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- rosetta.protocols.moves.Mover(builtins.object)
-
- CDRDihedralConstraintMover
- ParatopeEpitopeSiteConstraintMover
- ParatopeSiteConstraintMover
- rosetta.protocols.moves.MoverCreator(builtins.object)
-
- CDRDihedralConstraintMoverCreator
- ParatopeEpitopeSiteConstraintMoverCreator
- ParatopeSiteConstraintMoverCreator
class CDRDihedralConstraintMover(rosetta.protocols.moves.Mover) |
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Add Cluster or General Dihedral CircularHarmonic constraints to a CDR.
Cluster constraints currently only work for AHO renumbered CDRs.
(This will be rafactored to create constraints on-the-fly from cluster Mean/SD instead of from cst files.)
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- Method resolution order:
- CDRDihedralConstraintMover
- 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, ab_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType
3. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType
4. __init__(handle, rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover) -> 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.antibody.constraints.CDRDihedralConstraintMover, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, : rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover) -> rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover) -> rosetta.protocols.moves.Mover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover) -> str
- set_cdr(...) from builtins.PyCapsule
- set_cdr(self : rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, cdr : rosetta.protocols.antibody.CDRNameEnum) -> NoneType
- set_cluster_csts_data_cutoff(...) from builtins.PyCapsule
- set_cluster_csts_data_cutoff(self : rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, cutoff : int) -> NoneType
- set_cluster_csts_use_mean_cst_data(...) from builtins.PyCapsule
- set_cluster_csts_use_mean_cst_data(self : rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, use_mean_cst_data : bool) -> NoneType
Use constraints which have the means as the actual cluster means.
Setting this to false will use constraints that have the cst means set as cluster center data.
- set_cluster_csts_use_outlier_data(...) from builtins.PyCapsule
- set_cluster_csts_use_outlier_data(self : rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, use_outlier_data : bool) -> NoneType
- set_force_cluster(...) from builtins.PyCapsule
- set_force_cluster(self : rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, cluster : rosetta.protocols.antibody.clusters.CDRClusterEnum) -> NoneType
Do not use AntibodyInfo to for cluster - use this cluster instead
- set_general_phi_sd(...) from builtins.PyCapsule
- set_general_phi_sd(self : rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, phi_sd : float) -> NoneType
- set_general_psi_sd(...) from builtins.PyCapsule
- set_general_psi_sd(self : rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, psi_sd : float) -> NoneType
- set_ignore_pose_datacache(...) from builtins.PyCapsule
- set_ignore_pose_datacache(self : rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, ignore_pose_datacache : bool) -> NoneType
By default, if cluster information is present in the datacache, we attempt to use that first.
Override this behavior by setting this option to true.
- set_remove_any_set_forced_cluster(...) from builtins.PyCapsule
- set_remove_any_set_forced_cluster(rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover) -> NoneType
Remove any forced cluster settings.
- set_use_cluster_csts(...) from builtins.PyCapsule
- set_use_cluster_csts(self : rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, use_cluster_csts : bool) -> NoneType
Attempt to add cluster-based dihedral constraints. If this is set to false will simply add General Dihedral constraints instead.
Default True
- set_use_cluster_for_H3(...) from builtins.PyCapsule
- set_use_cluster_for_H3(self : rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, use_cluster_for_H3 : bool) -> NoneType
Set to use H3 cluster data for constraints if we are doing cluster-based constraints.
Default False - H3 does not cluster well. If use_general_data_on_failure is false, we will skip H3.
- set_use_general_csts_on_cluster_failure(...) from builtins.PyCapsule
- set_use_general_csts_on_cluster_failure(self : rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover, use_general_csts_on_failure : bool) -> NoneType
If we are set to use cluster csts and:
1) the cluster is NA,
2) there is sparse data for the cluster, or
3) The CDR is H3 and we have chosen not to use cluster data for H3 (default),
THEN add general dihedral constraints instead.
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 ParatopeEpitopeSiteConstraintMover(rosetta.protocols.moves.Mover) |
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Add SiteConstraints from the Epitope to the Paratope and from the Paratope to the Epitope.
Will only add the constraint if not already present.
If no paratope interface residues are given, detects the epitope at 10 A from antibody chain(s).
Optionally constrain to paratope CDRs or a specific set of paratope residues.
Uses a Linear Harmonic at 0, 1, 10 by default. Which means epitope will have penalty at greater than 10 A.
Linear Harmonic distance tolerance (last number) is set at the interface distance.
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- Method resolution order:
- ParatopeEpitopeSiteConstraintMover
- 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, ab_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType
3. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo, paratope_cdrs : rosetta.utility.vector1_protocols_antibody_CDRNameEnum) -> NoneType
4. __init__(self : handle, ab_info : rosetta.protocols.antibody.AntibodyInfo, paratope_cdrs : rosetta.utility.vector1_protocols_antibody_CDRNameEnum, epitope_residues : rosetta.utility.vector1_bool) -> NoneType
5. __init__(handle, rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover) -> 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.antibody.constraints.ParatopeEpitopeSiteConstraintMover, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, : rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover) -> rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover
- constrain_to_epitope_residues(...) from builtins.PyCapsule
- constrain_to_epitope_residues(*args, **kwargs)
Overloaded function.
