| | |
- builtins.object
-
- CentroidRotNum
- MakeRotLibOptionsData
- MakeRotLibPolymerType
- RotData
- TorsionRange
- rosetta.protocols.jd2.Job(builtins.object)
-
- MakeRotLibJob
- rosetta.protocols.jd2.JobInputter(builtins.object)
-
- MakeRotLibJobInputter
- rosetta.protocols.jd2.JobInputterCreator(builtins.object)
-
- MakeRotLibJobInputterCreator
- rosetta.protocols.moves.Mover(builtins.object)
-
- MakeRotLibMover
class MakeRotLibJob(rosetta.protocols.jd2.Job) |
| | |
- Method resolution order:
- MakeRotLibJob
- rosetta.protocols.jd2.Job
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, inner_job : rosetta.protocols.jd2.InnerJob, nstruct_index : int, omg : float, bbs : rosetta.utility.vector1_double, bb_ids : rosetta.utility.vector1_unsigned_long, eps : float, mrlod : rosetta.protocols.make_rot_lib.MakeRotLibOptionsData, semirotameric : bool) -> NoneType
2. __init__(handle, rosetta.protocols.make_rot_lib.MakeRotLibJob) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- get_bb(...) from builtins.PyCapsule
- get_bb(self : rosetta.protocols.make_rot_lib.MakeRotLibJob, i : int) -> float
- get_bb_ids(...) from builtins.PyCapsule
- get_bb_ids(rosetta.protocols.make_rot_lib.MakeRotLibJob) -> rosetta.utility.vector1_unsigned_long
- get_bbs(...) from builtins.PyCapsule
- get_bbs(rosetta.protocols.make_rot_lib.MakeRotLibJob) -> rosetta.utility.vector1_double
- get_eps(...) from builtins.PyCapsule
- get_eps(rosetta.protocols.make_rot_lib.MakeRotLibJob) -> float
- get_omg(...) from builtins.PyCapsule
- get_omg(rosetta.protocols.make_rot_lib.MakeRotLibJob) -> float
acessors
- get_options_data(...) from builtins.PyCapsule
- get_options_data(rosetta.protocols.make_rot_lib.MakeRotLibJob) -> rosetta.protocols.make_rot_lib.MakeRotLibOptionsData
- get_semirotameric(...) from builtins.PyCapsule
- get_semirotameric(rosetta.protocols.make_rot_lib.MakeRotLibJob) -> bool
Methods inherited from rosetta.protocols.jd2.Job:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.jd2.Job) -> str
- add_string(...) from builtins.PyCapsule
- add_string(self : rosetta.protocols.jd2.Job, string_in : str) -> NoneType
add an output string
- add_string_real_pair(...) from builtins.PyCapsule
- add_string_real_pair(self : rosetta.protocols.jd2.Job, string_in : str, real_in : float) -> NoneType
add a string/real pair
- add_string_string_pair(...) from builtins.PyCapsule
- add_string_string_pair(self : rosetta.protocols.jd2.Job, string1 : str, string2 : str) -> NoneType
add a string/string pair
- add_strings(...) from builtins.PyCapsule
- add_strings(self : rosetta.protocols.jd2.Job, : rosetta.std.list_std_string_std_allocator_std_string_t) -> NoneType
add output strings
- bad(...) from builtins.PyCapsule
- bad(rosetta.protocols.jd2.Job) -> bool
- call_output_observers(...) from builtins.PyCapsule
- call_output_observers(self : rosetta.protocols.jd2.Job, pose : rosetta.core.pose.Pose) -> NoneType
- can_be_deleted(...) from builtins.PyCapsule
- can_be_deleted(rosetta.protocols.jd2.Job) -> bool
Returns true iff this job can be deleted to free up memory.
Should only be true if the job has completed, is bad, or has failed.
- clear_output(...) from builtins.PyCapsule
- clear_output(rosetta.protocols.jd2.Job) -> NoneType
Delete the output strings, string/string pairs, and string/real pairs.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.jd2.Job) -> rosetta.protocols.jd2.Job
Return an owning pointer to a copy of this object.
