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- builtins.object
-
- BackboneGridSamplerHelper
- BundleGridSamplerHelper
- BundleReporterFilterBehaviour
- DoFType
- PertType
- PerturbBundleOptions
- rosetta.core.optimization.Multifunc(builtins.object)
-
- FitSimpleHelixMultiFunc
- rosetta.protocols.filters.Filter(builtins.object)
-
- BundleReporterFilter
- rosetta.protocols.filters.FilterCreator(builtins.object)
-
- BundleReporterFilterCreator
- rosetta.protocols.moves.Mover(builtins.object)
-
- BackboneGridSampler
- BundleGridSampler
- FitSimpleHelix
- MakeBundle
- MakeBundleHelix
- PerturbBundle
- PerturbBundleHelix
- rosetta.protocols.moves.MoverCreator(builtins.object)
-
- BackboneGridSamplerCreator
- BundleGridSamplerCreator
- FitSimpleHelixCreator
- MakeBundleCreator
- MakeBundleHelixCreator
- PerturbBundleCreator
- PerturbBundleHelixCreator
class BackboneGridSampler(rosetta.protocols.moves.Mover) |
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- Method resolution order:
- BackboneGridSampler
- 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.helical_bundle.BackboneGridSampler) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_torsion_to_fix(...) from builtins.PyCapsule
- add_torsion_to_fix(self : rosetta.protocols.helical_bundle.BackboneGridSampler, residue_index : int, torsion_index : int, torsion_value : float) -> NoneType
Add a mainchain torsion to fix, and that torsion's value.
The residue_index is the index of the residue in the repeating unit (1st, 2nd, 3rd, etc.).
The torsion_index is the mainchain torsion index in this residue, and the torsion_value is the
value at which to fix this residue.
- add_torsion_to_sample(...) from builtins.PyCapsule
- add_torsion_to_sample(self : rosetta.protocols.helical_bundle.BackboneGridSampler, residue_index : int, torsion_index : int, start_of_range : float, end_of_range : float, samples : int) -> NoneType
Add a mainchain torsion to sample, the range of values that will be sampled, and the number of samples.
The residue_index is the index in the repeating unit (1st residue, 2nd residue, etc.). The torsion_index
is the mainchain torsion index in this residue. Sampled values will go from start_of_range to end_of_range, with the
total number of samples given by the samples parameter. If the range is -180 to 180, the samples are adjusted so that
180 is not sampled twice.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.helical_bundle.BackboneGridSampler, pose : rosetta.core.pose.Pose) -> NoneType
Actually apply the mover to the pose.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.helical_bundle.BackboneGridSampler, : rosetta.protocols.helical_bundle.BackboneGridSampler) -> rosetta.protocols.helical_bundle.BackboneGridSampler
- cap_ends(...) from builtins.PyCapsule
- cap_ends(rosetta.protocols.helical_bundle.BackboneGridSampler) -> bool
Return whether the ends should be capped (N-acetyl, C-methylamide).
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.helical_bundle.BackboneGridSampler) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.helical_bundle.BackboneGridSampler) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.helical_bundle.BackboneGridSampler) -> str
- max_samples(...) from builtins.PyCapsule
- max_samples(rosetta.protocols.helical_bundle.BackboneGridSampler) -> int
Get the maximum number of samples for the mover.
If the number of gridpoints based on user options exceeds this number, an error is thrown
and the mover aborts. This is to prevent unreasonably large calculations from being attempted.
- nres(...) from builtins.PyCapsule
- nres(rosetta.protocols.helical_bundle.BackboneGridSampler) -> int
Get the number of residues in the pose to build.
This is actually the number of REPEATS. If there are two residues per repeat, you'd have twice this number of resiudes.
- nstruct_mode(...) from builtins.PyCapsule
- nstruct_mode(rosetta.protocols.helical_bundle.BackboneGridSampler) -> bool
Get the nstruct mode.
If true, each job samples one set of mainchain torsion values. If false, every job samples
every set of mainchain torsion values. False by default.
- nstruct_repeats(...) from builtins.PyCapsule
- nstruct_repeats(rosetta.protocols.helical_bundle.BackboneGridSampler) -> int
Get the nstruct repeats.
This is set to 1 by default, which means that each nstruct number correspnds to a different
set of mainchain torsion values. If set greater than 1, then multiple consecutive nstruct numbers will
correspond to the same mainchain torsion values. This allows combinatorially combining this mover's sampling
with another, similar mover's sampling.
- pdb_output(...) from builtins.PyCapsule
- pdb_output(rosetta.protocols.helical_bundle.BackboneGridSampler) -> bool
Returns whether the mover dumps pdbs or not.
- pdb_prefix(...) from builtins.PyCapsule
- pdb_prefix(rosetta.protocols.helical_bundle.BackboneGridSampler) -> str
Access the filename prefix for PDB output.
PDB files are of the form <prefix>_#####.pdb.
- peptide_stub_mover_initialized(...) from builtins.PyCapsule
- peptide_stub_mover_initialized(rosetta.protocols.helical_bundle.BackboneGridSampler) -> bool
Has the PeptideStubMover been initialized?
- prescoring_filter_exists(...) from builtins.PyCapsule
- prescoring_filter_exists(rosetta.protocols.helical_bundle.BackboneGridSampler) -> bool
Returns "true" if and only if a preselection filter has been assigned.
- prescoring_mover_exists(...) from builtins.PyCapsule
- prescoring_mover_exists(rosetta.protocols.helical_bundle.BackboneGridSampler) -> bool
Returns "true" if and only if a preselection mover has been assigned.
- reset_and_initialize_data(...) from builtins.PyCapsule
- reset_and_initialize_data(rosetta.protocols.helical_bundle.BackboneGridSampler) -> NoneType
Reset the torsions_to_sample_, torsions_to_fix_, and resname_ vectors, and
initialize them based on the value of residues_per_repeat_.
- residues_per_repeat(...) from builtins.PyCapsule
- residues_per_repeat(rosetta.protocols.helical_bundle.BackboneGridSampler) -> int
Get the number of residues per repeat.
- resname(...) from builtins.PyCapsule
- resname(self : rosetta.protocols.helical_bundle.BackboneGridSampler, res_index : int) -> str
Get the residue type.
Returns the residue type (full name string) for the nth residue in the list of residues defining the repeating unit.
- selection_low(...) from builtins.PyCapsule
- selection_low(rosetta.protocols.helical_bundle.BackboneGridSampler) -> bool
Returns whether the selection should be for the lowest score value (true) or highest (false).
- set_cap_ends(...) from builtins.PyCapsule
- set_cap_ends(self : rosetta.protocols.helical_bundle.BackboneGridSampler, cap : bool) -> NoneType
Set whether then ends should be capped (N-acetyl, C-methylamide).
- set_max_samples(...) from builtins.PyCapsule
- set_max_samples(self : rosetta.protocols.helical_bundle.BackboneGridSampler, val : int) -> NoneType
Set the maximum number of samples for the mover.
If the number of gridpoints based on user options exceeds this number, an error is thrown
and the mover aborts. This is to prevent unreasonably large calculations from being attempted.
- set_nres(...) from builtins.PyCapsule
- set_nres(self : rosetta.protocols.helical_bundle.BackboneGridSampler, nres_in : int) -> NoneType
Set the number of residues in the pose to build.
This is actually the number of REPEATS. If there are two residues per repeat, you'd have twice this number of resiudes.
- set_nstruct_mode(...) from builtins.PyCapsule
- set_nstruct_mode(self : rosetta.protocols.helical_bundle.BackboneGridSampler, val : bool) -> NoneType
Set the nstruct mode.
If true, each job samples one set of mainchain torsion values. If false, every job samples
every set of mainchain torsion values. False by default.
- set_nstruct_repeats(...) from builtins.PyCapsule
- set_nstruct_repeats(self : rosetta.protocols.helical_bundle.BackboneGridSampler, val : int) -> NoneType
Set the nstruct repeats.
This is set to 1 by default, which means that each nstruct number correspnds to a different
set of mainchain torsion values. If set greater than 1, then multiple consecutive nstruct numbers will
correspond to the same mainchain torsion values. This allows combinatorially combining this mover's sampling
with another, similar mover's sampling.
- set_pdb_output(...) from builtins.PyCapsule
- set_pdb_output(self : rosetta.protocols.helical_bundle.BackboneGridSampler, val : bool) -> NoneType
Set whether the mover dumps pdbs or not.
- set_pdb_prefix(...) from builtins.PyCapsule
- set_pdb_prefix(self : rosetta.protocols.helical_bundle.BackboneGridSampler, prefix : str) -> NoneType
Sets the filename prefix for PDB output.
PDB files are of the form <prefix>_#####.pdb.
- set_prescoring_filter(...) from builtins.PyCapsule
- set_prescoring_filter(self : rosetta.protocols.helical_bundle.BackboneGridSampler, filter : rosetta.protocols.filters.Filter) -> NoneType
Sets the filter that will be applied to all helical bundles generated prior to energy evaluation.
See the pre_scoring_filter_ private member variable for details.
- set_prescoring_mover(...) from builtins.PyCapsule
- set_prescoring_mover(self : rosetta.protocols.helical_bundle.BackboneGridSampler, mover : rosetta.protocols.moves.Mover) -> NoneType
Sets the mover that will be applied to all helical bundles generated prior to energy evaluation.
Note: if this is used, there is no guarantee that the resulting geometry will still lie within the
parameter space. (That is, this mover could move the backbone.)
- set_residues_per_repeat(...) from builtins.PyCapsule
- set_residues_per_repeat(self : rosetta.protocols.helical_bundle.BackboneGridSampler, val : int) -> NoneType
Set the number of residues per repeat.
This resets the torsions_to_sample_, torsions_to_fix_, and resname_ vectors, and
must therefore be called BEFORE setting up the torsions to sample, torsions to fix, or
residue types.
- set_resname(...) from builtins.PyCapsule
- set_resname(self : rosetta.protocols.helical_bundle.BackboneGridSampler, res_index : int, resname_in : str) -> NoneType
Set the residue type.
Sets the residue type for the nth residue in the list of residues defining the repeating unit.
- set_selection_low(...) from builtins.PyCapsule
- set_selection_low(self : rosetta.protocols.helical_bundle.BackboneGridSampler, val : bool) -> NoneType
Sets whether the selection should be for the lowest score value (true) or highest (false).
- set_sfxn(...) from builtins.PyCapsule
- set_sfxn(self : rosetta.protocols.helical_bundle.BackboneGridSampler, sfxn_in : rosetta.core.scoring.ScoreFunction) -> NoneType
Sets the scorefunction for this mover.
This must be done before calling the apply() function.
- set_up_peptide_stub_mover(...) from builtins.PyCapsule
- set_up_peptide_stub_mover(rosetta.protocols.helical_bundle.BackboneGridSampler) -> NoneType
Set up the PeptideStubMover object that will be used to build geometry.
- sfxn_set(...) from builtins.PyCapsule
- sfxn_set(rosetta.protocols.helical_bundle.BackboneGridSampler) -> bool
Returns whether the scorefunction has been set.
