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- rosetta.protocols.moves.Mover(builtins.object)
-
- BDR
- VarLengthBuild
class BDR(rosetta.protocols.moves.Mover) |
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- Method resolution order:
- BDR
- 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.forge.components.BDR) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_instruction(...) from builtins.PyCapsule
- add_instruction(*args, **kwargs)
Overloaded function.
1. add_instruction(self : rosetta.protocols.forge.components.BDR, bi : rosetta.protocols.forge.build.BuildInstruction) -> NoneType
add instruction to the manager of this BDR (no copy)
BuildInstruction
The allowed amino acid sequence
during design. Only applicable to BuildInstructions like
SegmentRebuild and SegmentInsert. Make sure the length of this
string matches up properly, and remember to use any special characters,
e.g. the insertion character for SegmentInsert
2. add_instruction(self : rosetta.protocols.forge.components.BDR, bi : rosetta.protocols.forge.build.BuildInstruction, aa_during_design_refine : str) -> NoneType
add instruction to the manager of this BDR (no copy)
BuildInstruction
The allowed amino acid sequence
during design. Only applicable to BuildInstructions like
SegmentRebuild and SegmentInsert. Make sure the length of this
string matches up properly, and remember to use any special characters,
e.g. the insertion character for SegmentInsert
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.forge.components.BDR, pose : rosetta.core.pose.Pose) -> NoneType
apply defined moves to given Pose
- centroid_loop_mover_str(...) from builtins.PyCapsule
- centroid_loop_mover_str(*args, **kwargs)
Overloaded function.
1. centroid_loop_mover_str(rosetta.protocols.forge.components.BDR) -> str
the loop mover string to use during centroid build
(default "RemodelLoopMover")
set to either a string the create_loop_mover() LoopMoverFactory
recognizes or the "RemodelLoopMover"
2. centroid_loop_mover_str(self : rosetta.protocols.forge.components.BDR, loop_mover_str : str) -> NoneType
the loop mover string to use during centroid build
set to either a string the create_loop_mover() LoopMoverFactory
recognizes or the "RemodelLoopMover"
- centroid_scorefunction(...) from builtins.PyCapsule
- centroid_scorefunction(*args, **kwargs)
Overloaded function.
1. centroid_scorefunction(rosetta.protocols.forge.components.BDR) -> rosetta.core.scoring.ScoreFunction
the centroid level score function, default "remodel_cen"
2. centroid_scorefunction(self : rosetta.protocols.forge.components.BDR, sfx : rosetta.core.scoring.ScoreFunction) -> NoneType
set the centroid level score function
3. centroid_scorefunction(self : rosetta.protocols.forge.components.BDR, sfx : rosetta.core.scoring.ScoreFunction) -> NoneType
set the centroid level score function
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.forge.components.BDR) -> rosetta.protocols.moves.Mover
clone this object
- create_directed_dependency(...) from builtins.PyCapsule
- create_directed_dependency(self : rosetta.protocols.forge.components.BDR, u : rosetta.protocols.forge.build.BuildInstruction, v : rosetta.protocols.forge.build.BuildInstruction) -> NoneType
create directed dependency between two instructions
- dr_cycles(...) from builtins.PyCapsule
- dr_cycles(*args, **kwargs)
Overloaded function.
1. dr_cycles(rosetta.protocols.forge.components.BDR) -> int
the number of design-refine cycles to perform, default 3
2. dr_cycles(self : rosetta.protocols.forge.components.BDR, cycles : int) -> NoneType
set the number of design-refine cycles to perform
set this to 0 to skip design-refine
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.forge.components.BDR) -> rosetta.protocols.moves.Mover
create this type of object
- fullatom_scorefunction(...) from builtins.PyCapsule
- fullatom_scorefunction(*args, **kwargs)
Overloaded function.