- completed(...) from builtins.PyCapsule
- completed(rosetta.protocols.jd2.Job) -> bool
- copy_without_output(...) from builtins.PyCapsule
- copy_without_output(rosetta.protocols.jd2.Job) -> rosetta.protocols.jd2.Job
returns a copy of this object whose "output fields" are zeroed
out. Used by the JobDistributor in cases where the job fails and must be
retried to prevent accumulation of Job state after a failure. This
implementation was chosen over a clear_all_output function to prevent
mover A from deleting mover B's hard work! You probably should not be
trying to call this function. The exception: If you want an
intermediate-output pose (not the final pose) to not have the aggregated
accessory data in the "real" Job object.
- elapsed_time(...) from builtins.PyCapsule
- elapsed_time(rosetta.protocols.jd2.Job) -> int
- end_time(...) from builtins.PyCapsule
- end_time(rosetta.protocols.jd2.Job) -> int
- end_timing(...) from builtins.PyCapsule
- end_timing(rosetta.protocols.jd2.Job) -> NoneType
- get_pose(...) from builtins.PyCapsule
- get_pose(*args, **kwargs)
Overloaded function.
1. get_pose(rosetta.protocols.jd2.Job) -> rosetta.core.pose.Pose
return a COP to the input pose
2. get_pose(self : rosetta.protocols.jd2.Job, : rosetta.core.pose.Pose) -> NoneType
in-place copy of input pose
- get_string_real_pairs(...) from builtins.PyCapsule
- get_string_real_pairs(rosetta.protocols.jd2.Job) -> rosetta.std.map_std_string_double
- get_string_string_pairs(...) from builtins.PyCapsule
- get_string_string_pairs(rosetta.protocols.jd2.Job) -> rosetta.std.map_std_string_std_string
- get_strings(...) from builtins.PyCapsule
- get_strings(rosetta.protocols.jd2.Job) -> rosetta.std.list_std_string_std_allocator_std_string_t
/////////////////////END SECTION//////////////////////////////////////////////////////////////////
- inner_job(...) from builtins.PyCapsule
- inner_job(rosetta.protocols.jd2.Job) -> protocols::jd2::InnerJob
access to inner-job ... use is discouraged - use sparingly!
--- DO NOT use my_job->inner_job()->get_pose()
INSTEAD use my_job->get_pose()
- inner_job_nonconst(...) from builtins.PyCapsule
- inner_job_nonconst(rosetta.protocols.jd2.Job) -> protocols::jd2::InnerJob
nonconst access is intended only for the JobInputter to load poses into the InnerJob, and the Parser to add constraints, and the JobDistributor to delete completed inputs (recycle memory)
- input_tag(...) from builtins.PyCapsule
- input_tag(rosetta.protocols.jd2.Job) -> str
return the input tag (a short string, generally)
- nstruct_index(...) from builtins.PyCapsule
- nstruct_index(rosetta.protocols.jd2.Job) -> int
- nstruct_max(...) from builtins.PyCapsule
- nstruct_max(rosetta.protocols.jd2.Job) -> int
- output_string_real_pairs_begin(...) from builtins.PyCapsule
- output_string_real_pairs_begin(rosetta.protocols.jd2.Job) -> std::_Rb_tree_const_iterator<std::pair<std::string const, double> >
- output_string_real_pairs_end(...) from builtins.PyCapsule
- output_string_real_pairs_end(rosetta.protocols.jd2.Job) -> std::_Rb_tree_const_iterator<std::pair<std::string const, double> >
- output_string_string_pairs_begin(...) from builtins.PyCapsule
- output_string_string_pairs_begin(rosetta.protocols.jd2.Job) -> std::_Rb_tree_const_iterator<std::pair<std::string const, std::string> >
- output_string_string_pairs_end(...) from builtins.PyCapsule
- output_string_string_pairs_end(rosetta.protocols.jd2.Job) -> std::_Rb_tree_const_iterator<std::pair<std::string const, std::string> >
- output_strings_begin(...) from builtins.PyCapsule
- output_strings_begin(rosetta.protocols.jd2.Job) -> std::_List_const_iterator<std::string>
/////////////////THIS SECTION OF FUNCTIONS IS FORBIDDEN FOR USE BY MOVERS//////////////////////////////////
- output_strings_end(...) from builtins.PyCapsule
- output_strings_end(rosetta.protocols.jd2.Job) -> std::_List_const_iterator<std::string>
- set_bad(...) from builtins.PyCapsule
- set_bad(*args, **kwargs)
Overloaded function.