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 BackboneGridSamplerHelper(builtins.object) |
| |
BackboneGridSamplerHelper class, which stores options for the PerturbBundle mover.
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) -> 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.helical_bundle.BackboneGridSamplerHelper, : rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) -> rosetta.protocols.helical_bundle.BackboneGridSamplerHelper
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) -> rosetta.protocols.helical_bundle.BackboneGridSamplerHelper
Copy this BackboneGridSamplerHelper object( allocate actual memory for it )
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) -> rosetta.protocols.helical_bundle.BackboneGridSamplerHelper
self pointers
2. get_self_ptr(rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) -> rosetta.protocols.helical_bundle.BackboneGridSamplerHelper
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) -> rosetta.std.weak_ptr_const_protocols_helical_bundle_BackboneGridSamplerHelper_t
2. get_self_weak_ptr(rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) -> rosetta.std.weak_ptr_protocols_helical_bundle_BackboneGridSamplerHelper_t
- increment_cur_indices(...) from builtins.PyCapsule
- increment_cur_indices(rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) -> NoneType
RECURSIVE function that increments the current sample index.
This function adds 1 to the last torsion index. If the last torsion
index value exceeds the number of samples for that torsion, it resets that
torsion index and increments the second-last torsion index by 1 by recursively
calling itself. This function is overloaded; the public version by
default tries to increment the last index, while the private version
can be called recursively.
- n_torsions(...) from builtins.PyCapsule
- n_torsions(self : rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, res_index : int) -> int
Returns the number of different mainchain torsions that the BackboneGridSampler will sample over.
Returns a value for the residue in the repeating unit with index res_index.
- n_torsions_total(...) from builtins.PyCapsule
- n_torsions_total(rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) -> int
Returns the total number of mainchain torsions over which we will sample.
This is the sum of the n_torsions_ entries for each residue in the repeating
unit, and is initialized by the initialize_samples() function.
- reset(...) from builtins.PyCapsule
- reset(rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) -> NoneType
Reset this BackboneGridSamplerHelper object.
Clears all internal data.
- residue_index(...) from builtins.PyCapsule
- residue_index(self : rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, index : int) -> int
Returns the residue index in the repeating unit (1st, 2nd, 3rd etc.) corresponding to a
given torsion index.
- residues_per_repeat(...) from builtins.PyCapsule
- residues_per_repeat(rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) -> int
Returns the number of residues per repeat, set by the initialize_data() function.
- torsion_id(...) from builtins.PyCapsule
- torsion_id(self : rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, index : int) -> int
Returns the torsion ID for the specified torsion index.
- torsion_sample_value(...) from builtins.PyCapsule
- torsion_sample_value(self : rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, index : int) -> float
Returns the current sample value for the specified torsion.
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class BundleGridSampler(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- BundleGridSampler
- 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.helical_bundle.BundleGridSampler) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_helix(...) from builtins.PyCapsule
- add_helix(rosetta.protocols.helical_bundle.BundleGridSampler) -> int
Add options for a new helix
Return value is the current total number of helices after the addition.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.helical_bundle.BundleGridSampler, pose : rosetta.core.pose.Pose) -> NoneType
Actually apply the mover to the pose.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.helical_bundle.BundleGridSampler, : rosetta.protocols.helical_bundle.BundleGridSampler) -> rosetta.protocols.helical_bundle.BundleGridSampler
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.helical_bundle.BundleGridSampler) -> rosetta.protocols.moves.Mover
- default_delta_omega0(...) from builtins.PyCapsule
- default_delta_omega0(*args, **kwargs)
Overloaded function.
1. default_delta_omega0(rosetta.protocols.helical_bundle.BundleGridSampler) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_delta_omega0_ BundleOptions object.
2. default_delta_omega0(rosetta.protocols.helical_bundle.BundleGridSampler) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_delta_omega0_ BundleOptions object (const-access).
- default_delta_omega1(...) from builtins.PyCapsule
- default_delta_omega1(*args, **kwargs)
Overloaded function.
1. default_delta_omega1(rosetta.protocols.helical_bundle.BundleGridSampler) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_delta_omega1_ BundleOptions object.
2. default_delta_omega1(rosetta.protocols.helical_bundle.BundleGridSampler) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_delta_omega1_ BundleOptions object (const-access).
- default_delta_t(...) from builtins.PyCapsule
- default_delta_t(*args, **kwargs)
Overloaded function.
1. default_delta_t(rosetta.protocols.helical_bundle.BundleGridSampler) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_delta_t_ BundleOptions object.
2. default_delta_t(rosetta.protocols.helical_bundle.BundleGridSampler) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_delta_t_ BundleOptions object (const-access).
- default_omega0(...) from builtins.PyCapsule
- default_omega0(*args, **kwargs)
Overloaded function.
1. default_omega0(rosetta.protocols.helical_bundle.BundleGridSampler) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_omega0_ BundleOptions object.
2. default_omega0(rosetta.protocols.helical_bundle.BundleGridSampler) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_omega0_ BundleOptions object (const-access).
- default_r0(...) from builtins.PyCapsule
- default_r0(*args, **kwargs)
Overloaded function.
1. default_r0(rosetta.protocols.helical_bundle.BundleGridSampler) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_r0_ BundleOptions object.
2. default_r0(rosetta.protocols.helical_bundle.BundleGridSampler) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_r0_ BundleOptions object (const-access).
- default_z0_offset(...) from builtins.PyCapsule
- default_z0_offset(*args, **kwargs)
Overloaded function.
1. default_z0_offset(rosetta.protocols.helical_bundle.BundleGridSampler) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_z0_offset_ BundleOptions object.
2. default_z0_offset(rosetta.protocols.helical_bundle.BundleGridSampler) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_z0_offset_ BundleOptions object (const-access).
- default_z1_offset(...) from builtins.PyCapsule
- default_z1_offset(*args, **kwargs)
Overloaded function.
1. default_z1_offset(rosetta.protocols.helical_bundle.BundleGridSampler) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_z1_offset_ BundleOptions object.
2. default_z1_offset(rosetta.protocols.helical_bundle.BundleGridSampler) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_z1_offset_ BundleOptions object (const-access).
- delta_omega0(...) from builtins.PyCapsule
- delta_omega0(*args, **kwargs)
Overloaded function.
1. delta_omega0(self : rosetta.protocols.helical_bundle.BundleGridSampler, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the delta_omega0_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
2. delta_omega0(self : rosetta.protocols.helical_bundle.BundleGridSampler, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the delta_omega0_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
- delta_omega1(...) from builtins.PyCapsule
- delta_omega1(*args, **kwargs)
Overloaded function.
1. delta_omega1(self : rosetta.protocols.helical_bundle.BundleGridSampler, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the delta_omega1_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
2. delta_omega1(self : rosetta.protocols.helical_bundle.BundleGridSampler, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the delta_omega1_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
- delta_t(...) from builtins.PyCapsule
- delta_t(*args, **kwargs)
Overloaded function.
1. delta_t(self : rosetta.protocols.helical_bundle.BundleGridSampler, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the delta_t_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
2. delta_t(self : rosetta.protocols.helical_bundle.BundleGridSampler, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the delta_t_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.helical_bundle.BundleGridSampler) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.helical_bundle.BundleGridSampler) -> str
- increment_helix_count(...) from builtins.PyCapsule
- increment_helix_count(rosetta.protocols.helical_bundle.BundleGridSampler) -> NoneType
Increments the number of helices that have been defined.
- max_samples(...) from builtins.PyCapsule
- max_samples(rosetta.protocols.helical_bundle.BundleGridSampler) -> int
Get the maximum number of samples for the mover.
If the number of gridpoints based on user options exceeds this number, an error is thrown
and the mover aborts. This is to prevent unreasonably large calculations from being attempted.
- n_helices(...) from builtins.PyCapsule
- n_helices(rosetta.protocols.helical_bundle.BundleGridSampler) -> int
Returns the number of helices that have been defined.
- nstruct_mode(...) from builtins.PyCapsule
- nstruct_mode(rosetta.protocols.helical_bundle.BundleGridSampler) -> bool
Get the nstruct mode.
If true, each job samples one set of Crick parameters. If false, every job samples
every set of Crick parameters. False by default.
- nstruct_repeats(...) from builtins.PyCapsule
- nstruct_repeats(rosetta.protocols.helical_bundle.BundleGridSampler) -> int
Get the nstruct repeats.
This is set to 1 by default, which means that each nstruct number correspnds to a different
set of Crick parameters. If set greater than 1, then multiple consecutive nstruct numbers will
correspond to the same Crick parameters. This allows combinatorially combining this mover's sampling
with another, similar mover's sampling.
- omega0(...) from builtins.PyCapsule
- omega0(*args, **kwargs)
Overloaded function.
1. omega0(self : rosetta.protocols.helical_bundle.BundleGridSampler, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the omega0_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
2. omega0(self : rosetta.protocols.helical_bundle.BundleGridSampler, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the omega0_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
- pdb_output(...) from builtins.PyCapsule
- pdb_output(rosetta.protocols.helical_bundle.BundleGridSampler) -> bool
Returns whether the mover dumps pdbs or not.
- pdb_prefix(...) from builtins.PyCapsule
- pdb_prefix(rosetta.protocols.helical_bundle.BundleGridSampler) -> str
Access the filename prefix for PDB output.
PDB files are of the form <prefix>_#####.pdb.
- preselection_filter_exists(...) from builtins.PyCapsule
- preselection_filter_exists(rosetta.protocols.helical_bundle.BundleGridSampler) -> bool
Returns "true" if and only if a preselection filter has been assigned.
- preselection_mover_exists(...) from builtins.PyCapsule
- preselection_mover_exists(rosetta.protocols.helical_bundle.BundleGridSampler) -> bool
Returns "true" if and only if a preselection mover has been assigned.
- r0(...) from builtins.PyCapsule
- r0(*args, **kwargs)
Overloaded function.
1. r0(self : rosetta.protocols.helical_bundle.BundleGridSampler, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the r0_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
2. r0(self : rosetta.protocols.helical_bundle.BundleGridSampler, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the r0_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
- reset_mode(...) from builtins.PyCapsule
- reset_mode(rosetta.protocols.helical_bundle.BundleGridSampler) -> bool
Get the reset mode.
If true (default), the pose is reset before generating bundles. If false, it is not.
- selection_low(...) from builtins.PyCapsule
- selection_low(rosetta.protocols.helical_bundle.BundleGridSampler) -> bool
Returns whether the selection should be for the lowest score value (true) or highest (false).
- set_max_samples(...) from builtins.PyCapsule
- set_max_samples(self : rosetta.protocols.helical_bundle.BundleGridSampler, val : int) -> NoneType
Set the maximum number of samples for the mover.
If the number of gridpoints based on user options exceeds this number, an error is thrown
and the mover aborts. This is to prevent unreasonably large calculations from being attempted.
