMethod
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.stepwise.modeler.rna.checker.VDWGridEnergy) -> rosetta.core.scoring.methods.EnergyMethod
clone
- finalize_total_energy(...) from builtins.PyCapsule
- finalize_total_energy(self : rosetta.protocols.stepwise.modeler.rna.checker.VDWGridEnergy, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector) -> NoneType
//////////////////////////////////////////////////////////////////////////
- indicate_required_context_graphs(...) from builtins.PyCapsule
- indicate_required_context_graphs(self : rosetta.protocols.stepwise.modeler.rna.checker.VDWGridEnergy, : rosetta.utility.vector1_bool) -> NoneType
VDWGridEnergy is context independent; indicates that no
context graphs are required
- version(...) from builtins.PyCapsule
- version(rosetta.protocols.stepwise.modeler.rna.checker.VDWGridEnergy) -> int
Methods inherited from rosetta.core.scoring.methods.WholeStructureEnergy:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.scoring.methods.WholeStructureEnergy, : rosetta.core.scoring.methods.WholeStructureEnergy) -> rosetta.core.scoring.methods.WholeStructureEnergy
- atomic_interaction_cutoff(...) from builtins.PyCapsule
- atomic_interaction_cutoff(rosetta.core.scoring.methods.WholeStructureEnergy) -> float
how far apart must two heavy atoms be to have a zero interaction energy?
If hydrogen atoms interact at the same range as heavy atoms, then
this distance should build-in a 2 * max-bound-h-distance-cutoff buffer.
There is an improper mixing here between run-time aquired chemical knowledge
(max-bound-h-distance-cutoff) and compile time aquired scoring knowledge
(max atom cutoff); this could be resolved by adding a boolean
uses_hydrogen_interaction_distance() to the SRTBEnergy class along with
a method of the ChemicalManager max_bound_h_distance_cutoff().
This method allows the WholeStructureEnergy class to define which edges
should be included in the EnergyGraph so that during the finalize() method
the Energy class can iterate across the EnergyGraph. This iteration occurrs
in the SecondaryStructureEnergy class, where the edges must span 12 angstroms
between the centroids. Arguably, the SecondaryStructureEnergy class could use
the TwelveANeighborGraph (a context graph) and not require that the EnergyGraph
span such long distances.
- method_type(...) from builtins.PyCapsule
- method_type(rosetta.core.scoring.methods.WholeStructureEnergy) -> rosetta.core.scoring.methods.EnergyMethodType
Methods inherited from rosetta.core.scoring.methods.EnergyMethod:
- defines_high_order_terms(...) from builtins.PyCapsule
- defines_high_order_terms(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose) -> bool
Should this EnergyMethod have score and derivative evaluation
evaluated both in the context of the whole Pose and in the context
of residue or residue-pairs? This covers scoring terms like env-smooth
wherein the CBeta's get derivatives for increasing the neighbor counts
for surrounding residues, and terms like constraints, which are definable
on arbitrary number of residues (e.g. more than 2); both of these terms
could be used in RTMin, and both should use the residue and residue-pair
evaluation scheme with the MinimizationGraph for the majority of the
work they do. (Now, high-order constraints (3-body or above) will not
be properly evaluated within RTMin.). The default implementation
returns "false".
- eval_atom_derivative(...) from builtins.PyCapsule
- eval_atom_derivative(self : rosetta.core.scoring.methods.EnergyMethod, id : rosetta.core.id.AtomID, pose : rosetta.core.pose.Pose, domain_map : ObjexxFCL::FArray1D<int>, sfxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType
Evaluate the XYZ derivative for an atom in the pose.
Called during the atomtree derivative calculation, atom_tree_minimize.cc,
through the ScoreFunction::eval_atom_derivative intermediary.
F1 and F2 should not zeroed, rather, this class should accumulate its contribution
from this atom's XYZ derivative
The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984)
"Rapid Calculation of First and Second Derivatives of Conformational Energy with
Respect to Dihedral Angles for Proteins. General Recurrent Equations"
Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga,
respectively, of equations 7a & 7b in that paper.
- finalize_after_derivatives(...) from builtins.PyCapsule
- finalize_after_derivatives(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction) -> NoneType
called at the end of derivatives evaluation
- minimize_in_whole_structure_context(...) from builtins.PyCapsule
- minimize_in_whole_structure_context(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose) -> bool
Should this EnergyMethod have score and derivative evaluation
evaluated only in the context of the whole Pose, or can it be included
in a decomposed manner for a residue or a set of residue-pairs that are
not part of the Pose that's serving as their context? The default
method implemented in the base class returns true in order to grandfather
in EnergyMethods that have not had their derivatives changed to take
advantage of the new derivative-evaluation machinery. Methods that return
"true" will not have their residue-energy(-ext) / residue-pair-energy(-ext)
methods invoked by the ScoreFunction during its traversal of the
MinimizationGraph, and instead will be asked to perform all their work
during finalize_total_energies(). Similarly, they will be expected to
perform all their work during eval_atom_deriv() instead of during the
ScoreFunction's traversal of the MinimizationGraph for derivative evaluation.
IMPORTANT: Methods that return "true" cannot be included in RTMin.
- prepare_rotamers_for_packing(...) from builtins.PyCapsule
- prepare_rotamers_for_packing(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, : rosetta.core.conformation.RotamerSetBase) -> NoneType
If an energy method needs to cache data in a packing::RotamerSet object before
rotamer energies are calculated, it does so during this function. The packer
must ensure this function is called. The default behavior is to do nothing.
- score_types(...) from builtins.PyCapsule
- score_types(rosetta.core.scoring.methods.EnergyMethod) -> rosetta.utility.vector1_core_scoring_ScoreType
Returns the score types that this energy method computes.
- setup_for_derivatives(...) from builtins.PyCapsule
- setup_for_derivatives(self : rosetta.core.scoring.methods.EnergyMethod, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
Called immediately before atom- and DOF-derivatives are calculated
allowing the derived class a chance to prepare for future calls.
- setup_for_minimizing(...) from builtins.PyCapsule
- setup_for_minimizing(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, : rosetta.core.kinematics.MinimizerMapBase) -> NoneType
Called at the beginning of atom tree minimization, this method
allows the derived class the opportunity to initialize pertinent data
that will be used during minimization. During minimzation, the chemical
structure of the pose is constant, so assumptions on the number of atoms
per residue and their identities are safe so long as the pose's Energies
object's "use_nblist()" method returns true.
- setup_for_packing(...) from builtins.PyCapsule
- setup_for_packing(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, : rosetta.utility.vector1_bool) -> NoneType
if an energy method needs to cache data in the Energies object,
before packing begins, then it does so during this function. The packer
must ensure this function is called. The default behavior is to do nothing.
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction) -> NoneType
if an energy method needs to cache something in the pose (e.g. in pose.energies()),
before scoring begins, it must do so in this method. All long range energy
functions must initialize their LREnergyContainers before scoring begins.
The default is to do nothing.
- update_residue_for_packing(...) from builtins.PyCapsule
- update_residue_for_packing(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, resid : int) -> NoneType
If the pose changes in the middle of a packing (as happens in rotamer trials) and if
an energy method needs to cache data in the pose that corresponds to its current state,
then the method must update that data when this function is called. The packer must
ensure this function gets called. The default behavior is to do nothing.
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