Bindings for protocols::cluster namespace

Classes
		builtins.object APCluster Cluster DataPoint Exemplar rosetta.protocols.moves.Mover(builtins.object) GatherPosesMover AssignToClustersMover ClusterBase ClusterPhilStyle ClusterPhilStyle_Loop ClusterPhilStyle_PoseReporter EnsembleConstraints EnsembleConstraints_Simple   class APCluster(builtins.object)     Public interface for doing affinity propagation clustering.     Based on Frey and Dueck, "Clustering by Passing Messages Between Data Points", Science 315 (2007). Useful for choosing a set of representative data points (exemplars) out of a large set (e.g. all decoys from a large Rosetta run) given a measure of similarity (e.g. RMSD, maxsub, GDT, ...).   As I understand it, this procedures tries to maximize the sum of similarities between each data point and its exemplar, while balancing that with total number of clusters. Reasonable measures of similarity would be negative RMSD, log-likelihoods, or squared distance (i.e. squared error), depending on what the points represent. Note there is no requirement for symmetry:  s(i,j) need not equal s(j,i). The self-similarity s(k,k) ("preference") for each point controls the likelihood it will be selected as an exemplar, and thus indirectly controls the total number of clusters. There is no way to directly specify a specific number of clusters. The authors suggest that using the median of all other similarities will give a moderate number of clusters, and using the minimum of the other similaries will give a small number of clusters.   This implementation is designed for clustering very large numbers of data points with sparse similarity [ s(i,k) = -Inf for most i,k ]. Similarities for each input point are kept in a heap so that you can limit to only the L highest for each. (This scheme is quite likely to break symmetry, as some points will have more close neighbors than others.) Alternately, you may choose to do your own pre-filtering and only enter the G globally highest similarities between any points in the data set. Run time (per cycle) is linear in the number of similarities, or O(N^2) in the limit of a dense similarity matrix.   I follow the conventions of the original paper, where "i" is the index of some generic data point, and "k" is the index of a data point being considered as an exemplar (cluster center).     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, int) -> NoneType   doc   2. __init__(self : handle, total_pts : int, max_sims_per_pt : int) -> 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.cluster.APCluster,  : rosetta.protocols.cluster.APCluster) -> rosetta.protocols.cluster.APCluster cluster(...) from builtins.PyCapsule cluster(self : rosetta.protocols.cluster.APCluster, maxits : int, convits : int, lambda : float) -> bool   Run the actual clustering algorithm. get_all_exemplars(...) from builtins.PyCapsule get_all_exemplars(self : rosetta.protocols.cluster.APCluster, exemplars : rosetta.utility.vector1_unsigned_long) -> NoneType   Return the indices of data points chosen as exemplars (cluster centers). get_cluster_for(...) from builtins.PyCapsule get_cluster_for(self : rosetta.protocols.cluster.APCluster, k : int, cluster : rosetta.utility.vector1_unsigned_long) -> NoneType   Returns the indices of points with the specified exemplar k.  Note that k is the index of an (input) data point that was chosen as an exemplar,  not some "cluster index" between 1 and get_num_exemplars(). get_exemplar_for(...) from builtins.PyCapsule get_exemplar_for(self : rosetta.protocols.cluster.APCluster, i : int) -> int   Return the index of the point that is the exemplar for point i. get_net_sim(...) from builtins.PyCapsule get_net_sim(rosetta.protocols.cluster.APCluster) -> float   The sum of similarities s(i,k) between every data point i and its exemplar k,  plus the self preferences of the exemplars.  The algorithm *should* minimize this value -- if it dips and climbs again, increase lambda. get_num_exemplars(...) from builtins.PyCapsule get_num_exemplars(rosetta.protocols.cluster.APCluster) -> int   The number of exemplars selected (number of clusters).  