- set_nstruct_mode(...) from builtins.PyCapsule
- set_nstruct_mode(self : rosetta.protocols.helical_bundle.BundleGridSampler, val : bool) -> NoneType
Set the nstruct mode.
If true, each job samples one set of Crick parameters. If false, every job samples
every set of Crick parameters. False by default.
- set_nstruct_repeats(...) from builtins.PyCapsule
- set_nstruct_repeats(self : rosetta.protocols.helical_bundle.BundleGridSampler, val : int) -> NoneType
Set the nstruct repeats.
This is set to 1 by default, which means that each nstruct number correspnds to a different
set of Crick parameters. If set greater than 1, then multiple consecutive nstruct numbers will
correspond to the same Crick parameters. This allows combinatorially combining this mover's sampling
with another, similar mover's sampling.
- set_pdb_output(...) from builtins.PyCapsule
- set_pdb_output(self : rosetta.protocols.helical_bundle.BundleGridSampler, val : bool) -> NoneType
Set whether the mover dumps pdbs or not.
- set_pdb_prefix(...) from builtins.PyCapsule
- set_pdb_prefix(self : rosetta.protocols.helical_bundle.BundleGridSampler, prefix : str) -> NoneType
Sets the filename prefix for PDB output.
PDB files are of the form <prefix>_#####.pdb.
- set_preselection_filter(...) from builtins.PyCapsule
- set_preselection_filter(self : rosetta.protocols.helical_bundle.BundleGridSampler, filter : rosetta.protocols.filters.Filter) -> NoneType
Sets the filter that will be applied to all helical bundles generated prior to energy evaluation.
See the pre_selection_filter_ private member variable for details.
- set_preselection_mover(...) from builtins.PyCapsule
- set_preselection_mover(self : rosetta.protocols.helical_bundle.BundleGridSampler, mover : rosetta.protocols.moves.Mover) -> NoneType
Sets the mover that will be applied to all helical bundles generated prior to energy evaluation.
Note: if this is used, there is no guarantee that the resulting geometry will still lie within the
parameter space. (That is, this mover could move the backbone.)
- set_reset_mode(...) from builtins.PyCapsule
- set_reset_mode(self : rosetta.protocols.helical_bundle.BundleGridSampler, val : bool) -> NoneType
Set the reset mode.
If true (default), the pose is reset before generating bundles. If false, it is not.
- set_selection_low(...) from builtins.PyCapsule
- set_selection_low(self : rosetta.protocols.helical_bundle.BundleGridSampler, val : bool) -> NoneType
Sets whether the selection should be for the lowest score value (true) or highest (false).
- set_sfxn(...) from builtins.PyCapsule
- set_sfxn(self : rosetta.protocols.helical_bundle.BundleGridSampler, sfxn_in : rosetta.core.scoring.ScoreFunction) -> NoneType
Sets the scorefunction for this mover.
This must be done before calling the apply() function.
- sfxn_set(...) from builtins.PyCapsule
- sfxn_set(rosetta.protocols.helical_bundle.BundleGridSampler) -> bool
Returns whether the scorefunction has been set.
- z0_offset(...) from builtins.PyCapsule
- z0_offset(*args, **kwargs)
Overloaded function.
1. z0_offset(self : rosetta.protocols.helical_bundle.BundleGridSampler, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the z0_offset_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
2. z0_offset(self : rosetta.protocols.helical_bundle.BundleGridSampler, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the z0_offset_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
- z1_offset(...) from builtins.PyCapsule
- z1_offset(*args, **kwargs)
Overloaded function.
1. z1_offset(self : rosetta.protocols.helical_bundle.BundleGridSampler, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the z1_offset_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
2. z1_offset(self : rosetta.protocols.helical_bundle.BundleGridSampler, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the z1_offset_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
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 BundleGridSamplerHelper(builtins.object) |
| |
BundleGridSamplerHelper class, which stores options for the PerturbBundle mover.
|
| |
Methods defined here:
- DoF_helix_index(...) from builtins.PyCapsule
- DoF_helix_index(self : rosetta.protocols.helical_bundle.BundleGridSamplerHelper, index : int) -> int
Returns the helix index of the specified DoF.
- DoF_name(...) from builtins.PyCapsule
- DoF_name(self : rosetta.protocols.helical_bundle.BundleGridSamplerHelper, type : rosetta.protocols.helical_bundle.DoFType) -> str
Return the name of a DoF type given its enum.
- DoF_sample_value(...) from builtins.PyCapsule
- DoF_sample_value(self : rosetta.protocols.helical_bundle.BundleGridSamplerHelper, index : int) -> float
Returns the current sample value for the specified DoF.
- DoF_type(...) from builtins.PyCapsule
- DoF_type(self : rosetta.protocols.helical_bundle.BundleGridSamplerHelper, index : int) -> rosetta.protocols.helical_bundle.DoFType
Returns the DoF type of the specified DoF.
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.helical_bundle.BundleGridSamplerHelper) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_DoF(...) from builtins.PyCapsule
- add_DoF(self : rosetta.protocols.helical_bundle.BundleGridSamplerHelper, doftype : rosetta.protocols.helical_bundle.DoFType, helix_index : int, n_samples : int, lower_val : float, upper_val : float) -> NoneType
Add an allowed DoF that the BundleGridSampler will sample over.
Must specify the DoF type, the helix index, the number of samples,
and the lower and upper bounds of the range to be sampled.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.helical_bundle.BundleGridSamplerHelper, : rosetta.protocols.helical_bundle.BundleGridSamplerHelper) -> rosetta.protocols.helical_bundle.BundleGridSamplerHelper
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.helical_bundle.BundleGridSamplerHelper) -> rosetta.protocols.helical_bundle.BundleGridSamplerHelper
Copy this BundleGridSamplerHelper object( allocate actual memory for it )
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.helical_bundle.BundleGridSamplerHelper) -> rosetta.protocols.helical_bundle.BundleGridSamplerHelper
self pointers
2. get_self_ptr(rosetta.protocols.helical_bundle.BundleGridSamplerHelper) -> rosetta.protocols.helical_bundle.BundleGridSamplerHelper
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.helical_bundle.BundleGridSamplerHelper) -> rosetta.std.weak_ptr_const_protocols_helical_bundle_BundleGridSamplerHelper_t
2. get_self_weak_ptr(rosetta.protocols.helical_bundle.BundleGridSamplerHelper) -> rosetta.std.weak_ptr_protocols_helical_bundle_BundleGridSamplerHelper_t
- increment_cur_indices(...) from builtins.PyCapsule
- increment_cur_indices(rosetta.protocols.helical_bundle.BundleGridSamplerHelper) -> NoneType
RECURSIVE function that increments the current sample index.
This function adds 1 to the last DoF index. If the last DoF
index value exceeds the number of samples for that DoF, it resets that
DoF index and increments the second-last DoF index by 1 by recursively
calling itself. This function is overloaded; the public version by
default tries to increment the last index, while the private version
can be called recursively.
- initialize_samples(...) from builtins.PyCapsule
- initialize_samples(rosetta.protocols.helical_bundle.BundleGridSamplerHelper) -> NoneType
Perform the pre-calculation that sets up the lists of parameter values to be sampled.
- nDoFs(...) from builtins.PyCapsule
- nDoFs(rosetta.protocols.helical_bundle.BundleGridSamplerHelper) -> int
Returns the number of different DoFs that the BundleGridSampler will sample over.
- reset(...) from builtins.PyCapsule
- reset(rosetta.protocols.helical_bundle.BundleGridSamplerHelper) -> NoneType
Reset this BundleGridSamplerHelper object.
Clears all internal data.
|
class BundleReporterFilter(rosetta.protocols.filters.Filter) |
| | |
- Method resolution order:
- BundleReporterFilter
- rosetta.protocols.filters.Filter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.helical_bundle.BundleReporterFilter) -> 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.helical_bundle.BundleReporterFilter, pose : rosetta.core.pose.Pose) -> bool
Actually apply the filter to a pose.
This scores the pose with the scorefunction, writes out the energy and the
bundle parameters (if any) to the REPORT tracer, then applies the selected behaviour
of the filter (always true, always false, or actually filtering by score).
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.helical_bundle.BundleReporterFilter) -> rosetta.protocols.filters.Filter
Returns an owning pointer to a new instance of this filter, with copied
variables (a copy of this filter).
- compute(...) from builtins.PyCapsule
- compute(self : rosetta.protocols.helical_bundle.BundleReporterFilter, pose : rosetta.core.pose.Pose) -> float
Computes the energy of the pose.
the energy function must be suitable for residue type set of the pose,
and must be symmetric if this is a symmetric pose.
- filter_behaviour(...) from builtins.PyCapsule
- filter_behaviour(rosetta.protocols.helical_bundle.BundleReporterFilter) -> rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour
Get the filter behaviour.
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.helical_bundle.BundleReporterFilter) -> rosetta.protocols.filters.Filter
Returns an owning pointer to a new instance of this filter, with default
initialization (NOT a copy).
- generate_full_tracer_report(...) from builtins.PyCapsule
- generate_full_tracer_report(self : rosetta.protocols.helical_bundle.BundleReporterFilter, jobno : int, score : float, pose : rosetta.core.pose.Pose) -> str
Generates the text of the full report that the filter writes out to the REPORT tracer.
Called by the APPLY function. Jobno is the RosettaScripts job number; ignored if set to 0.
- report_sequence(...) from builtins.PyCapsule
- report_sequence(rosetta.protocols.helical_bundle.BundleReporterFilter) -> bool
Get whether we report sequences.
- report_sm(...) from builtins.PyCapsule
- report_sm(self : rosetta.protocols.helical_bundle.BundleReporterFilter, pose : rosetta.core.pose.Pose) -> float
Allows reporting of the filter value to a float.
- score_type(...) from builtins.PyCapsule
- score_type(rosetta.protocols.helical_bundle.BundleReporterFilter) -> rosetta.core.scoring.ScoreType
Get the score type.
- score_type_threshold(...) from builtins.PyCapsule
- score_type_threshold(rosetta.protocols.helical_bundle.BundleReporterFilter) -> float
Get the score threshold.
- scorefxn(...) from builtins.PyCapsule
- scorefxn(rosetta.protocols.helical_bundle.BundleReporterFilter) -> rosetta.core.scoring.ScoreFunction
Get the scorefunction (by owning pointer).
Non-const access.
- set_filter_behaviour(...) from builtins.PyCapsule
- set_filter_behaviour(*args, **kwargs)
Overloaded function.
1. set_filter_behaviour(self : rosetta.protocols.helical_bundle.BundleReporterFilter, behaviour_string : str) -> NoneType
Set the behaviour by string.
Options are "ALWAYS_TRUE", "ALWAYS_FALSE", or "FILTER".
2. set_filter_behaviour(self : rosetta.protocols.helical_bundle.BundleReporterFilter, behaviour_in : rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour) -> NoneType
Set the behaviour by enum.
Options are brf_always_true, brf_always_false, or brf_filter_by_energy.
- set_report_sequence(...) from builtins.PyCapsule
- set_report_sequence(*args, **kwargs)
Overloaded function.