1. fullatom_scorefunction(rosetta.protocols.forge.components.BDR) -> rosetta.core.scoring.ScoreFunction
the full-atom level score function, default score12
2. fullatom_scorefunction(self : rosetta.protocols.forge.components.BDR, sfx : rosetta.core.scoring.ScoreFunction) -> NoneType
set the full-atom level score function
3. fullatom_scorefunction(self : rosetta.protocols.forge.components.BDR, sfx : rosetta.core.scoring.ScoreFunction) -> NoneType
set the full-atom level score function
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.forge.components.BDR) -> str
- loops_buns_polar_calc_name(...) from builtins.PyCapsule
- loops_buns_polar_calc_name() -> str
the name for the loops' buried unsatisfied polars
calculator
- max_linear_chainbreak(...) from builtins.PyCapsule
- max_linear_chainbreak(*args, **kwargs)
Overloaded function.
1. max_linear_chainbreak(rosetta.protocols.forge.components.BDR) -> float
the maximum allowed linear chainbreak (default 0.07)
2. max_linear_chainbreak(self : rosetta.protocols.forge.components.BDR, threshold : float) -> NoneType
the maximum allowed linear chainbreak
- neighborhood_buns_polar_calc_name(...) from builtins.PyCapsule
- neighborhood_buns_polar_calc_name() -> str
the name for the loops' neighborhood buried unsatisfied polars
calculator
- neighborhood_calc_name(...) from builtins.PyCapsule
- neighborhood_calc_name() -> str
the name for the loops' neighborhood calculator
- redesign_loop_neighborhood(...) from builtins.PyCapsule
- redesign_loop_neighborhood(*args, **kwargs)
Overloaded function.
1. redesign_loop_neighborhood(rosetta.protocols.forge.components.BDR) -> bool
redesign the neighborhood around the loop? if false, then just
repacks during the design phase (default true)
2. redesign_loop_neighborhood(self : rosetta.protocols.forge.components.BDR, flag : bool) -> NoneType
redesign the neighborhood around the loop? if false, then just
repacks during the design phase
- resfile(...) from builtins.PyCapsule
- resfile(*args, **kwargs)
Overloaded function.
1. resfile(rosetta.protocols.forge.components.BDR) -> str
name of the resfile to use during design-refine; empty string
implies no resfile
2. resfile(self : rosetta.protocols.forge.components.BDR, filename : str) -> NoneType
name of the resfile to use during design-refine; empty string
implies no resfile
- use_fullmer(...) from builtins.PyCapsule
- use_fullmer(*args, **kwargs)
Overloaded function.
1. use_fullmer(rosetta.protocols.forge.components.BDR) -> bool
use full-mer fragments when building the loop? (default false)
2. use_fullmer(self : rosetta.protocols.forge.components.BDR, flag : bool) -> NoneType
use full-mer fragments when building the loop?
- use_sequence_bias(...) from builtins.PyCapsule
- use_sequence_bias(*args, **kwargs)
Overloaded function.
1. use_sequence_bias(rosetta.protocols.forge.components.BDR) -> bool
use sequence biased fragments when building the loop? (default false)
2. use_sequence_bias(self : rosetta.protocols.forge.components.BDR, flag : bool) -> NoneType
use sequence biased fragments when building the loop? (default false)
Methods inherited from rosetta.protocols.moves.Mover:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.moves.Mover, other : rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- 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 VarLengthBuild(rosetta.protocols.moves.Mover) |
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Component that performs a protocol for user-specified variable length
remodeling of protein backbone segments.
This bootstrap implementation performs centroid level loop building
using 9,3,1-mer fragments and running a LoopMover with the Remodel 'remodel_cen'
score function. The default loop mover is the forge RemodelLoopMover.
It does not yet handle extensions or continuous replacements.
This class is under heavy development, expect many changes to both API and
internals.