Monotonically related to the self-preferences s(k,k). load_binary(...) from builtins.PyCapsule load_binary(self : rosetta.protocols.cluster.APCluster, filename : str) -> bool   Wipes all currently held data and reads in similarity values and cluster assignments.  Afterwards, points may be re-clustered with different parameters if desired.  File format is custom binary and is not portable (host endian-ness). num_pts(...) from builtins.PyCapsule num_pts(rosetta.protocols.cluster.APCluster) -> int save_binary(...) from builtins.PyCapsule save_binary(self : rosetta.protocols.cluster.APCluster, filename : str) -> bool   Saves the (sparse) similarity matrix and current cluster assignments (if any),  but not the accumulated evidence from the last clustering [ r(i,k) and a(i,k) ].  File format is custom binary and is not portable (host endian-ness). set_sim(...) from builtins.PyCapsule set_sim(self : rosetta.protocols.cluster.APCluster, i : int, k : int, sim : float) -> NoneType   How appropriate is k as an exemplar for i?   class AssignToClustersMover(GatherPosesMover)       Method resolution order: AssignToClustersMover GatherPosesMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, cluster_base : rosetta.protocols.cluster.ClusterBase) -> NoneType   2. __init__(handle, rosetta.protocols.cluster.AssignToClustersMover) -> 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.cluster.AssignToClustersMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.cluster.AssignToClustersMover,  : rosetta.protocols.cluster.AssignToClustersMover) -> rosetta.protocols.cluster.AssignToClustersMover clone(...) from builtins.PyCapsule clone(rosetta.protocols.cluster.AssignToClustersMover) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.cluster.AssignToClustersMover) -> str Methods inherited from GatherPosesMover: check_tag(...) from builtins.PyCapsule check_tag(self : rosetta.protocols.cluster.GatherPosesMover, query_tag : str) -> bool clear(...) from builtins.PyCapsule clear(rosetta.protocols.cluster.GatherPosesMover) -> NoneType get_distance_measure(...) from builtins.PyCapsule get_distance_measure(self : rosetta.protocols.cluster.GatherPosesMover, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> float get_filter(...) from builtins.PyCapsule get_filter(rosetta.protocols.cluster.GatherPosesMover) -> float get_pose_list(...) from builtins.PyCapsule get_pose_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_core_pose_Pose get_tag_list(...) from builtins.PyCapsule get_tag_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_std_string nposes(...) from builtins.PyCapsule nposes(rosetta.protocols.cluster.GatherPosesMover) -> int   Return the number of poses gathered by this mover  This is the post-filtered number of poses. push_back(...) from builtins.PyCapsule push_back(self : rosetta.protocols.cluster.GatherPosesMover, pose : rosetta.core.pose.Pose) -> NoneType set_cluster_by_all_atom(...) from builtins.PyCapsule set_cluster_by_all_atom(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_cluster_by_protein_backbone(...) from builtins.PyCapsule set_cluster_by_protein_backbone(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_filter(...) from builtins.PyCapsule set_filter(self : rosetta.protocols.cluster.GatherPosesMover, filter : float) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.protocols.cluster.GatherPosesMover, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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   class Cluster(builtins.object)       Methods defined here: __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.protocols.cluster.Cluster, index : int) -> int   2. __getitem__(self : rosetta.protocols.cluster.Cluster, index : int) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.cluster.Cluster) -> NoneType   2. __init__(self : rosetta.protocols.cluster.Cluster, new_cluster_center : int) -> NoneType   3. __init__(self : rosetta.protocols.cluster.Cluster,  : rosetta.protocols.cluster.Cluster) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_member(...) from builtins.PyCapsule add_member(self : rosetta.protocols.cluster.Cluster, new_member : int) -> NoneType add_member_front(...) from builtins.PyCapsule add_member_front(self : rosetta.protocols.cluster.Cluster, new_member : int) -> NoneType clear(...) from builtins.PyCapsule clear(rosetta.protocols.cluster.Cluster) -> NoneType erase(...) from builtins.PyCapsule erase(self : rosetta.protocols.cluster.Cluster, j : int) -> NoneType get_cluster_center(...) from builtins.PyCapsule get_cluster_center(rosetta.protocols.cluster.Cluster) -> int group_size(...) from builtins.PyCapsule group_size(rosetta.protocols.cluster.Cluster) -> int push_back(...) from builtins.PyCapsule push_back(self : rosetta.protocols.cluster.Cluster, new_member : int) -> NoneType push_front(...) from builtins.PyCapsule push_front(self : rosetta.protocols.cluster.Cluster, new_member : int) -> NoneType remove_member(...) from builtins.PyCapsule remove_member(self : rosetta.protocols.cluster.Cluster, old_member : int) -> NoneType shuffle(...) from builtins.PyCapsule shuffle(rosetta.protocols.cluster.Cluster) -> NoneType size(...) from builtins.PyCapsule size(rosetta.protocols.cluster.Cluster) -> int Data descriptors defined here: cluster_center_ group_size_ member   class ClusterBase(GatherPosesMover)       Method resolution order: ClusterBase GatherPosesMover 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.cluster.ClusterBase) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_structure(...) from builtins.PyCapsule add_structure(self : rosetta.protocols.cluster.ClusterBase, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.cluster.ClusterBase,  : rosetta.protocols.cluster.ClusterBase) -> rosetta.protocols.cluster.ClusterBase calculate_distance_matrix(...) from builtins.PyCapsule calculate_distance_matrix(rosetta.protocols.cluster.ClusterBase) -> NoneType clean_pose_store(...) from builtins.PyCapsule clean_pose_store(rosetta.protocols.cluster.ClusterBase) -> NoneType create_constraints(...) from builtins.PyCapsule create_constraints(self : rosetta.protocols.cluster.ClusterBase, prefix : str, constraint_maker : rosetta.protocols.cluster.EnsembleConstraints) -> NoneType export_only_low(...) from builtins.PyCapsule export_only_low(*args, **kwargs) Overloaded function.   1. export_only_low(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. export_only_low(self : rosetta.protocols.cluster.ClusterBase, value : bool) -> NoneType get_cluster_list(...) from builtins.PyCapsule get_cluster_list(rosetta.protocols.cluster.ClusterBase) -> rosetta.std.vector_protocols_cluster_Cluster get_cluster_radius(...) from builtins.PyCapsule get_cluster_radius(rosetta.protocols.cluster.ClusterBase) -> float get_median_rms(...) from builtins.PyCapsule get_median_rms(rosetta.protocols.cluster.ClusterBase) -> float get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.cluster.ClusterBase) -> str limit_groups(...) from builtins.PyCapsule limit_groups(*args, **kwargs) Overloaded function.   1. limit_groups(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. limit_groups(self : rosetta.protocols.cluster.ClusterBase, limit : int) -> NoneType limit_groupsize(...) from builtins.PyCapsule limit_groupsize(*args, **kwargs) Overloaded function.   1. limit_groupsize(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. limit_groupsize(self : rosetta.protocols.cluster.ClusterBase, limit : int) -> NoneType   3. limit_groupsize(self : rosetta.protocols.cluster.ClusterBase, percent_limit : float) -> NoneType limit_total_structures(...) from builtins.PyCapsule limit_total_structures(*args, **kwargs) Overloaded function.   