1. set_report_sequence(rosetta.protocols.helical_bundle.BundleReporterFilter) -> NoneType
Set whether we report sequences.
2. set_report_sequence(self : rosetta.protocols.helical_bundle.BundleReporterFilter, val : bool) -> NoneType
Set whether we report sequences.
- set_score_type(...) from builtins.PyCapsule
- set_score_type(self : rosetta.protocols.helical_bundle.BundleReporterFilter, type : rosetta.core.scoring.ScoreType) -> NoneType
Set the score type.
- set_score_type_threshold(...) from builtins.PyCapsule
- set_score_type_threshold(self : rosetta.protocols.helical_bundle.BundleReporterFilter, val : float) -> NoneType
Set the score threshold.
- set_scorefxn(...) from builtins.PyCapsule
- set_scorefxn(self : rosetta.protocols.helical_bundle.BundleReporterFilter, scorefxn_in : rosetta.core.scoring.ScoreFunction) -> NoneType
Set the scorefunction.
- set_use_threeletter(...) from builtins.PyCapsule
- set_use_threeletter(*args, **kwargs)
Overloaded function.
1. set_use_threeletter(rosetta.protocols.helical_bundle.BundleReporterFilter) -> NoneType
Set whether we report three-letter codes.
2. set_use_threeletter(self : rosetta.protocols.helical_bundle.BundleReporterFilter, val : bool) -> NoneType
Set whether we report three-letter codes.
- use_threeletter(...) from builtins.PyCapsule
- use_threeletter(rosetta.protocols.helical_bundle.BundleReporterFilter) -> bool
Get whether we report three-letter codes.
Methods inherited from rosetta.protocols.filters.Filter:
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.filters.Filter) -> NoneType
used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.filters.Filter) -> str
- get_user_defined_name(...) from builtins.PyCapsule
- get_user_defined_name(rosetta.protocols.filters.Filter) -> str
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.filters.Filter) -> str
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.filters.Filter, pose : rosetta.core.pose.Pose) -> float
- set_user_defined_name(...) from builtins.PyCapsule
- set_user_defined_name(self : rosetta.protocols.filters.Filter, name : str) -> NoneType
|
class DoFType(builtins.object) |
| |
The type of bundle parameter that will be sampled by the
BundleGridSampler mover.
|
| |
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(rosetta.protocols.helical_bundle.DoFType, rosetta.protocols.helical_bundle.DoFType) -> bool
- __hash__(...) from builtins.PyCapsule
- __hash__(rosetta.protocols.helical_bundle.DoFType) -> int
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.helical_bundle.DoFType, int) -> NoneType
2. __init__(rosetta.protocols.helical_bundle.DoFType, int) -> NoneType
- __int__(...) from builtins.PyCapsule
- __int__(rosetta.protocols.helical_bundle.DoFType) -> int
- __ne__(...) from builtins.PyCapsule
- __ne__(rosetta.protocols.helical_bundle.DoFType, rosetta.protocols.helical_bundle.DoFType) -> bool
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __repr__(...) from builtins.PyCapsule
- __repr__(rosetta.protocols.helical_bundle.DoFType) -> str
Data and other attributes defined here:
- bgsh_delta_omega0 = DoFType.bgsh_delta_omega0
- bgsh_delta_omega1 = DoFType.bgsh_delta_omega1
- bgsh_delta_t = DoFType.bgsh_delta_t
- bgsh_omega0 = DoFType.bgsh_omega0
- bgsh_r0 = DoFType.bgsh_r0
- bgsh_undefined_dof = DoFType.bgsh_undefined_dof
- bgsh_z0_offset = DoFType.bgsh_z0_offset
- bgsh_z1_offset = DoFType.bgsh_z1_offset
|
class FitSimpleHelix(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- FitSimpleHelix
- 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.helical_bundle.FitSimpleHelix) -> 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.helical_bundle.FitSimpleHelix, pose : rosetta.core.pose.Pose) -> NoneType
Actually apply the mover to the pose.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.helical_bundle.FitSimpleHelix, : rosetta.protocols.helical_bundle.FitSimpleHelix) -> rosetta.protocols.helical_bundle.FitSimpleHelix
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.helical_bundle.FitSimpleHelix) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.helical_bundle.FitSimpleHelix) -> rosetta.protocols.moves.Mover
- get_crick_parameters(...) from builtins.PyCapsule
- get_crick_parameters(self : rosetta.protocols.helical_bundle.FitSimpleHelix, r1_out : rosetta.utility.vector1_double, omega1_out : float, z1_out : float, delta_omega1_out : rosetta.utility.vector1_double, delta_z1_out : rosetta.utility.vector1_double) -> NoneType
Function to retrieve the final values of the helical parameters, post-fit.
Call this function after the "apply" function, and pass it containers for
the data to be retrieved.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.helical_bundle.FitSimpleHelix) -> str
- reference_residue(...) from builtins.PyCapsule
- reference_residue(rosetta.protocols.helical_bundle.FitSimpleHelix) -> int
Get the reference residue index in the repeating unit.
- residues_per_repeat(...) from builtins.PyCapsule
- residues_per_repeat(rosetta.protocols.helical_bundle.FitSimpleHelix) -> int
Get the number of residues per repeating unit in the helix.
- set_delta_omega1_guesses(...) from builtins.PyCapsule
- set_delta_omega1_guesses(self : rosetta.protocols.helical_bundle.FitSimpleHelix, delta_omega1_guesses_in : rosetta.utility.vector1_double) -> NoneType
Load in guesses for the delta_omega1 values (optional during fitter setup).
- set_delta_z1_guesses(...) from builtins.PyCapsule
- set_delta_z1_guesses(self : rosetta.protocols.helical_bundle.FitSimpleHelix, delta_z1_guesses_in : rosetta.utility.vector1_double) -> NoneType
Load in guesses for the delta_z1 values (optional during fitter setup).
- set_initial_guesses(...) from builtins.PyCapsule
- set_initial_guesses(self : rosetta.protocols.helical_bundle.FitSimpleHelix, r1_initial : float, omega1_initial : float, dz1_initial : float) -> NoneType
- set_min_tolerance(...) from builtins.PyCapsule
- set_min_tolerance(self : rosetta.protocols.helical_bundle.FitSimpleHelix, min_tol_in : float) -> NoneType
Set the minimizer tolerance (defaults to 1E-7, the default for many other protocols).
- set_min_type(...) from builtins.PyCapsule
- set_min_type(self : rosetta.protocols.helical_bundle.FitSimpleHelix, min_type : str) -> NoneType
Set the minimization type (e.g. dfpmin, linmin, etc.)
Defaults to dfpmin if not set.
- set_r1_guesses(...) from builtins.PyCapsule
- set_r1_guesses(self : rosetta.protocols.helical_bundle.FitSimpleHelix, r1_guesses_in : rosetta.utility.vector1_double) -> NoneType
Load in guesses for the radii (optional during fitter setup).
- set_range(...) from builtins.PyCapsule
- set_range(self : rosetta.protocols.helical_bundle.FitSimpleHelix, start : int, end : int) -> NoneType
- set_reference_atom(...) from builtins.PyCapsule
- set_reference_atom(self : rosetta.protocols.helical_bundle.FitSimpleHelix, ref_atom_in : str) -> NoneType
Set the mainchain atom that will be fit first, and used as the reference for other mainchain atoms.
If not set, this defaults to "CA".
- set_reference_residue(...) from builtins.PyCapsule
- set_reference_residue(self : rosetta.protocols.helical_bundle.FitSimpleHelix, ref_res_in : int) -> NoneType
Set the residue in the repeating unit (1, 2, 3, etc.) that contains the reference atom.
If not set, this defaults to 1.
- set_residues_per_repeat(...) from builtins.PyCapsule
- set_residues_per_repeat(self : rosetta.protocols.helical_bundle.FitSimpleHelix, count_in : int) -> NoneType
Set the number of residues per repeating unit in the helix.
If not set, this defaults to 1.
- set_rms_offset(...) from builtins.PyCapsule
- set_rms_offset(self : rosetta.protocols.helical_bundle.FitSimpleHelix, rms_offset_in : float) -> NoneType
Set the small float used to offset certain values in the RMS calculation to avoid zero determinants.
If fits produce bad geometry, this may need to be increased slightly.
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 FitSimpleHelixMultiFunc(rosetta.core.optimization.Multifunc) |
| |
Multifunction class for fitting a simple (straight) helix to the Crick parameters.
|
| |
- Method resolution order:
- FitSimpleHelixMultiFunc
- rosetta.core.optimization.Multifunc
- builtins.object
Methods defined here:
- __call__(...) from builtins.PyCapsule
- __call__(self : rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc, vars : rosetta.utility.vector1_double) -> float
Calculate function value (rms squared)
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, pose : rosetta.core.pose.Pose, atom_name : str, first_res_index : int, res_per_repeat : int, start_index : int, end_index : int, minimization_mode : int, rms_offset : float) -> NoneType
2. __init__(handle, rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc) -> 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.helical_bundle.FitSimpleHelixMultiFunc, : rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc) -> rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc
- dfunc(...) from builtins.PyCapsule
- dfunc(self : rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc, vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double) -> NoneType
Calculate function value derivatives
- dump(...) from builtins.PyCapsule
- dump(self : rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc, vars : rosetta.utility.vector1_double, vars2 : rosetta.utility.vector1_double) -> NoneType
Error state reached -- derivative does not match gradient
Methods inherited from rosetta.core.optimization.Multifunc:
- abort_min(...) from builtins.PyCapsule
- abort_min(self : rosetta.core.optimization.Multifunc, : rosetta.utility.vector1_double) -> bool
Christophe added the following to allow premature end of minimization
If you want to abort the minimizer under specific circonstances
overload this function and return true if you want to stop, false if you want to continue.
FOR THE MOMENT, ONLY IN DFPMIN!
|
class MakeBundle(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- MakeBundle
- 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.helical_bundle.MakeBundle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_helix(...) from builtins.PyCapsule
- add_helix(rosetta.protocols.helical_bundle.MakeBundle) -> NoneType
Function to add a helix.
This creates a MakeBundleHelix mover that will be called at apply time.
The new mover is only initialized if default values are provided by THIS mover.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.helical_bundle.MakeBundle, pose : rosetta.core.pose.Pose) -> NoneType
Actually apply the mover to the pose.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.helical_bundle.MakeBundle, : rosetta.protocols.helical_bundle.MakeBundle) -> rosetta.protocols.helical_bundle.MakeBundle
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.helical_bundle.MakeBundle) -> rosetta.protocols.moves.Mover
- convert_angle(...) from builtins.PyCapsule
- convert_angle(self : rosetta.protocols.helical_bundle.MakeBundle, val : float) -> float
Ensure that an angle value is in radians.
Checks the use_degrees_ boolean. If true, converts degrees to radians; if false, returns input value.