1. constrain_to_epitope_residues(self : rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, epitope_residues : rosetta.utility.vector1_protocols_antibody_design_PDBNumbering, pose : rosetta.core.pose.Pose) -> NoneType
Manually set the epitope residues via PDB Numbering
2. constrain_to_epitope_residues(self : rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, epitope_residues : rosetta.utility.vector1_bool) -> NoneType
Manually set the epitope residues via pose Numbering
- constrain_to_paratope_cdrs(...) from builtins.PyCapsule
- constrain_to_paratope_cdrs(*args, **kwargs)
Overloaded function.
1. constrain_to_paratope_cdrs(self : rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, paratope_cdrs : rosetta.utility.vector1_protocols_antibody_CDRNameEnum) -> NoneType
2. constrain_to_paratope_cdrs(self : rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, paratope_cdrs : rosetta.utility.vector1_bool) -> NoneType
- constrain_to_paratope_residues(...) from builtins.PyCapsule
- constrain_to_paratope_residues(self : rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, paratope_residues : rosetta.utility.vector1_bool) -> NoneType
- get_epitope_residues(...) from builtins.PyCapsule
- get_epitope_residues(rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover) -> rosetta.utility.vector1_bool
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover) -> str
- remove(...) from builtins.PyCapsule
- remove(self : rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, pose : rosetta.core.pose.Pose) -> NoneType
- set_constraint_func(...) from builtins.PyCapsule
- set_constraint_func(self : rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, constraint_func : rosetta.core.scoring.func.Func) -> NoneType
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover) -> NoneType
- set_interface_distance(...) from builtins.PyCapsule
- set_interface_distance(self : rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover, distance : float) -> NoneType
The interface distance for antigen epitope auto-detection and the distance at which the default
at which the default flat-harmonic constraint will give a penalty. 10A default.
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
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class ParatopeSiteConstraintMover(rosetta.protocols.moves.Mover) |
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Adds and removes ambiguous site constraints for the Antibody Paratope to antigen,
defined for simplicity as the CDRs, however a set of paratope residues can be given to the class to use instead.
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- Method resolution order:
- ParatopeSiteConstraintMover
- 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, ab_info : rosetta.protocols.antibody.AntibodyInfo) -> NoneType
3. __init__(handle, rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover) -> 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.antibody.constraints.ParatopeSiteConstraintMover, pose : rosetta.core.pose.Pose) -> NoneType
Add AmbiguousSiteConstraints to specified paratope residues, or each CDR set. Default is all of them.
If there are already exits AmbiguousSiteConstraints from the antigen to the residue, add them.
If they are missing, such as after a graft, add them.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, : rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover) -> rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover
- constrain_to_antigen_chains(...) from builtins.PyCapsule
- constrain_to_antigen_chains(self : rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, antigen_chains : rosetta.utility.vector1_unsigned_long) -> NoneType
Optionally constrain to a set of antigen chains instead of all of them
- constrain_to_paratope_cdrs(...) from builtins.PyCapsule
- constrain_to_paratope_cdrs(*args, **kwargs)
Overloaded function.
1. constrain_to_paratope_cdrs(self : rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, paratope_cdrs : rosetta.utility.vector1_protocols_antibody_CDRNameEnum) -> NoneType
Optionally use only these CDRs as the paratope. Useful for constraining to Light or Heavy chain CDRs
2. constrain_to_paratope_cdrs(self : rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, paratope_cdrs : rosetta.utility.vector1_bool) -> NoneType
- constrain_to_paratope_residues(...) from builtins.PyCapsule
- constrain_to_paratope_residues(self : rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, paratope_residues : rosetta.utility.vector1_bool) -> NoneType
Optionally constrain to a set of pre-determined paratope residues
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover) -> str
- remove(...) from builtins.PyCapsule
- remove(*args, **kwargs)
Overloaded function.
1. remove(self : rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, pose : rosetta.core.pose.Pose) -> NoneType
Remove constraints from each paratope residue and antigen chain set. If reset_paratope_residues is true, then it will update the
set of paratope residues it has. This is used after pose length changes such as CDR insertion or deletion.
2. remove(self : rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, pose : rosetta.core.pose.Pose, reset_paratope_residues : bool) -> NoneType
Remove constraints from each paratope residue and antigen chain set. If reset_paratope_residues is true, then it will update the
set of paratope residues it has. This is used after pose length changes such as CDR insertion or deletion.
- set_constraint_func(...) from builtins.PyCapsule
- set_constraint_func(self : rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, constraint_func : rosetta.core.scoring.func.Func) -> NoneType
Optionally set the Func that will be used for the constraint. Default is the Flat_Harmonic at 0, 1, 5
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover) -> NoneType
- set_interface_distance(...) from builtins.PyCapsule
- set_interface_distance(self : rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover, interface_distance : float) -> NoneType
Set the interface distance that will be only be used as the tolerance for the linear harmonic constraint
if no constraint func is 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
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
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