1. set_bad(rosetta.protocols.jd2.Job) -> NoneType
2. set_bad(self : rosetta.protocols.jd2.Job, value : bool) -> NoneType
- set_can_be_deleted(...) from builtins.PyCapsule
- set_can_be_deleted(*args, **kwargs)
Overloaded function.
1. set_can_be_deleted(rosetta.protocols.jd2.Job) -> NoneType
Set whether this job can be deleted to free up memory.
2. set_can_be_deleted(self : rosetta.protocols.jd2.Job, value : bool) -> NoneType
Set whether this job can be deleted to free up memory.
- set_completed(...) from builtins.PyCapsule
- set_completed(*args, **kwargs)
Overloaded function.
1. set_completed(rosetta.protocols.jd2.Job) -> NoneType
2. set_completed(self : rosetta.protocols.jd2.Job, value : bool) -> NoneType
- set_status_prefix(...) from builtins.PyCapsule
- set_status_prefix(self : rosetta.protocols.jd2.Job, prefix : str) -> NoneType
- start_time(...) from builtins.PyCapsule
- start_time(rosetta.protocols.jd2.Job) -> int
- start_timing(...) from builtins.PyCapsule
- start_timing(rosetta.protocols.jd2.Job) -> NoneType
- status_prefix(...) from builtins.PyCapsule
- status_prefix(rosetta.protocols.jd2.Job) -> str
- timestamp(...) from builtins.PyCapsule
- timestamp(rosetta.protocols.jd2.Job) -> str
- to_do(...) from builtins.PyCapsule
- to_do(rosetta.protocols.jd2.Job) -> bool
|
class MakeRotLibJobInputter(rosetta.protocols.jd2.JobInputter) |
| |
JobInputter that creats jobs based on MakeRotLib option files.
|
| |
- Method resolution order:
- MakeRotLibJobInputter
- rosetta.protocols.jd2.JobInputter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.make_rot_lib.MakeRotLibJobInputter) -> 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.make_rot_lib.MakeRotLibJobInputter, : rosetta.protocols.make_rot_lib.MakeRotLibJobInputter) -> rosetta.protocols.make_rot_lib.MakeRotLibJobInputter
- fill_jobs(...) from builtins.PyCapsule
- fill_jobs(self : rosetta.protocols.make_rot_lib.MakeRotLibJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType
Determines what jobs exist from the make_rot_lib options file
- input_source(...) from builtins.PyCapsule
- input_source(rosetta.protocols.make_rot_lib.MakeRotLibJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum
Return the type of input source that the MakeRotLibJobInputter is currently using.
- pose_from_job(...) from builtins.PyCapsule
- pose_from_job(self : rosetta.protocols.make_rot_lib.MakeRotLibJobInputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType
this function is responsible for filling the pose reference with the pose indicated by the job
Methods inherited from rosetta.protocols.jd2.JobInputter:
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter
Get self const owning pointers.
2. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter
Get self owning pointers.
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_const_protocols_jd2_JobInputter_t
Get self const weak pointers.
2. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_protocols_jd2_JobInputter_t
Get self weak pointers.
- job_inputter_input_source_to_string(...) from builtins.PyCapsule
- job_inputter_input_source_to_string(source : rosetta.protocols.jd2.JobInputterInputSource.Enum) -> str
call this with input_source() to get the input source of a
particular job inputter
- update_jobs_list(...) from builtins.PyCapsule
- update_jobs_list(self : rosetta.protocols.jd2.JobInputter, jobs : protocols::jd2::JobsContainer) -> NoneType
This function is only called by certain JobInputters to update the jobs list after it has already been created.