1. limit_total_structures(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. limit_total_structures(self : rosetta.protocols.cluster.ClusterBase, limit : int) -> NoneType print_cluster_PDBs(...) from builtins.PyCapsule print_cluster_PDBs(self : rosetta.protocols.cluster.ClusterBase, prefix : str) -> NoneType print_cluster_assignment(...) from builtins.PyCapsule print_cluster_assignment(rosetta.protocols.cluster.ClusterBase) -> NoneType print_clusters_silentfile(...) from builtins.PyCapsule print_clusters_silentfile(self : rosetta.protocols.cluster.ClusterBase, prefix : str) -> NoneType print_raw_numbers(...) from builtins.PyCapsule print_raw_numbers(rosetta.protocols.cluster.ClusterBase) -> NoneType print_summary(...) from builtins.PyCapsule print_summary(rosetta.protocols.cluster.ClusterBase) -> NoneType random_limit_groupsize(...) from builtins.PyCapsule random_limit_groupsize(self : rosetta.protocols.cluster.ClusterBase, percent_limit : float) -> NoneType remove_highest_energy_member_of_each_group(...) from builtins.PyCapsule remove_highest_energy_member_of_each_group(rosetta.protocols.cluster.ClusterBase) -> NoneType remove_singletons(...) from builtins.PyCapsule remove_singletons(rosetta.protocols.cluster.ClusterBase) -> NoneType return_lowest_poses_in_clusters(...) from builtins.PyCapsule return_lowest_poses_in_clusters(rosetta.protocols.cluster.ClusterBase) -> rosetta.std.vector_std_shared_ptr_core_pose_Pose_t return_top_poses_in_clusters(...) from builtins.PyCapsule return_top_poses_in_clusters(self : rosetta.protocols.cluster.ClusterBase, count : int) -> rosetta.std.vector_std_shared_ptr_core_pose_Pose_t set_cluster_radius(...) from builtins.PyCapsule set_cluster_radius(self : rosetta.protocols.cluster.ClusterBase, cluster_radius : float) -> NoneType set_population_weight(...) from builtins.PyCapsule set_population_weight(self : rosetta.protocols.cluster.ClusterBase, population_weight : float) -> NoneType sort_each_group_by_energy(...) from builtins.PyCapsule sort_each_group_by_energy(rosetta.protocols.cluster.ClusterBase) -> NoneType sort_groups_by_energy(...) from builtins.PyCapsule sort_groups_by_energy(rosetta.protocols.cluster.ClusterBase) -> NoneType Methods inherited from GatherPosesMover: apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.cluster.GatherPosesMover, pose : rosetta.core.pose.Pose) -> NoneType check_tag(...) from builtins.PyCapsule check_tag(self : rosetta.protocols.cluster.GatherPosesMover, query_tag : str) -> bool clear(...) from builtins.PyCapsule clear(rosetta.protocols.cluster.GatherPosesMover) -> NoneType get_distance_measure(...) from builtins.PyCapsule get_distance_measure(self : rosetta.protocols.cluster.GatherPosesMover, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> float get_filter(...) from builtins.PyCapsule get_filter(rosetta.protocols.cluster.GatherPosesMover) -> float get_pose_list(...) from builtins.PyCapsule get_pose_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_core_pose_Pose get_tag_list(...) from builtins.PyCapsule get_tag_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_std_string nposes(...) from builtins.PyCapsule nposes(rosetta.protocols.cluster.GatherPosesMover) -> int   Return the number of poses gathered by this mover  This is the post-filtered number of poses. push_back(...) from builtins.PyCapsule push_back(self : rosetta.protocols.cluster.GatherPosesMover, pose : rosetta.core.pose.Pose) -> NoneType set_cluster_by_all_atom(...) from builtins.PyCapsule set_cluster_by_all_atom(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_cluster_by_protein_backbone(...) from builtins.PyCapsule set_cluster_by_protein_backbone(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_filter(...) from builtins.PyCapsule set_filter(self : rosetta.protocols.cluster.GatherPosesMover, filter : float) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.protocols.cluster.GatherPosesMover, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class ClusterPhilStyle(ClusterBase)       Method resolution order: ClusterPhilStyle ClusterBase GatherPosesMover 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.cluster.ClusterPhilStyle) -> 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.cluster.ClusterPhilStyle,  : rosetta.protocols.cluster.ClusterPhilStyle) -> rosetta.protocols.cluster.ClusterPhilStyle