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- Method resolution order:
- VarLengthBuild
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, manager : rosetta.protocols.forge.build.BuildManager) -> NoneType
3. __init__(self : handle, manager : rosetta.protocols.forge.build.BuildManager, remodel_data : rosetta.protocols.forge.remodel.RemodelData) -> NoneType
4. __init__(handle, rosetta.protocols.forge.components.VarLengthBuild) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_rcg(...) from builtins.PyCapsule
- add_rcg(self : rosetta.protocols.forge.components.VarLengthBuild, rcg : protocols::forge::remodel::RemodelConstraintGenerator) -> NoneType
- add_setup_mover(...) from builtins.PyCapsule
- add_setup_mover(self : rosetta.protocols.forge.components.VarLengthBuild, mover_in : rosetta.protocols.moves.Mover) -> NoneType
- add_user_provided_mover(...) from builtins.PyCapsule
- add_user_provided_mover(self : rosetta.protocols.forge.components.VarLengthBuild, mover_in : rosetta.protocols.moves.Mover) -> NoneType
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.forge.components.VarLengthBuild, pose : rosetta.core.pose.Pose) -> NoneType
run protocol on given Pose
if procedure successful, return Pose with modifications and a
sealed fold tree, otherwise return Pose with modifications and the
in-progress cut fold tree
Before invoking this function it's best to make sure
the secondary structure in the Pose is marked via the method
that you would prefer, e.g. by Dssp (protocols::jumping::Dssp),
by the old Rosetta++ binning method (core::pose::set_ss_from_phipsi)
or by external method such as reading in a file.
- cache_fragments(...) from builtins.PyCapsule
- cache_fragments(*args, **kwargs)
Overloaded function.
1. cache_fragments(rosetta.protocols.forge.components.VarLengthBuild) -> bool
cache fragments after picking? (default true)
If true, will cache fragments and reuse them upon each
apply() call instead of repicking every time.
2. cache_fragments(self : rosetta.protocols.forge.components.VarLengthBuild, flag : bool) -> NoneType
cache fragments after picking?
If true, will cache fragments and reuse them upon each
apply() call instead of repicking every time.
- clear_fragments(...) from builtins.PyCapsule
- clear_fragments(rosetta.protocols.forge.components.VarLengthBuild) -> NoneType
clear any currently cached fragments
- clear_rcgs(...) from builtins.PyCapsule
- clear_rcgs(rosetta.protocols.forge.components.VarLengthBuild) -> NoneType
- clear_setup_movers(...) from builtins.PyCapsule
- clear_setup_movers(rosetta.protocols.forge.components.VarLengthBuild) -> NoneType
- clear_user_provided_movers(...) from builtins.PyCapsule
- clear_user_provided_movers(rosetta.protocols.forge.components.VarLengthBuild) -> NoneType
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.forge.components.VarLengthBuild) -> rosetta.protocols.moves.Mover
clone this object
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.forge.components.VarLengthBuild) -> rosetta.protocols.moves.Mover
create a new instance of this type of object
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.forge.components.VarLengthBuild) -> str
- ignore_cmdline_enzdes_cstfile(...) from builtins.PyCapsule
- ignore_cmdline_enzdes_cstfile(self : rosetta.protocols.forge.components.VarLengthBuild, flag : bool) -> NoneType
- loop_mover_fold_tree_constant(...) from builtins.PyCapsule
- loop_mover_fold_tree_constant(self : rosetta.protocols.forge.components.VarLengthBuild, flag : bool) -> NoneType
- loop_mover_str(...) from builtins.PyCapsule
- loop_mover_str(*args, **kwargs)
Overloaded function.
1. loop_mover_str(rosetta.protocols.forge.components.VarLengthBuild) -> str
the string id of the loop mover to use
(default "RemodelLoopMover")
"RemodelLoopMover" for the forge RemodelLoopMover, otherwise a
string recognized by create_loop_mover() in the "LoopMoverFactory".
2. loop_mover_str(self : rosetta.protocols.forge.components.VarLengthBuild, str : str) -> NoneType
set the loop mover to use via string
use "RemodelLoopMover" for the forge RemodelLoopMover,
otherwise set it to a string recognized by
create_loop_mover() in the "LoopMoverFactory".