An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back.
- updates_jobs_list(...) from builtins.PyCapsule
- updates_jobs_list(rosetta.protocols.jd2.JobInputter) -> bool
Does this type of JobInputter update the jobs list?
False by default. Override this function in derived classes to make it true.
|
class MakeRotLibMover(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- MakeRotLibMover
- 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.make_rot_lib.MakeRotLibMover) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- angle_diff(...) from builtins.PyCapsule
- angle_diff(self : rosetta.protocols.make_rot_lib.MakeRotLibMover, a1 : float, a2 : float) -> float
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.make_rot_lib.MakeRotLibMover, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.make_rot_lib.MakeRotLibMover, : rosetta.protocols.make_rot_lib.MakeRotLibMover) -> rosetta.protocols.make_rot_lib.MakeRotLibMover
- bbs_appropriate_for_definitions(...) from builtins.PyCapsule
- bbs_appropriate_for_definitions(self : rosetta.protocols.make_rot_lib.MakeRotLibMover, bbs : rosetta.utility.vector1_double) -> bool
- calc_all_dist(...) from builtins.PyCapsule
- calc_all_dist(rosetta.protocols.make_rot_lib.MakeRotLibMover) -> NoneType
- calc_centroids(...) from builtins.PyCapsule
- calc_centroids(rosetta.protocols.make_rot_lib.MakeRotLibMover) -> bool
- calc_dist(...) from builtins.PyCapsule
- calc_dist(self : rosetta.protocols.make_rot_lib.MakeRotLibMover, rd1 : rosetta.protocols.make_rot_lib.RotData, rd2 : rosetta.protocols.make_rot_lib.RotData) -> float
- calc_final_rotamer_probs(...) from builtins.PyCapsule
- calc_final_rotamer_probs(rosetta.protocols.make_rot_lib.MakeRotLibMover) -> NoneType
- calc_final_rotamers(...) from builtins.PyCapsule
- calc_final_rotamers(rosetta.protocols.make_rot_lib.MakeRotLibMover) -> NoneType
- calc_medoids(...) from builtins.PyCapsule
- calc_medoids(rosetta.protocols.make_rot_lib.MakeRotLibMover) -> bool
- calc_rotamer_clusters(...) from builtins.PyCapsule
- calc_rotamer_clusters(rosetta.protocols.make_rot_lib.MakeRotLibMover) -> bool
- calc_running_avg(...) from builtins.PyCapsule
- calc_running_avg(self : rosetta.protocols.make_rot_lib.MakeRotLibMover, angle_new : float, angle_old : float, count : int) -> NoneType
- calc_standard_deviations(...) from builtins.PyCapsule
- calc_standard_deviations(self : rosetta.protocols.make_rot_lib.MakeRotLibMover, pose : rosetta.core.pose.Pose, bbs : rosetta.utility.vector1_double, bb_ids : rosetta.utility.vector1_unsigned_long, polymer_type : rosetta.protocols.make_rot_lib.MakeRotLibPolymerType) -> NoneType
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.make_rot_lib.MakeRotLibMover) -> str
- init_centroids(...) from builtins.PyCapsule
- init_centroids(self : rosetta.protocols.make_rot_lib.MakeRotLibMover, centroid_data : rosetta.utility.vector1_utility_vector1_protocols_make_rot_lib_CentroidRotNum_std_allocator_protocols_make_rot_lib_CentroidRotNum_t, num_chi : int, semirotameric : bool) -> NoneType
- init_rotamers(...) from builtins.PyCapsule
- init_rotamers(self : rosetta.protocols.make_rot_lib.MakeRotLibMover, chi_ranges : rosetta.utility.vector1_protocols_make_rot_lib_TorsionRange, num_clusters : int, omg : float, bbs : rosetta.utility.vector1_double, bbids : rosetta.utility.vector1_unsigned_long, eps : float, semirotameric : bool) -> NoneType