clone(...) from builtins.PyCapsule clone(rosetta.protocols.cluster.ClusterPhilStyle) -> rosetta.protocols.moves.Mover do_clustering(...) from builtins.PyCapsule do_clustering(self : rosetta.protocols.cluster.ClusterPhilStyle, max_total_cluster : int) -> NoneType do_redistribution(...) from builtins.PyCapsule do_redistribution(rosetta.protocols.cluster.ClusterPhilStyle) -> NoneType get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.cluster.ClusterPhilStyle) -> str Methods inherited from ClusterBase: add_structure(...) from builtins.PyCapsule add_structure(self : rosetta.protocols.cluster.ClusterBase, pose : rosetta.core.pose.Pose) -> NoneType calculate_distance_matrix(...) from builtins.PyCapsule calculate_distance_matrix(rosetta.protocols.cluster.ClusterBase) -> NoneType clean_pose_store(...) from builtins.PyCapsule clean_pose_store(rosetta.protocols.cluster.ClusterBase) -> NoneType create_constraints(...) from builtins.PyCapsule create_constraints(self : rosetta.protocols.cluster.ClusterBase, prefix : str, constraint_maker : rosetta.protocols.cluster.EnsembleConstraints) -> NoneType export_only_low(...) from builtins.PyCapsule export_only_low(*args, **kwargs) Overloaded function.   1. export_only_low(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. export_only_low(self : rosetta.protocols.cluster.ClusterBase, value : bool) -> NoneType get_cluster_list(...) from builtins.PyCapsule get_cluster_list(rosetta.protocols.cluster.ClusterBase) -> rosetta.std.vector_protocols_cluster_Cluster get_cluster_radius(...) from builtins.PyCapsule get_cluster_radius(rosetta.protocols.cluster.ClusterBase) -> float get_median_rms(...) from builtins.PyCapsule get_median_rms(rosetta.protocols.cluster.ClusterBase) -> float limit_groups(...) from builtins.PyCapsule limit_groups(*args, **kwargs) Overloaded function.   1. limit_groups(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. limit_groups(self : rosetta.protocols.cluster.ClusterBase, limit : int) -> NoneType limit_groupsize(...) from builtins.PyCapsule limit_groupsize(*args, **kwargs) Overloaded function.   1. limit_groupsize(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. limit_groupsize(self : rosetta.protocols.cluster.ClusterBase, limit : int) -> NoneType   3. limit_groupsize(self : rosetta.protocols.cluster.ClusterBase, percent_limit : float) -> NoneType limit_total_structures(...) from builtins.PyCapsule limit_total_structures(*args, **kwargs) Overloaded function.   1. limit_total_structures(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. limit_total_structures(self : rosetta.protocols.cluster.ClusterBase, limit : int) -> NoneType print_cluster_PDBs(...) from builtins.PyCapsule print_cluster_PDBs(self : rosetta.protocols.cluster.ClusterBase, prefix : str) -> NoneType print_cluster_assignment(...) from builtins.PyCapsule print_cluster_assignment(rosetta.protocols.cluster.ClusterBase) -> NoneType print_clusters_silentfile(...) from builtins.PyCapsule print_clusters_silentfile(self : rosetta.protocols.cluster.ClusterBase, prefix : str) -> NoneType print_raw_numbers(...) from builtins.PyCapsule print_raw_numbers(rosetta.protocols.cluster.ClusterBase) -> NoneType print_summary(...) from builtins.PyCapsule print_summary(rosetta.protocols.cluster.ClusterBase) -> NoneType random_limit_groupsize(...) from builtins.PyCapsule random_limit_groupsize(self : rosetta.protocols.cluster.ClusterBase, percent_limit : float) -> NoneType remove_highest_energy_member_of_each_group(...) from builtins.PyCapsule remove_highest_energy_member_of_each_group(rosetta.protocols.cluster.ClusterBase) -> NoneType remove_singletons(...) from builtins.PyCapsule remove_singletons(rosetta.protocols.cluster.ClusterBase) -> NoneType return_lowest_poses_in_clusters(...) from builtins.PyCapsule return_lowest_poses_in_clusters(rosetta.protocols.cluster.ClusterBase) -> rosetta.std.vector_std_shared_ptr_core_pose_Pose_t return_top_poses_in_clusters(...) from builtins.PyCapsule return_top_poses_in_clusters(self : rosetta.protocols.cluster.ClusterBase, count : int) -> rosetta.std.vector_std_shared_ptr_core_pose_Pose_t set_cluster_radius(...) from builtins.PyCapsule set_cluster_radius(self : rosetta.protocols.cluster.ClusterBase, cluster_radius : float) -> NoneType set_population_weight(...) from builtins.PyCapsule set_population_weight(self : rosetta.protocols.cluster.ClusterBase, population_weight : float) -> NoneType sort_each_group_by_energy(...) from builtins.PyCapsule sort_each_group_by_energy(rosetta.protocols.cluster.ClusterBase) -> NoneType sort_groups_by_energy(...) from builtins.PyCapsule sort_groups_by_energy(rosetta.protocols.cluster.ClusterBase) -> NoneType Methods inherited from GatherPosesMover: apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.cluster.GatherPosesMover, pose : rosetta.core.pose.Pose) -> NoneType check_tag(...) from builtins.PyCapsule check_tag(self : rosetta.protocols.cluster.GatherPosesMover, query_tag : str) -> bool clear(...) from builtins.PyCapsule clear(rosetta.protocols.cluster.GatherPosesMover) -> NoneType get_distance_measure(...) from builtins.PyCapsule get_distance_measure(self : rosetta.protocols.cluster.GatherPosesMover, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> float get_filter(...) from builtins.PyCapsule get_filter(rosetta.protocols.cluster.GatherPosesMover) -> float get_pose_list(...) from builtins.PyCapsule get_pose_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_core_pose_Pose get_tag_list(...) from builtins.PyCapsule get_tag_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_std_string nposes(...) from builtins.PyCapsule nposes(rosetta.protocols.cluster.GatherPosesMover) -> int   Return the number of poses gathered by this mover  This is the post-filtered number of poses. push_back(...) from builtins.PyCapsule push_back(self : rosetta.protocols.cluster.GatherPosesMover, pose : rosetta.core.pose.Pose) -> NoneType set_cluster_by_all_atom(...) from builtins.PyCapsule set_cluster_by_all_atom(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_cluster_by_protein_backbone(...) from builtins.PyCapsule set_cluster_by_protein_backbone(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_filter(...) from builtins.PyCapsule set_filter(self : rosetta.protocols.cluster.GatherPosesMover, filter : float) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.protocols.cluster.GatherPosesMover, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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   class ClusterPhilStyle_Loop(ClusterPhilStyle)       Method resolution order: ClusterPhilStyle_Loop ClusterPhilStyle ClusterBase GatherPosesMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, loop_def : rosetta.protocols.loops.Loops) -> NoneType   2. __init__(handle, rosetta.protocols.cluster.ClusterPhilStyle_Loop) -> 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.cluster.ClusterPhilStyle_Loop,  : rosetta.protocols.cluster.ClusterPhilStyle_Loop) -> rosetta.protocols.cluster.ClusterPhilStyle_Loop clone(...) from builtins.PyCapsule clone(rosetta.protocols.cluster.ClusterPhilStyle_Loop) -> rosetta.protocols.moves.Mover get_distance_measure(...) from builtins.PyCapsule get_distance_measure(self : rosetta.protocols.cluster.ClusterPhilStyle_Loop, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> float get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.cluster.ClusterPhilStyle_Loop) -> str Methods inherited from ClusterPhilStyle: do_clustering(...) from builtins.PyCapsule do_clustering(self : rosetta.protocols.cluster.ClusterPhilStyle, max_total_cluster : int) -> NoneType do_redistribution(...) from builtins.PyCapsule do_redistribution(rosetta.protocols.cluster.ClusterPhilStyle) -> NoneType Methods inherited from ClusterBase: add_structure(...) from builtins.PyCapsule add_structure(self : rosetta.protocols.cluster.ClusterBase, pose : rosetta.core.pose.Pose) -> NoneType calculate_distance_matrix(...) from builtins.PyCapsule calculate_distance_matrix(rosetta.protocols.cluster.ClusterBase) -> NoneType clean_pose_store(...) from builtins.PyCapsule clean_pose_store(rosetta.protocols.cluster.ClusterBase) -> NoneType create_constraints(...) from builtins.PyCapsule create_constraints(self : rosetta.protocols.cluster.ClusterBase, prefix : str, constraint_maker : rosetta.protocols.cluster.EnsembleConstraints) -> NoneType export_only_low(...) from builtins.PyCapsule export_only_low(*args, **kwargs) Overloaded function.   