- manager(...) from builtins.PyCapsule
- manager(*args, **kwargs)
Overloaded function.
1. manager(rosetta.protocols.forge.components.VarLengthBuild) -> rosetta.protocols.forge.build.BuildManager
build manager
2. manager(self : rosetta.protocols.forge.components.VarLengthBuild, manager : rosetta.protocols.forge.build.BuildManager) -> NoneType
set build manager; also clears any cached fragments
- max_linear_chainbreak(...) from builtins.PyCapsule
- max_linear_chainbreak(*args, **kwargs)
Overloaded function.
1. max_linear_chainbreak(rosetta.protocols.forge.components.VarLengthBuild) -> float
return the highest linear chainbreak score a chainbreak can have
and still be considered closed
default 0.07
2. max_linear_chainbreak(self : rosetta.protocols.forge.components.VarLengthBuild, tol : float) -> NoneType
set the highest linear chainbreak score a chainbreak can have
and still be considered closed
- new_secondary_structure_override(...) from builtins.PyCapsule
- new_secondary_structure_override(*args, **kwargs)
Overloaded function.
1. new_secondary_structure_override(rosetta.protocols.forge.components.VarLengthBuild) -> str
full sequence string with length corresponding to the *new*
modified pose used to pick secondary structure biased fragments.
IMPORTANT: This is an override! If this string is filled,
it will be used as the string to pick secondary structure biased
fragments without modification. All secondary structure settings
that might be taken from the original Pose or from the BuildInstructions
*will be ignored*. The length of this string must be equal to the
length of the *NEW* modified pose, otherwise the protocol will stop
with error -- you can use BuildManager::dummy_modify() to help
figure things out.
2. new_secondary_structure_override(self : rosetta.protocols.forge.components.VarLengthBuild, str : str) -> NoneType
full sequence string with length corresponding to the *new*
modified pose used to pick secondary structure biased fragments.
String with length equals to the *new* modified pose.
See remarks for help on how to determine this. String is allowed
to be empty, in which case it will clear the setting.
IMPORTANT: This is an override! If this string is filled,
it will be used as the string to pick secondary structure biased
fragments without modification. All secondary structure settings
that might be taken from the original Pose or from the BuildInstructions
*will be ignored*. The length of this string must be equal to the
length of the *NEW* modified pose, otherwise the protocol will stop
with error -- you can use BuildManager::dummy_modify() to help
figure things out.
- new_sequence_override(...) from builtins.PyCapsule
- new_sequence_override(*args, **kwargs)
Overloaded function.
1. new_sequence_override(rosetta.protocols.forge.components.VarLengthBuild) -> str
full amino acid string with length corresponding to the *new*
modified pose used to pick sequence biased fragments.
IMPORTANT: This is an override! If this string is filled,
it will be used as the string to pick sequence biased
fragments without modification. All sequence settings
that might be taken from the original Pose or from the BuildInstructions
*will be ignored*. The length of this string must be equal to the
length of the *NEW* modified pose, otherwise the protocol will stop
with error -- you can use BuildManager::dummy_modify() to help
figure things out.
2. new_sequence_override(self : rosetta.protocols.forge.components.VarLengthBuild, str : str) -> NoneType
full amino acid string with length corresponding to the *new*
modified pose used to pick sequence biased fragments.
String with length equals to the *new* modified pose.
See remarks for help on how to determine this. String is allowed
to be empty, in which case it will clear the setting.
IMPORTANT: This is an override! If this string is filled,
it will be used as the string to pick sequence biased
fragments without modification. All sequence settings
that might be taken from the original Pose or from the BuildInstructions
*will be ignored*. The length of this string must be equal to the
length of the *NEW* modified pose, otherwise the protocol will stop
with error -- you can use BuildManager::dummy_modify() to help
figure things out.
- num_fragpick(...) from builtins.PyCapsule
- num_fragpick(*args, **kwargs)
Overloaded function.