- make_three_fold_symmetry_90_210_330(...) from builtins.PyCapsule
- make_three_fold_symmetry_90_210_330(self : rosetta.protocols.make_rot_lib.MakeRotLibMover, rdv : rosetta.utility.vector1_protocols_make_rot_lib_RotData, chi_num : int) -> NoneType
- make_two_fold_symmetry_0_180(...) from builtins.PyCapsule
- make_two_fold_symmetry_0_180(self : rosetta.protocols.make_rot_lib.MakeRotLibMover, rdv : rosetta.utility.vector1_protocols_make_rot_lib_RotData, chi_num : int) -> NoneType
- make_two_fold_symmetry_135_315(...) from builtins.PyCapsule
- make_two_fold_symmetry_135_315(self : rosetta.protocols.make_rot_lib.MakeRotLibMover, rdv : rosetta.utility.vector1_protocols_make_rot_lib_RotData, chi_num : int) -> NoneType
- minimize_all_rotamers(...) from builtins.PyCapsule
- minimize_all_rotamers(self : rosetta.protocols.make_rot_lib.MakeRotLibMover, pose : rosetta.core.pose.Pose, bbs : rosetta.utility.vector1_double, bb_ids : rosetta.utility.vector1_unsigned_long, polymer_type : rosetta.protocols.make_rot_lib.MakeRotLibPolymerType) -> NoneType
- minimize_rotamer(...) from builtins.PyCapsule
- minimize_rotamer(self : rosetta.protocols.make_rot_lib.MakeRotLibMover, rd : rosetta.protocols.make_rot_lib.RotData, pose : rosetta.core.pose.Pose, bbs : rosetta.utility.vector1_double, bb_ids : rosetta.utility.vector1_unsigned_long, polymer_type : rosetta.protocols.make_rot_lib.MakeRotLibPolymerType) -> NoneType
- seed_centroids(...) from builtins.PyCapsule
- seed_centroids(self : rosetta.protocols.make_rot_lib.MakeRotLibMover, semirotameric : bool) -> NoneType
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- 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 RotData(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.make_rot_lib.RotData, NumChi : int, NumCluster : int) -> NoneType
2. __init__(self : rosetta.protocols.make_rot_lib.RotData, NumChi : int, NumCluster : int, semirotameric : bool) -> NoneType
3. __init__(self : rosetta.protocols.make_rot_lib.RotData, NumChi : int, NumBBs : int, NumCluster : int) -> NoneType
4. __init__(self : rosetta.protocols.make_rot_lib.RotData, NumChi : int, NumBBs : int, NumCluster : int, semirotameric : bool) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- get_bb(...) from builtins.PyCapsule
- get_bb(self : rosetta.protocols.make_rot_lib.RotData, i : int) -> float
- get_bb_id(...) from builtins.PyCapsule
- get_bb_id(self : rosetta.protocols.make_rot_lib.RotData, i : int) -> int
- get_bbs(...) from builtins.PyCapsule
- get_bbs(rosetta.protocols.make_rot_lib.RotData) -> rosetta.utility.vector1_double
- get_cen_dist(...) from builtins.PyCapsule
- get_cen_dist(self : rosetta.protocols.make_rot_lib.RotData, num : int) -> float
- get_cluster_num(...) from builtins.PyCapsule
- get_cluster_num(rosetta.protocols.make_rot_lib.RotData) -> int
- get_energy(...) from builtins.PyCapsule
- get_energy(rosetta.protocols.make_rot_lib.RotData) -> float
- get_eps(...) from builtins.PyCapsule
- get_eps(rosetta.protocols.make_rot_lib.RotData) -> float
- get_inp_chi(...) from builtins.PyCapsule
- get_inp_chi(self : rosetta.protocols.make_rot_lib.RotData, num : int) -> float
- get_inter_atr(...) from builtins.PyCapsule
- get_inter_atr(rosetta.protocols.make_rot_lib.RotData) -> float