- default_allow_bondangles(...) from builtins.PyCapsule
- default_allow_bondangles(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns the default for whether bond lengths should be set by the mover
- default_allow_bondangles_set(...) from builtins.PyCapsule
- default_allow_bondangles_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default for whether bond lengths should be set by the mover has been set
- default_allow_bondlengths(...) from builtins.PyCapsule
- default_allow_bondlengths(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns the default for whether bond lengths should be set by the mover
- default_allow_bondlengths_set(...) from builtins.PyCapsule
- default_allow_bondlengths_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default for whether bond lengths should be set by the mover has been set
- default_allow_dihedrals(...) from builtins.PyCapsule
- default_allow_dihedrals(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns the default for whether bond lengths should be set by the mover
- default_allow_dihedrals_set(...) from builtins.PyCapsule
- default_allow_dihedrals_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default for whether bond lengths should be set by the mover has been set
- default_crick_params_file(...) from builtins.PyCapsule
- default_crick_params_file(rosetta.protocols.helical_bundle.MakeBundle) -> str
Returns the default Crick params file name.
- default_crick_params_file_set(...) from builtins.PyCapsule
- default_crick_params_file_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default Crick params file name has been set.
- default_delta_omega0(...) from builtins.PyCapsule
- default_delta_omega0(rosetta.protocols.helical_bundle.MakeBundle) -> float
Returns the default delta_omega0 value (major helix turn).
- default_delta_omega0_set(...) from builtins.PyCapsule
- default_delta_omega0_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default delta_omega0 value (major helix turn) has been set
- default_delta_omega1_all(...) from builtins.PyCapsule
- default_delta_omega1_all(rosetta.protocols.helical_bundle.MakeBundle) -> float
Returns the default delta_omega1_all value (minor helix rotation).
- default_delta_omega1_all_set(...) from builtins.PyCapsule
- default_delta_omega1_all_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default delta_omega1_all value (minor helix rotation) has been set
- default_delta_t(...) from builtins.PyCapsule
- default_delta_t(rosetta.protocols.helical_bundle.MakeBundle) -> float
Returns the default delta_t value (residue offset).
- default_delta_t_set(...) from builtins.PyCapsule
- default_delta_t_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default delta_t value (residue offset) has been set.
- default_helix_length(...) from builtins.PyCapsule
- default_helix_length(rosetta.protocols.helical_bundle.MakeBundle) -> int
Returns the default number of residues per helix.
- default_helix_length_set(...) from builtins.PyCapsule
- default_helix_length_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default number of residues per helix has been set
- default_invert(...) from builtins.PyCapsule
- default_invert(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns the default invert value (should the helix be flipped?)
- default_invert_set(...) from builtins.PyCapsule
- default_invert_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default invert value (should the helix be flipped?) has been set
- default_omega0(...) from builtins.PyCapsule
- default_omega0(rosetta.protocols.helical_bundle.MakeBundle) -> float
Returns the default omega0 value (major helix rise per residue).
- default_omega0_set(...) from builtins.PyCapsule
- default_omega0_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default omega0 value (major helix rise per residue) has been set
- default_omega1(...) from builtins.PyCapsule
- default_omega1(rosetta.protocols.helical_bundle.MakeBundle) -> float
Returns the default omega1 value (minor helix turn per residue).
- default_omega1_set(...) from builtins.PyCapsule
- default_omega1_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default omega1 value (minor helix turn per residue) has been set
- default_r0(...) from builtins.PyCapsule
- default_r0(rosetta.protocols.helical_bundle.MakeBundle) -> float
Returns the default r0 value (major helix radius).
- default_r0_set(...) from builtins.PyCapsule
- default_r0_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default r0 value (major helix radius) has been set
- default_repeating_unit_offset(...) from builtins.PyCapsule
- default_repeating_unit_offset(rosetta.protocols.helical_bundle.MakeBundle) -> int
Returns the default repeating unit offset value.
An offset of 0 means that the first residue of the helix is the first residue of the repeating unit. An offset
of 1 means that the first residue of the helix is the second residue of the repeating unit, etc.
- default_repeating_unit_offset_set(...) from builtins.PyCapsule
- default_repeating_unit_offset_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default repeating unit offset has been set.
An offset of 0 means that the first residue of the helix is the first residue of the repeating unit. An offset
of 1 means that the first residue of the helix is the second residue of the repeating unit, etc.
- default_residue_name(...) from builtins.PyCapsule
- default_residue_name(*args, **kwargs)
Overloaded function.
1. default_residue_name(self : rosetta.protocols.helical_bundle.MakeBundle, index_in_repeating_unit : int) -> str
Returns the default residue name for a particular position in the repeating unit.
2. default_residue_name(rosetta.protocols.helical_bundle.MakeBundle) -> rosetta.utility.vector1_std_string
Returns the default residue name vector.
- default_residue_name_set(...) from builtins.PyCapsule
- default_residue_name_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default residue name has been set
- default_z0_offset(...) from builtins.PyCapsule
- default_z0_offset(rosetta.protocols.helical_bundle.MakeBundle) -> float
Returns the default z0_offset value (helix offset along the major helix axis).
- default_z0_offset_set(...) from builtins.PyCapsule
- default_z0_offset_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default z0_offset value (helix offset along the major helix axis) has been set.
- default_z1(...) from builtins.PyCapsule
- default_z1(rosetta.protocols.helical_bundle.MakeBundle) -> float
Returns the default z1 value (minor helix rise per residue).
- default_z1_offset(...) from builtins.PyCapsule
- default_z1_offset(rosetta.protocols.helical_bundle.MakeBundle) -> float
Returns the default z1_offset value (helix offset along the minor helix axis).
- default_z1_offset_set(...) from builtins.PyCapsule
- default_z1_offset_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default z1_offset value (helix offset along the minor helix axis) has been set.
- default_z1_set(...) from builtins.PyCapsule
- default_z1_set(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true if and only if the default z1 value (minor helix rise per residue) has been set
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.helical_bundle.MakeBundle) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.helical_bundle.MakeBundle) -> str
- helix(...) from builtins.PyCapsule
- helix(self : rosetta.protocols.helical_bundle.MakeBundle, index : int) -> rosetta.protocols.helical_bundle.MakeBundleHelix
Non-const access to helix in the bundle.
- helix_cop(...) from builtins.PyCapsule
- helix_cop(self : rosetta.protocols.helical_bundle.MakeBundle, index : int) -> rosetta.protocols.helical_bundle.MakeBundleHelix
Const access to helix in the bundle.
- last_apply_failed(...) from builtins.PyCapsule
- last_apply_failed(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns true or false based on whether the last call to the apply() function
failed (true) or succeeded (false).
The apply() function calls the private function set_last_apply_failed() to
set this.
- n_helices(...) from builtins.PyCapsule
- n_helices(rosetta.protocols.helical_bundle.MakeBundle) -> int
Returns the number of helices.
Note that this is not multiplied by the number of symmetry repeats. That is,
if the bundle has 3-fold symmetry and 2 helices are defined, there will be 6 helices in
the final structure, but this function would still return 2.
- reset_pose(...) from builtins.PyCapsule
- reset_pose(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Returns a bool indicating whether the input pose will be reset prior to
building a helix.
- set_default_allow_bondangles(...) from builtins.PyCapsule
- set_default_allow_bondangles(self : rosetta.protocols.helical_bundle.MakeBundle, val : bool) -> NoneType
Set the default for whether bond lengths should be set by the mover
- set_default_allow_bondlengths(...) from builtins.PyCapsule
- set_default_allow_bondlengths(self : rosetta.protocols.helical_bundle.MakeBundle, val : bool) -> NoneType
Set the default for whether bond lengths should be set by the mover
- set_default_allow_dihedrals(...) from builtins.PyCapsule
- set_default_allow_dihedrals(self : rosetta.protocols.helical_bundle.MakeBundle, val : bool) -> NoneType
Set the default for whether bond lengths should be set by the mover
- set_default_crick_params_file(...) from builtins.PyCapsule
- set_default_crick_params_file(self : rosetta.protocols.helical_bundle.MakeBundle, input_string : str) -> NoneType
Set the default Crick params file name.
- set_default_delta_omega0(...) from builtins.PyCapsule
- set_default_delta_omega0(self : rosetta.protocols.helical_bundle.MakeBundle, val : float) -> NoneType
Set the default delta_omega0 value (major helix turn)
- set_default_delta_omega1_all(...) from builtins.PyCapsule
- set_default_delta_omega1_all(self : rosetta.protocols.helical_bundle.MakeBundle, val : float) -> NoneType
Set the default delta_omega1_all value (minor helix rotation)
- set_default_delta_t(...) from builtins.PyCapsule
- set_default_delta_t(self : rosetta.protocols.helical_bundle.MakeBundle, val : float) -> NoneType
Set the default delta_t value (residue offset).
- set_default_helix_length(...) from builtins.PyCapsule
- set_default_helix_length(self : rosetta.protocols.helical_bundle.MakeBundle, val : int) -> NoneType
Set the default number of residues per helix
- set_default_invert(...) from builtins.PyCapsule
- set_default_invert(self : rosetta.protocols.helical_bundle.MakeBundle, val : bool) -> NoneType
Set the default invert value (should the helix be flipped?)
- set_default_omega0(...) from builtins.PyCapsule
- set_default_omega0(self : rosetta.protocols.helical_bundle.MakeBundle, val : float) -> NoneType
Set the default omega0 value (major helix rise per residue)
- set_default_omega1(...) from builtins.PyCapsule
- set_default_omega1(self : rosetta.protocols.helical_bundle.MakeBundle, val : float) -> NoneType
Set the default omega1 value (minor helix turn per residue)
- set_default_r0(...) from builtins.PyCapsule
- set_default_r0(self : rosetta.protocols.helical_bundle.MakeBundle, val : float) -> NoneType
Set the default r0 value (major helix radius)
- set_default_repeating_unit_offset(...) from builtins.PyCapsule
- set_default_repeating_unit_offset(self : rosetta.protocols.helical_bundle.MakeBundle, offset : int) -> NoneType
Set the default repeating unit offset
An offset of 0 means that the first residue of the helix is the first residue of the repeating unit. An offset
of 1 means that the first residue of the helix is the second residue of the repeating unit, etc.
- set_default_residue_name(...) from builtins.PyCapsule
- set_default_residue_name(self : rosetta.protocols.helical_bundle.MakeBundle, names : rosetta.utility.vector1_std_string) -> NoneType
Set the default residue name
- set_default_z0_offset(...) from builtins.PyCapsule
- set_default_z0_offset(self : rosetta.protocols.helical_bundle.MakeBundle, val : float) -> NoneType
Set the default z0_offset value (helix offset along the major helix axis).
- set_default_z1(...) from builtins.PyCapsule
- set_default_z1(self : rosetta.protocols.helical_bundle.MakeBundle, val : float) -> NoneType
Set the default z1 value (minor helix rise per residue)
- set_default_z1_offset(...) from builtins.PyCapsule
- set_default_z1_offset(self : rosetta.protocols.helical_bundle.MakeBundle, val : float) -> NoneType
Set the default z1_offset value (helix offset along the minor helix axis).