1. num_fragpick(rosetta.protocols.forge.components.VarLengthBuild) -> int
the number of fragments to pick at each position
(default 200)
2. num_fragpick(self : rosetta.protocols.forge.components.VarLengthBuild, num : int) -> NoneType
the number of fragments to pick at each position (default 200)
- original_sequence(...) from builtins.PyCapsule
- original_sequence(*args, **kwargs)
Overloaded function.
1. original_sequence(rosetta.protocols.forge.components.VarLengthBuild) -> str
full sequence string corresponding to original input pose
used to pick sequence biased fragments; if empty, sequence bias
is not used when picking fragments
2. original_sequence(self : rosetta.protocols.forge.components.VarLengthBuild, seq : str) -> NoneType
full sequence string corresponding to original input pose
used to pick sequence biased fragments; if empty, sequence bias
is not used when picking fragments
- recover_original_on_failure(...) from builtins.PyCapsule
- recover_original_on_failure(*args, **kwargs)
Overloaded function.
1. recover_original_on_failure(rosetta.protocols.forge.components.VarLengthBuild) -> bool
at the end of apply(), reset the Pose to the original Pose if
mover was not successful? (default true)
2. recover_original_on_failure(self : rosetta.protocols.forge.components.VarLengthBuild, flag : bool) -> NoneType
at the end of apply(), reset the Pose to the original Pose if
mover was not successful?
- restart_mode(...) from builtins.PyCapsule
- restart_mode(*args, **kwargs)
Overloaded function.
1. restart_mode(rosetta.protocols.forge.components.VarLengthBuild) -> bool
Flag to turn on restart mode, in which VLB assumes that the Pose
fed to it during apply() has already been modified by the manager.
(default False)
In restart mode, VLB only runs the manager's dummy modify
capability during apply() to get the mapping info.
2. restart_mode(self : rosetta.protocols.forge.components.VarLengthBuild, flag : bool) -> NoneType
Flag to turn on restart mode, in which VLB assumes that the Pose
fed to it during apply() has already been modified by the manager.
(default False)
In restart mode, VLB only runs the manager's dummy modify
capability during apply() to get the mapping info.
- scorefunction(...) from builtins.PyCapsule
- scorefunction(*args, **kwargs)
Overloaded function.
1. scorefunction(self : rosetta.protocols.forge.components.VarLengthBuild, sfx : rosetta.core.scoring.ScoreFunction) -> NoneType
set ScoreFunction used during build
2. scorefunction(self : rosetta.protocols.forge.components.VarLengthBuild, sfx : rosetta.core.scoring.ScoreFunction) -> NoneType
set ScoreFunction used during build
- set_abego(...) from builtins.PyCapsule
- set_abego(self : rosetta.protocols.forge.components.VarLengthBuild, abego : rosetta.utility.vector1_std_string) -> NoneType
set abego definition for fragments
- use_fullmer(...) from builtins.PyCapsule
- use_fullmer(*args, **kwargs)
Overloaded function.
1. use_fullmer(rosetta.protocols.forge.components.VarLengthBuild) -> bool
also use fragments spanning the entire length of a loop?
(default false)
2. use_fullmer(self : rosetta.protocols.forge.components.VarLengthBuild, flag : bool) -> NoneType
also use fragments spanning the entire length of a loop?
- vall_memory_usage(...) from builtins.PyCapsule
- vall_memory_usage(*args, **kwargs)
Overloaded function.
1. vall_memory_usage(rosetta.protocols.forge.components.VarLengthBuild) -> rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum
option dictating whether to keep VallLibrary in memory or clear
it under certain circumstances after picking fragments.
(default KEEP_IN_MEMORY)
2. vall_memory_usage(self : rosetta.protocols.forge.components.VarLengthBuild, level : rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum) -> NoneType
option dictating whether to keep VallLibrary in memory or clear
it under certain circumstances after picking fragments.
Methods inherited from rosetta.protocols.moves.Mover:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.moves.Mover, other : rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- 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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