- get_inter_rep(...) from builtins.PyCapsule
- get_inter_rep(rosetta.protocols.make_rot_lib.RotData) -> float
- get_intra_atr(...) from builtins.PyCapsule
- get_intra_atr(rosetta.protocols.make_rot_lib.RotData) -> float
- get_intra_rep(...) from builtins.PyCapsule
- get_intra_rep(rosetta.protocols.make_rot_lib.RotData) -> float
- get_lib_chi_val(...) from builtins.PyCapsule
- get_lib_chi_val(self : rosetta.protocols.make_rot_lib.RotData, num : int) -> float
- get_min_cent_dist(...) from builtins.PyCapsule
- get_min_cent_dist(rosetta.protocols.make_rot_lib.RotData) -> int
- get_min_chi(...) from builtins.PyCapsule
- get_min_chi(self : rosetta.protocols.make_rot_lib.RotData, num : int) -> float
- get_min_eps(...) from builtins.PyCapsule
- get_min_eps(rosetta.protocols.make_rot_lib.RotData) -> float
- get_min_omg(...) from builtins.PyCapsule
- get_min_omg(rosetta.protocols.make_rot_lib.RotData) -> float
- get_num_bbs(...) from builtins.PyCapsule
- get_num_bbs(rosetta.protocols.make_rot_lib.RotData) -> int
- get_num_chi(...) from builtins.PyCapsule
- get_num_chi(rosetta.protocols.make_rot_lib.RotData) -> int
- get_num_clusters(...) from builtins.PyCapsule
- get_num_clusters(rosetta.protocols.make_rot_lib.RotData) -> int
- get_omg(...) from builtins.PyCapsule
- get_omg(rosetta.protocols.make_rot_lib.RotData) -> float
////////////////////////////////////////////////////////
- get_phi(...) from builtins.PyCapsule
- get_phi(rosetta.protocols.make_rot_lib.RotData) -> float
- get_probability(...) from builtins.PyCapsule
- get_probability(rosetta.protocols.make_rot_lib.RotData) -> float
- get_psi(...) from builtins.PyCapsule
- get_psi(rosetta.protocols.make_rot_lib.RotData) -> float
- get_semi_energy_dist(...) from builtins.PyCapsule
- get_semi_energy_dist(self : rosetta.protocols.make_rot_lib.RotData, i : int) -> float
- get_semi_prob_dist(...) from builtins.PyCapsule
- get_semi_prob_dist(self : rosetta.protocols.make_rot_lib.RotData, i : int) -> float
- get_semirotameric(...) from builtins.PyCapsule
- get_semirotameric(rosetta.protocols.make_rot_lib.RotData) -> bool
- get_solvation(...) from builtins.PyCapsule
- get_solvation(rosetta.protocols.make_rot_lib.RotData) -> float
- get_std_dev(...) from builtins.PyCapsule
- get_std_dev(self : rosetta.protocols.make_rot_lib.RotData, num : int) -> float
- get_twist(...) from builtins.PyCapsule
- get_twist(rosetta.protocols.make_rot_lib.RotData) -> float
- resize_bb_ids(...) from builtins.PyCapsule
- resize_bb_ids(self : rosetta.protocols.make_rot_lib.RotData, i : int) -> NoneType
- resize_bbs(...) from builtins.PyCapsule
- resize_bbs(self : rosetta.protocols.make_rot_lib.RotData, i : int) -> NoneType
- resize_semi_vectors(...) from builtins.PyCapsule
- resize_semi_vectors(self : rosetta.protocols.make_rot_lib.RotData, i : int) -> NoneType
- set_bb(...) from builtins.PyCapsule
- set_bb(self : rosetta.protocols.make_rot_lib.RotData, i : int, BB : float) -> NoneType
- set_bb_id(...) from builtins.PyCapsule
- set_bb_id(self : rosetta.protocols.make_rot_lib.RotData, i : int, bbid : int) -> NoneType
- set_cen_dist(...) from builtins.PyCapsule
- set_cen_dist(self : rosetta.protocols.make_rot_lib.RotData, dist : float, num : int) -> NoneType
- set_cluster_num(...) from builtins.PyCapsule