- set_dofs_from_tag(...) from builtins.PyCapsule
- set_dofs_from_tag(self : rosetta.protocols.helical_bundle.MakeBundle, tag : rosetta.utility.tag.Tag) -> NoneType
Set defaults for whether the mover can set bond lengths, bond angles, and dihedrals.
- set_helix_params_from_tag(...) from builtins.PyCapsule
- set_helix_params_from_tag(self : rosetta.protocols.helical_bundle.MakeBundle, helix_index : int, tag : rosetta.utility.tag.Tag) -> NoneType
Set crick_params_file, set_bondlengths, set_bondangles, and set_dihedrals options for a single helix, based on an input tag.
- set_minor_helix_params_from_tag(...) from builtins.PyCapsule
- set_minor_helix_params_from_tag(self : rosetta.protocols.helical_bundle.MakeBundle, helix_index : int, tag : rosetta.utility.tag.Tag) -> NoneType
Set omega1, z1, and delta_omega1 for a single helix, based on an input tag.
- set_minorhelix_defaults_from_tag(...) from builtins.PyCapsule
- set_minorhelix_defaults_from_tag(self : rosetta.protocols.helical_bundle.MakeBundle, tag : rosetta.utility.tag.Tag) -> NoneType
Set the crick_params_file, omega1, and z1 default values from a tag.
- set_other_defaults_from_tag(...) from builtins.PyCapsule
- set_other_defaults_from_tag(self : rosetta.protocols.helical_bundle.MakeBundle, tag : rosetta.utility.tag.Tag) -> NoneType
Set the residue_name, invert, and helix_length default values based on an input tag.
- set_other_helix_params_from_tag(...) from builtins.PyCapsule
- set_other_helix_params_from_tag(self : rosetta.protocols.helical_bundle.MakeBundle, helix_index : int, tag : rosetta.utility.tag.Tag) -> NoneType
Set residue_name, invert, and helix_length for a single helix, based on an input tag.
- set_reset_pose(...) from builtins.PyCapsule
- set_reset_pose(self : rosetta.protocols.helical_bundle.MakeBundle, reset_in : bool) -> NoneType
Set whether the input pose should be reset prior to building a helix.
- set_symmetry(...) from builtins.PyCapsule
- set_symmetry(self : rosetta.protocols.helical_bundle.MakeBundle, symmetry_in : int) -> NoneType
Set the symmetry of the bundle.
See bundle_symmetry_ member variable for details.
- set_symmetry_copies(...) from builtins.PyCapsule
- set_symmetry_copies(self : rosetta.protocols.helical_bundle.MakeBundle, symmetry_copies_in : int) -> NoneType
Set how many of the symmetry copies actually get generated.
See bundle_symmetry_copies_ member variable for details.
- set_symmetry_options_from_tag(...) from builtins.PyCapsule
- set_symmetry_options_from_tag(self : rosetta.protocols.helical_bundle.MakeBundle, tag : rosetta.utility.tag.Tag) -> NoneType
Set symmetry and symmetry_copies options based on an input tag.
- set_use_degrees(...) from builtins.PyCapsule
- set_use_degrees(*args, **kwargs)
Overloaded function.
1. set_use_degrees(rosetta.protocols.helical_bundle.MakeBundle) -> NoneType
Set whether we're using degrees (true) or radians (false).
2. set_use_degrees(self : rosetta.protocols.helical_bundle.MakeBundle, val : bool) -> NoneType
Set whether we're using degrees (true) or radians (false).
- symmetry(...) from builtins.PyCapsule
- symmetry(rosetta.protocols.helical_bundle.MakeBundle) -> int
Get the symmetry of the bundle.
See bundle_symmetry_ member variable for details.
- symmetry_copies(...) from builtins.PyCapsule
- symmetry_copies(rosetta.protocols.helical_bundle.MakeBundle) -> int
Get how many of the symmetry copies actually get generated.
See bundle_symmetry_copies_ member variable for details.
- use_degrees(...) from builtins.PyCapsule
- use_degrees(rosetta.protocols.helical_bundle.MakeBundle) -> bool
Get whether we're using degrees (true) or radians (false).
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 MakeBundleHelix(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- MakeBundleHelix
- 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.helical_bundle.MakeBundleHelix) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- allow_bondangles(...) from builtins.PyCapsule
- allow_bondangles(rosetta.protocols.helical_bundle.MakeBundleHelix) -> bool
Returns "true" if and only if this mover is allowed to set mainchain bond angles.
- allow_bondlengths(...) from builtins.PyCapsule
- allow_bondlengths(rosetta.protocols.helical_bundle.MakeBundleHelix) -> bool
Returns "true" if and only if this mover is allowed to set mainchain bond lengths.
- allow_dihedrals(...) from builtins.PyCapsule
- allow_dihedrals(rosetta.protocols.helical_bundle.MakeBundleHelix) -> bool
Returns "true" if and only if this mover is allowed to set mainchain dihedrals.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.helical_bundle.MakeBundleHelix, pose : rosetta.core.pose.Pose) -> NoneType
Actually apply the mover to the pose.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.helical_bundle.MakeBundleHelix, : rosetta.protocols.helical_bundle.MakeBundleHelix) -> rosetta.protocols.helical_bundle.MakeBundleHelix
- atoms_per_residue(...) from builtins.PyCapsule
- atoms_per_residue(rosetta.protocols.helical_bundle.MakeBundleHelix) -> rosetta.utility.vector1_unsigned_long
Get the atoms per residue vector (const-access).
- bundle_parameters(...) from builtins.PyCapsule
- bundle_parameters(rosetta.protocols.helical_bundle.MakeBundleHelix) -> rosetta.protocols.helical_bundle.parameters.BundleParameters
Const-access to bundle parameters.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.helical_bundle.MakeBundleHelix) -> rosetta.protocols.moves.Mover
- delta_omega0(...) from builtins.PyCapsule
- delta_omega0(rosetta.protocols.helical_bundle.MakeBundleHelix) -> float
Get the delta_omega0 value.
- delta_omega1(...) from builtins.PyCapsule
- delta_omega1(self : rosetta.protocols.helical_bundle.MakeBundleHelix, index : int) -> float
Get the delta_omega1 value for a given mainchain atom.
- delta_omega1_all(...) from builtins.PyCapsule
- delta_omega1_all(rosetta.protocols.helical_bundle.MakeBundleHelix) -> float
Get global omega1 offset
The overall omega1 offset is the sum of this global value and the per-atom
delta_omega1 values.
- delta_omega1_vect(...) from builtins.PyCapsule
- delta_omega1_vect(rosetta.protocols.helical_bundle.MakeBundleHelix) -> rosetta.utility.vector1_double
Const-access to the whole delta_omega1 vector.
- delta_t(...) from builtins.PyCapsule
- delta_t(rosetta.protocols.helical_bundle.MakeBundleHelix) -> float
Get the delta_t value.
- delta_z1(...) from builtins.PyCapsule
- delta_z1(self : rosetta.protocols.helical_bundle.MakeBundleHelix, index : int) -> float
Get the delta_z1 value for a given mainchain atom.
- delta_z1_vect(...) from builtins.PyCapsule
- delta_z1_vect(rosetta.protocols.helical_bundle.MakeBundleHelix) -> rosetta.utility.vector1_double
Const-access to the whole delta_z1 vector.
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.helical_bundle.MakeBundleHelix) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.helical_bundle.MakeBundleHelix) -> str
- helix_length(...) from builtins.PyCapsule
- helix_length(rosetta.protocols.helical_bundle.MakeBundleHelix) -> int
Returns a bool indicating whether the input pose will be reset prior to
building a helix.
- invert_helix(...) from builtins.PyCapsule
- invert_helix(rosetta.protocols.helical_bundle.MakeBundleHelix) -> bool
Return whether the helix direction will be inverted.
- last_apply_failed(...) from builtins.PyCapsule
- last_apply_failed(rosetta.protocols.helical_bundle.MakeBundleHelix) -> bool
Returns "true" if the last call to the apply function failed, false otherwise.
- omega0(...) from builtins.PyCapsule
- omega0(rosetta.protocols.helical_bundle.MakeBundleHelix) -> float
Get the omega0 value.
- omega1(...) from builtins.PyCapsule
- omega1(rosetta.protocols.helical_bundle.MakeBundleHelix) -> float
Get the omega1 value.
- r0(...) from builtins.PyCapsule
- r0(rosetta.protocols.helical_bundle.MakeBundleHelix) -> float
Get the r0 value.
- r1(...) from builtins.PyCapsule
- r1(self : rosetta.protocols.helical_bundle.MakeBundleHelix, index : int) -> float
Get the r1 value for a given mainchain atom.
- r1_vect(...) from builtins.PyCapsule
- r1_vect(rosetta.protocols.helical_bundle.MakeBundleHelix) -> rosetta.utility.vector1_double
Const-access to the whole r1 vector.
- repeating_unit_offset(...) from builtins.PyCapsule
- repeating_unit_offset(rosetta.protocols.helical_bundle.MakeBundleHelix) -> int
Get the repeating unit offset.
An offset of 0 means that the first residue in the helix is the first
residue of the repeating unit. An offset of 1 means that the first residue in
the helix is the second residue in the repeating unit, etc.
- reset_pose(...) from builtins.PyCapsule
- reset_pose(rosetta.protocols.helical_bundle.MakeBundleHelix) -> bool
Returns a bool indicating whether the input pose will be reset prior to
building a helix.
- residue_name(...) from builtins.PyCapsule
- residue_name(self : rosetta.protocols.helical_bundle.MakeBundleHelix, repeat_index : int) -> str
Get the name (full name, not 3-letter code) of one of the residue types in the repeating
unit that will make up the helix.
- residues_per_repeat(...) from builtins.PyCapsule
- residues_per_repeat(rosetta.protocols.helical_bundle.MakeBundleHelix) -> int
Get the residues per repeat.
- set_allow_bondangles(...) from builtins.PyCapsule
- set_allow_bondangles(self : rosetta.protocols.helical_bundle.MakeBundleHelix, val : bool) -> NoneType
Sets whether this mover is allowed to set mainchain bond angles.
- set_allow_bondlengths(...) from builtins.PyCapsule
- set_allow_bondlengths(self : rosetta.protocols.helical_bundle.MakeBundleHelix, val : bool) -> NoneType
Sets whether this mover is allowed to set mainchain bond lengths.
- set_allow_dihedrals(...) from builtins.PyCapsule
- set_allow_dihedrals(self : rosetta.protocols.helical_bundle.MakeBundleHelix, val : bool) -> NoneType
Sets whether this mover is allowed to set mainchain dihedrals.
- set_bundle_parameters(...) from builtins.PyCapsule
- set_bundle_parameters(self : rosetta.protocols.helical_bundle.MakeBundleHelix, newparams : rosetta.protocols.helical_bundle.parameters.BundleParameters) -> NoneType
Set a new set of bundle parameters.