- set_cluster_num(self : rosetta.protocols.make_rot_lib.RotData, Cluster_Num : int) -> NoneType
- set_energy(...) from builtins.PyCapsule
- set_energy(self : rosetta.protocols.make_rot_lib.RotData, Energy : float) -> NoneType
- set_eps(...) from builtins.PyCapsule
- set_eps(self : rosetta.protocols.make_rot_lib.RotData, Epsilon : float) -> NoneType
- set_inp_chi(...) from builtins.PyCapsule
- set_inp_chi(self : rosetta.protocols.make_rot_lib.RotData, angle : float, num : int) -> NoneType
- set_inter_atr(...) from builtins.PyCapsule
- set_inter_atr(self : rosetta.protocols.make_rot_lib.RotData, inter_atr : float) -> NoneType
- set_inter_rep(...) from builtins.PyCapsule
- set_inter_rep(self : rosetta.protocols.make_rot_lib.RotData, inter_rep : float) -> NoneType
- set_intra_atr(...) from builtins.PyCapsule
- set_intra_atr(self : rosetta.protocols.make_rot_lib.RotData, intra_atr : float) -> NoneType
- set_intra_rep(...) from builtins.PyCapsule
- set_intra_rep(self : rosetta.protocols.make_rot_lib.RotData, intra_rep : float) -> NoneType
- set_lib_chi_val(...) from builtins.PyCapsule
- set_lib_chi_val(self : rosetta.protocols.make_rot_lib.RotData, val : int, num : int) -> NoneType
- set_min_chi(...) from builtins.PyCapsule
- set_min_chi(self : rosetta.protocols.make_rot_lib.RotData, angle : float, num : int) -> NoneType
- set_min_eps(...) from builtins.PyCapsule
- set_min_eps(self : rosetta.protocols.make_rot_lib.RotData, MinEpsilon : float) -> NoneType
- set_min_omg(...) from builtins.PyCapsule
- set_min_omg(self : rosetta.protocols.make_rot_lib.RotData, MinOmega : float) -> NoneType
- set_num_bbs(...) from builtins.PyCapsule
- set_num_bbs(self : rosetta.protocols.make_rot_lib.RotData, i : int) -> NoneType
- set_num_chi(...) from builtins.PyCapsule
- set_num_chi(self : rosetta.protocols.make_rot_lib.RotData, Num_Chi : int) -> NoneType
- set_num_clusters(...) from builtins.PyCapsule
- set_num_clusters(self : rosetta.protocols.make_rot_lib.RotData, num : int) -> NoneType
- set_omg(...) from builtins.PyCapsule
- set_omg(self : rosetta.protocols.make_rot_lib.RotData, Omega : float) -> NoneType
////////////////////////////////////////////////////////
- set_phi(...) from builtins.PyCapsule
- set_phi(self : rosetta.protocols.make_rot_lib.RotData, Phi : float) -> NoneType
- set_probability(...) from builtins.PyCapsule
- set_probability(self : rosetta.protocols.make_rot_lib.RotData, Probability : float) -> NoneType
- set_psi(...) from builtins.PyCapsule
- set_psi(self : rosetta.protocols.make_rot_lib.RotData, Psi : float) -> NoneType
- set_semi_energy_dist(...) from builtins.PyCapsule
- set_semi_energy_dist(self : rosetta.protocols.make_rot_lib.RotData, i : int, setting : float) -> NoneType
- set_semi_prob_dist(...) from builtins.PyCapsule
- set_semi_prob_dist(self : rosetta.protocols.make_rot_lib.RotData, i : int, setting : float) -> NoneType
- set_solvation(...) from builtins.PyCapsule
- set_solvation(self : rosetta.protocols.make_rot_lib.RotData, solvation : float) -> NoneType
- set_std_dev(...) from builtins.PyCapsule
- set_std_dev(self : rosetta.protocols.make_rot_lib.RotData, STD : float, num : int) -> NoneType
- set_twist(...) from builtins.PyCapsule
- set_twist(self : rosetta.protocols.make_rot_lib.RotData, twist : float) -> NoneType
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