- set_delta_omega0(...) from builtins.PyCapsule
- set_delta_omega0(self : rosetta.protocols.helical_bundle.MakeBundleHelix, delta_omega0_in : float) -> NoneType
Set the delta_omega0 value.
- set_delta_omega1_all(...) from builtins.PyCapsule
- set_delta_omega1_all(self : rosetta.protocols.helical_bundle.MakeBundleHelix, delta_omega1_all_in : float) -> NoneType
Set global omega1 offset
The overall omega1 offset is the sum of this global value and the per-atom
delta_omega1 values.
- set_delta_t(...) from builtins.PyCapsule
- set_delta_t(self : rosetta.protocols.helical_bundle.MakeBundleHelix, delta_t_in : float) -> NoneType
Set delta_t
- set_helix_length(...) from builtins.PyCapsule
- set_helix_length(self : rosetta.protocols.helical_bundle.MakeBundleHelix, helix_length_in : int) -> NoneType
Set the length of the helix, in residues.
- set_invert_helix(...) from builtins.PyCapsule
- set_invert_helix(self : rosetta.protocols.helical_bundle.MakeBundleHelix, invert_in : bool) -> NoneType
Set whether the helix direction should be inverted.
- set_major_helix_params(...) from builtins.PyCapsule
- set_major_helix_params(self : rosetta.protocols.helical_bundle.MakeBundleHelix, r0_in : float, omega0_in : float, delta_omega0_in : float) -> NoneType
Set the major helix parameters
- set_minor_helix_params(...) from builtins.PyCapsule
- set_minor_helix_params(self : rosetta.protocols.helical_bundle.MakeBundleHelix, r1_in : rosetta.utility.vector1_double, omega1_in : float, z1_in : float, delta_omega1_in : rosetta.utility.vector1_double, delta_z1_in : rosetta.utility.vector1_double) -> NoneType
Set the minor helix parameters
- set_minor_helix_params_from_file(...) from builtins.PyCapsule
- set_minor_helix_params_from_file(self : rosetta.protocols.helical_bundle.MakeBundleHelix, filename : str) -> NoneType
Set the minor helix parameters by reading them in from a file.
- set_omega0(...) from builtins.PyCapsule
- set_omega0(self : rosetta.protocols.helical_bundle.MakeBundleHelix, val : float) -> NoneType
Set the omega0 value.
- set_omega1(...) from builtins.PyCapsule
- set_omega1(self : rosetta.protocols.helical_bundle.MakeBundleHelix, val : float) -> NoneType
Set the omega1 value.
- set_r0(...) from builtins.PyCapsule
- set_r0(self : rosetta.protocols.helical_bundle.MakeBundleHelix, val : float) -> NoneType
Set the r0 value.
- set_repeating_unit_offset(...) from builtins.PyCapsule
- set_repeating_unit_offset(self : rosetta.protocols.helical_bundle.MakeBundleHelix, val : int) -> NoneType
Set the repeating unit offset.
An offset of 0 means that the first residue of the helix is the first residue of the repeating unit. An offset
of 1 means that the first residue of the helix is the SECOND residue of the repeating unit, etc.
- set_reset_pose(...) from builtins.PyCapsule
- set_reset_pose(self : rosetta.protocols.helical_bundle.MakeBundleHelix, reset_in : bool) -> NoneType
Set whether the input pose should be reset prior to building a helix.
- set_residue_name(...) from builtins.PyCapsule
- set_residue_name(self : rosetta.protocols.helical_bundle.MakeBundleHelix, names : rosetta.utility.vector1_std_string) -> NoneType
Set the residue type(s) (full name, not 3-letter code) that will make up the helix.
If there is more than one residue per repeating unit in the minor helix, one residue
name must be provided for each residue in the repeating unit. Note that there is no check that
the size of the residue_name_ vector matches the number of residues in the repeating unit until
apply time.
- set_tail_residue_name(...) from builtins.PyCapsule
- set_tail_residue_name(self : rosetta.protocols.helical_bundle.MakeBundleHelix, name : str) -> NoneType
Set the residue type (full name, not 3-letter code) that will cap the helix.
Set this to "" for no cap.
- set_z0_offset(...) from builtins.PyCapsule
- set_z0_offset(self : rosetta.protocols.helical_bundle.MakeBundleHelix, val : float) -> NoneType
Set z0_offset, the offset along the major helix axis for the whole helix.
- set_z1(...) from builtins.PyCapsule
- set_z1(self : rosetta.protocols.helical_bundle.MakeBundleHelix, val : float) -> NoneType
Set the z1 value.
- set_z1_offset(...) from builtins.PyCapsule
- set_z1_offset(self : rosetta.protocols.helical_bundle.MakeBundleHelix, val : float) -> NoneType
Set z1_offset, the offset along the minor helix axis for the whole helix.
- tail_residue_name(...) from builtins.PyCapsule
- tail_residue_name(rosetta.protocols.helical_bundle.MakeBundleHelix) -> str
Get the name of the residue type (full name, not 3-letter code) that will cap the helix.
Returns "" for no cap.
- z0_offset(...) from builtins.PyCapsule
- z0_offset(rosetta.protocols.helical_bundle.MakeBundleHelix) -> float
Get the z0_offset value (the offset of the helix along the major helix axis).
- z1(...) from builtins.PyCapsule
- z1(rosetta.protocols.helical_bundle.MakeBundleHelix) -> float
Get the z1 value.
- z1_offset(...) from builtins.PyCapsule
- z1_offset(rosetta.protocols.helical_bundle.MakeBundleHelix) -> float
Get the z1_offset value (the offset of the helix along the minor helix axis).
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 PertType(builtins.object) |
| |
The type of random perturbation that will be used.
|
| |
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(rosetta.protocols.helical_bundle.PertType, rosetta.protocols.helical_bundle.PertType) -> bool
- __hash__(...) from builtins.PyCapsule
- __hash__(rosetta.protocols.helical_bundle.PertType) -> int
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.helical_bundle.PertType, int) -> NoneType
2. __init__(rosetta.protocols.helical_bundle.PertType, int) -> NoneType
- __int__(...) from builtins.PyCapsule
- __int__(rosetta.protocols.helical_bundle.PertType) -> int
- __ne__(...) from builtins.PyCapsule
- __ne__(rosetta.protocols.helical_bundle.PertType, rosetta.protocols.helical_bundle.PertType) -> bool
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __repr__(...) from builtins.PyCapsule
- __repr__(rosetta.protocols.helical_bundle.PertType) -> str
Data and other attributes defined here:
- pt_gaussian = PertType.pt_gaussian
- pt_undefined_perturbation = PertType.pt_undefined_perturbation
- pt_uniform = PertType.pt_uniform
|
class PerturbBundle(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- PerturbBundle
- 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.helical_bundle.PerturbBundle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_helix(...) from builtins.PyCapsule
- add_helix(self : rosetta.protocols.helical_bundle.PerturbBundle, helix_index : int) -> int
Add options for a new helix
Return value is the current total number of helices after the addition.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.helical_bundle.PerturbBundle, pose : rosetta.core.pose.Pose) -> NoneType
Actually apply the mover to the pose.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.helical_bundle.PerturbBundle, : rosetta.protocols.helical_bundle.PerturbBundle) -> rosetta.protocols.helical_bundle.PerturbBundle
- bundleparametersset_index(...) from builtins.PyCapsule
- bundleparametersset_index(rosetta.protocols.helical_bundle.PerturbBundle) -> int
Returns a value indicating which bundle parameters set will be used, if more than one is defined in the pose's Conformation object.
A value of n indicates that the nth bundle paramets set encountered will be perturbed.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.helical_bundle.PerturbBundle) -> rosetta.protocols.moves.Mover
- convert_angle(...) from builtins.PyCapsule
- convert_angle(self : rosetta.protocols.helical_bundle.PerturbBundle, val : float) -> float
Ensure that an angle value is in radians.
Checks the use_degrees_ boolean. If true, converts degrees to radians; if false, returns input value.
- default_delta_omega0(...) from builtins.PyCapsule
- default_delta_omega0(*args, **kwargs)
Overloaded function.
1. default_delta_omega0(rosetta.protocols.helical_bundle.PerturbBundle) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_delta_omega0_ BundleOptions object.
2. default_delta_omega0(rosetta.protocols.helical_bundle.PerturbBundle) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_delta_omega0_ BundleOptions object (const-access).
- default_delta_omega1(...) from builtins.PyCapsule
- default_delta_omega1(*args, **kwargs)
Overloaded function.
1. default_delta_omega1(rosetta.protocols.helical_bundle.PerturbBundle) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_delta_omega1_ BundleOptions object.
2. default_delta_omega1(rosetta.protocols.helical_bundle.PerturbBundle) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_delta_omega1_ BundleOptions object (const-access).
- default_delta_t(...) from builtins.PyCapsule
- default_delta_t(*args, **kwargs)
Overloaded function.
1. default_delta_t(rosetta.protocols.helical_bundle.PerturbBundle) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_delta_t_ BundleOptions object.
2. default_delta_t(rosetta.protocols.helical_bundle.PerturbBundle) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_delta_t_ BundleOptions object (const-access).
- default_omega0(...) from builtins.PyCapsule
- default_omega0(*args, **kwargs)
Overloaded function.
1. default_omega0(rosetta.protocols.helical_bundle.PerturbBundle) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_omega0_ BundleOptions object.
2. default_omega0(rosetta.protocols.helical_bundle.PerturbBundle) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_omega0_ BundleOptions object (const-access).
- default_r0(...) from builtins.PyCapsule
- default_r0(*args, **kwargs)
Overloaded function.
1. default_r0(rosetta.protocols.helical_bundle.PerturbBundle) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_r0_ BundleOptions object.
2. default_r0(rosetta.protocols.helical_bundle.PerturbBundle) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_r0_ BundleOptions object (const-access).
- default_z0_offset(...) from builtins.PyCapsule
- default_z0_offset(*args, **kwargs)
Overloaded function.
1. default_z0_offset(rosetta.protocols.helical_bundle.PerturbBundle) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_z0_offset_ BundleOptions object.
2. default_z0_offset(rosetta.protocols.helical_bundle.PerturbBundle) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_z0_offset_ BundleOptions object (const-access).
- default_z1_offset(...) from builtins.PyCapsule
- default_z1_offset(*args, **kwargs)
Overloaded function.
1. default_z1_offset(rosetta.protocols.helical_bundle.PerturbBundle) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_z1_offset_ BundleOptions object.
2. default_z1_offset(rosetta.protocols.helical_bundle.PerturbBundle) -> protocols::helical_bundle::PerturbBundleOptions
Access the default_z1_offset_ BundleOptions object (const-access).
- delta_omega0(...) from builtins.PyCapsule
- delta_omega0(*args, **kwargs)
Overloaded function.
1. delta_omega0(self : rosetta.protocols.helical_bundle.PerturbBundle, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the delta_omega0_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
2. delta_omega0(self : rosetta.protocols.helical_bundle.PerturbBundle, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the delta_omega0_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
- delta_omega1(...) from builtins.PyCapsule
- delta_omega1(*args, **kwargs)
Overloaded function.
1. delta_omega1(self : rosetta.protocols.helical_bundle.PerturbBundle, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the delta_omega1_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
2. delta_omega1(self : rosetta.protocols.helical_bundle.PerturbBundle, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the delta_omega1_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
- delta_t(...) from builtins.PyCapsule
- delta_t(*args, **kwargs)
Overloaded function.
1. delta_t(self : rosetta.protocols.helical_bundle.PerturbBundle, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the delta_t_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
2. delta_t(self : rosetta.protocols.helical_bundle.PerturbBundle, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the delta_t_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.helical_bundle.PerturbBundle) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.helical_bundle.PerturbBundle) -> str
- omega0(...) from builtins.PyCapsule
- omega0(*args, **kwargs)
Overloaded function.
1. omega0(self : rosetta.protocols.helical_bundle.PerturbBundle, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the omega0_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
2. omega0(self : rosetta.protocols.helical_bundle.PerturbBundle, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the omega0_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
- r0(...) from builtins.PyCapsule
- r0(*args, **kwargs)
Overloaded function.
1. r0(self : rosetta.protocols.helical_bundle.PerturbBundle, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the r0_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
2. r0(self : rosetta.protocols.helical_bundle.PerturbBundle, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the r0_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
- set_bundleparametersset_index(...) from builtins.PyCapsule
- set_bundleparametersset_index(self : rosetta.protocols.helical_bundle.PerturbBundle, val : int) -> NoneType
Set which bundle parameters set will be used, if more than one is defined in the pose's Conformation object.
A value of n indicates that the nth bundle paramets set encountered will be perturbed.
- set_use_degrees(...) from builtins.PyCapsule
- set_use_degrees(self : rosetta.protocols.helical_bundle.PerturbBundle, val : bool) -> NoneType
Set whether user input is in degrees (true) or radians (false).
- use_degrees(...) from builtins.PyCapsule
- use_degrees(rosetta.protocols.helical_bundle.PerturbBundle) -> bool
Get whether user input is in degrees (true) or radians (false).
- z0_offset(...) from builtins.PyCapsule
- z0_offset(*args, **kwargs)
Overloaded function.
1. z0_offset(self : rosetta.protocols.helical_bundle.PerturbBundle, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the z0_offset_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
2. z0_offset(self : rosetta.protocols.helical_bundle.PerturbBundle, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the z0_offset_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
- z1_offset(...) from builtins.PyCapsule
- z1_offset(*args, **kwargs)
Overloaded function.
1. z1_offset(self : rosetta.protocols.helical_bundle.PerturbBundle, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the z1_offset_ BundleOptions object, by index.
This is the index in order of helices added, NOT necessarily the index of the helix.
2. z1_offset(self : rosetta.protocols.helical_bundle.PerturbBundle, index : int) -> protocols::helical_bundle::PerturbBundleOptions
Access the z1_offset_ BundleOptions object, by index. This provides const access.
This is the index in order of helices added, NOT necessarily the index of the helix.
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 PerturbBundleHelix(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- PerturbBundleHelix
- 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.helical_bundle.PerturbBundleHelix) -> 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.helical_bundle.PerturbBundleHelix, pose : rosetta.core.pose.Pose) -> NoneType
Actually apply the mover to the pose.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.helical_bundle.PerturbBundleHelix, : rosetta.protocols.helical_bundle.PerturbBundleHelix) -> rosetta.protocols.helical_bundle.PerturbBundleHelix
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.helical_bundle.PerturbBundleHelix) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.helical_bundle.PerturbBundleHelix) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.helical_bundle.PerturbBundleHelix) -> str
- last_apply_failed(...) from builtins.PyCapsule
- last_apply_failed(rosetta.protocols.helical_bundle.PerturbBundleHelix) -> bool
- parameters_index(...) from builtins.PyCapsule
- parameters_index(rosetta.protocols.helical_bundle.PerturbBundleHelix) -> int
Returns the index of the Parameters object in the ParametersSet object in the pose that's being perturbed.
This Parameters object contains the Crick parameters that define the helix that's being perturbed.
- parameters_set_index(...) from builtins.PyCapsule
- parameters_set_index(rosetta.protocols.helical_bundle.PerturbBundleHelix) -> int
Returns the index of the ParametersSet object in the pose that's being perturbed.
This ParametersSet contains the Parameters object that defines the helix that's being perturbed.
- set_parameters_index(...) from builtins.PyCapsule
- set_parameters_index(self : rosetta.protocols.helical_bundle.PerturbBundleHelix, index : int) -> NoneType
Sets the index of the Parameters object in the ParametersSet object in the pose that's being perturbed.
This Parameters object contains the Crick parameters that define the helix that's being perturbed.
- set_parameters_set_index(...) from builtins.PyCapsule
- set_parameters_set_index(self : rosetta.protocols.helical_bundle.PerturbBundleHelix, index : int) -> NoneType
Sets the index of the ParametersSet object in the pose that's being perturbed.
This ParametersSet contains the Parameters object that defines the helix that's being perturbed.
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 PerturbBundleOptions(builtins.object) |
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PerturbBundleOptions class, which stores options for the PerturbBundle mover.
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.helical_bundle.PerturbBundleOptions) -> 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.helical_bundle.PerturbBundleOptions, : rosetta.protocols.helical_bundle.PerturbBundleOptions) -> rosetta.protocols.helical_bundle.PerturbBundleOptions
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> rosetta.protocols.helical_bundle.PerturbBundleOptions
Copy this residue( allocate actual memory for it )
- default_value(...) from builtins.PyCapsule
- default_value(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> float
Returns the default value of this parameter.
This is used by the BundleGridSampler mover, but not the PerturbBundle mover.
- delta(...) from builtins.PyCapsule
- delta(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> float
Function to generate a random value, based on the perturbation type and perturbation magnitude.
Typically, one would then add this value to the current parameter value to perturb it.
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> rosetta.protocols.helical_bundle.PerturbBundleOptions
self pointers
2. get_self_ptr(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> rosetta.protocols.helical_bundle.PerturbBundleOptions
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> rosetta.std.weak_ptr_const_protocols_helical_bundle_PerturbBundleOptions_t
2. get_self_weak_ptr(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> rosetta.std.weak_ptr_protocols_helical_bundle_PerturbBundleOptions_t
- helix_index(...) from builtins.PyCapsule
- helix_index(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> int
Returns the index of the helix that these options refer to.
- is_copy(...) from builtins.PyCapsule
- is_copy(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> bool
Returns whether we're copying this value from another helix.
- is_perturbable(...) from builtins.PyCapsule
- is_perturbable(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> bool
Returns whether this option is set to be peturbable.
- lower_value(...) from builtins.PyCapsule
- lower_value(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> float
Returns the lower sampled value of this parameter.
This is used by the BundleGridSampler mover, but not the PerturbBundle mover.
- omega0_copies_pitch_instead(...) from builtins.PyCapsule
- omega0_copies_pitch_instead(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> bool
Special case: returns whether omega0 copying should use the pitch angle instead of the omega0 value.
Default false.
- other_helix(...) from builtins.PyCapsule
- other_helix(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> int
Returns the other helix index from which we're copying a value.
- perturbation_magnitude(...) from builtins.PyCapsule
- perturbation_magnitude(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> float
Returns the perturbation magnitude. Returns 0 if not perturbable.
- perturbation_type(...) from builtins.PyCapsule
- perturbation_type(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> rosetta.protocols.helical_bundle.PertType
Returns the perturbation type.
- samples(...) from builtins.PyCapsule
- samples(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> int
Returns the number of values to sample for this parameter.
This is used by the BundleGridSampler mover, but not the PerturbBundle mover. If the sample value is 0, no sampling occurs.
- set_default_value(...) from builtins.PyCapsule
- set_default_value(self : rosetta.protocols.helical_bundle.PerturbBundleOptions, val : float) -> NoneType
Set the default value of this parameter.
This is used by the BundleGridSampler mover, but not the PerturbBundle mover.
- set_helix_index(...) from builtins.PyCapsule
- set_helix_index(self : rosetta.protocols.helical_bundle.PerturbBundleOptions, val : int) -> NoneType
Sets the index of the helix that these options refer to.
- set_helix_to_copy(...) from builtins.PyCapsule
- set_helix_to_copy(self : rosetta.protocols.helical_bundle.PerturbBundleOptions, helix_index : int) -> NoneType
Sets the helix from which we should copy a parameter value. If set to zero, no copying occurs.
- set_lower_value(...) from builtins.PyCapsule
- set_lower_value(self : rosetta.protocols.helical_bundle.PerturbBundleOptions, val : float) -> NoneType
Set the lower sampled value of this parameter.
This is used by the BundleGridSampler mover, but not the PerturbBundle mover.
- set_omega0_copies_pitch_instead(...) from builtins.PyCapsule
- set_omega0_copies_pitch_instead(self : rosetta.protocols.helical_bundle.PerturbBundleOptions, copy_pitch : bool) -> NoneType
Special case: sets whether omega0 copying should copy the pitch angle instead of the omega0 value.
- set_perturbable(...) from builtins.PyCapsule
- set_perturbable(self : rosetta.protocols.helical_bundle.PerturbBundleOptions, val : bool) -> NoneType
Sets whether this option is peturbable.
- set_perturbation_magnitude(...) from builtins.PyCapsule
- set_perturbation_magnitude(self : rosetta.protocols.helical_bundle.PerturbBundleOptions, val : float) -> NoneType
Sets the perturbation magnitude. Sets perturbable to true in the process.
- set_perturbation_type(...) from builtins.PyCapsule
- set_perturbation_type(self : rosetta.protocols.helical_bundle.PerturbBundleOptions, type : rosetta.protocols.helical_bundle.PertType) -> NoneType
Sets the perturbation type.
- set_samples(...) from builtins.PyCapsule
- set_samples(self : rosetta.protocols.helical_bundle.PerturbBundleOptions, val : int) -> NoneType
Sets the number of values to sample for this parameter.
This is used by the BundleGridSampler mover, but not the PerturbBundle mover. If set to 0, no sampling occurs.
- set_upper_value(...) from builtins.PyCapsule
- set_upper_value(self : rosetta.protocols.helical_bundle.PerturbBundleOptions, val : float) -> NoneType
Set the upper sampled value of this parameter.
This is used by the BundleGridSampler mover, but not the PerturbBundle mover.
- set_use_defaults(...) from builtins.PyCapsule
- set_use_defaults(self : rosetta.protocols.helical_bundle.PerturbBundleOptions, val : bool) -> NoneType
Sets whether the default values should be used in lieu of whatever is set here.
- upper_value(...) from builtins.PyCapsule
- upper_value(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> float
Returns the upper sampled value of this parameter.
This is used by the BundleGridSampler mover, but not the PerturbBundle mover.
- use_defaults(...) from builtins.PyCapsule
- use_defaults(rosetta.protocols.helical_bundle.PerturbBundleOptions) -> bool
Returns whether the default values should be used in lieu of whatever is set here.
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