1. export_only_low(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. export_only_low(self : rosetta.protocols.cluster.ClusterBase, value : bool) -> NoneType get_cluster_list(...) from builtins.PyCapsule get_cluster_list(rosetta.protocols.cluster.ClusterBase) -> rosetta.std.vector_protocols_cluster_Cluster get_cluster_radius(...) from builtins.PyCapsule get_cluster_radius(rosetta.protocols.cluster.ClusterBase) -> float get_median_rms(...) from builtins.PyCapsule get_median_rms(rosetta.protocols.cluster.ClusterBase) -> float limit_groups(...) from builtins.PyCapsule limit_groups(*args, **kwargs) Overloaded function.   1. limit_groups(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. limit_groups(self : rosetta.protocols.cluster.ClusterBase, limit : int) -> NoneType limit_groupsize(...) from builtins.PyCapsule limit_groupsize(*args, **kwargs) Overloaded function.   1. limit_groupsize(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. limit_groupsize(self : rosetta.protocols.cluster.ClusterBase, limit : int) -> NoneType   3. limit_groupsize(self : rosetta.protocols.cluster.ClusterBase, percent_limit : float) -> NoneType limit_total_structures(...) from builtins.PyCapsule limit_total_structures(*args, **kwargs) Overloaded function.   1. limit_total_structures(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. limit_total_structures(self : rosetta.protocols.cluster.ClusterBase, limit : int) -> NoneType print_cluster_PDBs(...) from builtins.PyCapsule print_cluster_PDBs(self : rosetta.protocols.cluster.ClusterBase, prefix : str) -> NoneType print_cluster_assignment(...) from builtins.PyCapsule print_cluster_assignment(rosetta.protocols.cluster.ClusterBase) -> NoneType print_clusters_silentfile(...) from builtins.PyCapsule print_clusters_silentfile(self : rosetta.protocols.cluster.ClusterBase, prefix : str) -> NoneType print_raw_numbers(...) from builtins.PyCapsule print_raw_numbers(rosetta.protocols.cluster.ClusterBase) -> NoneType print_summary(...) from builtins.PyCapsule print_summary(rosetta.protocols.cluster.ClusterBase) -> NoneType random_limit_groupsize(...) from builtins.PyCapsule random_limit_groupsize(self : rosetta.protocols.cluster.ClusterBase, percent_limit : float) -> NoneType remove_highest_energy_member_of_each_group(...) from builtins.PyCapsule remove_highest_energy_member_of_each_group(rosetta.protocols.cluster.ClusterBase) -> NoneType remove_singletons(...) from builtins.PyCapsule remove_singletons(rosetta.protocols.cluster.ClusterBase) -> NoneType return_lowest_poses_in_clusters(...) from builtins.PyCapsule return_lowest_poses_in_clusters(rosetta.protocols.cluster.ClusterBase) -> rosetta.std.vector_std_shared_ptr_core_pose_Pose_t return_top_poses_in_clusters(...) from builtins.PyCapsule return_top_poses_in_clusters(self : rosetta.protocols.cluster.ClusterBase, count : int) -> rosetta.std.vector_std_shared_ptr_core_pose_Pose_t set_cluster_radius(...) from builtins.PyCapsule set_cluster_radius(self : rosetta.protocols.cluster.ClusterBase, cluster_radius : float) -> NoneType set_population_weight(...) from builtins.PyCapsule set_population_weight(self : rosetta.protocols.cluster.ClusterBase, population_weight : float) -> NoneType sort_each_group_by_energy(...) from builtins.PyCapsule sort_each_group_by_energy(rosetta.protocols.cluster.ClusterBase) -> NoneType sort_groups_by_energy(...) from builtins.PyCapsule sort_groups_by_energy(rosetta.protocols.cluster.ClusterBase) -> NoneType Methods inherited from GatherPosesMover: apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.cluster.GatherPosesMover, pose : rosetta.core.pose.Pose) -> NoneType check_tag(...) from builtins.PyCapsule check_tag(self : rosetta.protocols.cluster.GatherPosesMover, query_tag : str) -> bool clear(...) from builtins.PyCapsule clear(rosetta.protocols.cluster.GatherPosesMover) -> NoneType get_filter(...) from builtins.PyCapsule get_filter(rosetta.protocols.cluster.GatherPosesMover) -> float get_pose_list(...) from builtins.PyCapsule get_pose_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_core_pose_Pose get_tag_list(...) from builtins.PyCapsule get_tag_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_std_string nposes(...) from builtins.PyCapsule nposes(rosetta.protocols.cluster.GatherPosesMover) -> int   Return the number of poses gathered by this mover  This is the post-filtered number of poses. push_back(...) from builtins.PyCapsule push_back(self : rosetta.protocols.cluster.GatherPosesMover, pose : rosetta.core.pose.Pose) -> NoneType set_cluster_by_all_atom(...) from builtins.PyCapsule set_cluster_by_all_atom(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_cluster_by_protein_backbone(...) from builtins.PyCapsule set_cluster_by_protein_backbone(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_filter(...) from builtins.PyCapsule set_filter(self : rosetta.protocols.cluster.GatherPosesMover, filter : float) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.protocols.cluster.GatherPosesMover, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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   class ClusterPhilStyle_PoseReporter(ClusterPhilStyle)       Method resolution order: ClusterPhilStyle_PoseReporter ClusterPhilStyle ClusterBase GatherPosesMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, reporter : rosetta.protocols.rosetta_scripts.PosePropertyReporter) -> NoneType   2. __init__(handle, rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter) -> 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.cluster.ClusterPhilStyle_PoseReporter,  : rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter) -> rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter clone(...) from builtins.PyCapsule clone(rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter) -> rosetta.protocols.moves.Mover get_distance_measure(...) from builtins.PyCapsule get_distance_measure(self : rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> float get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter) -> str Methods inherited from ClusterPhilStyle: do_clustering(...) from builtins.PyCapsule do_clustering(self : rosetta.protocols.cluster.ClusterPhilStyle, max_total_cluster : int) -> NoneType do_redistribution(...) from builtins.PyCapsule do_redistribution(rosetta.protocols.cluster.ClusterPhilStyle) -> NoneType Methods inherited from ClusterBase: add_structure(...) from builtins.PyCapsule add_structure(self : rosetta.protocols.cluster.ClusterBase, pose : rosetta.core.pose.Pose) -> NoneType calculate_distance_matrix(...) from builtins.PyCapsule calculate_distance_matrix(rosetta.protocols.cluster.ClusterBase) -> NoneType clean_pose_store(...) from builtins.PyCapsule clean_pose_store(rosetta.protocols.cluster.ClusterBase) -> NoneType create_constraints(...) from builtins.PyCapsule create_constraints(self : rosetta.protocols.cluster.ClusterBase, prefix : str, constraint_maker : rosetta.protocols.cluster.EnsembleConstraints) -> NoneType export_only_low(...) from builtins.PyCapsule export_only_low(*args, **kwargs) Overloaded function.   1. export_only_low(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. export_only_low(self : rosetta.protocols.cluster.ClusterBase, value : bool) -> NoneType get_cluster_list(...) from builtins.PyCapsule get_cluster_list(rosetta.protocols.cluster.ClusterBase) -> rosetta.std.vector_protocols_cluster_Cluster get_cluster_radius(...) from builtins.PyCapsule get_cluster_radius(rosetta.protocols.cluster.ClusterBase) -> float get_median_rms(...) from builtins.PyCapsule get_median_rms(rosetta.protocols.cluster.ClusterBase) -> float limit_groups(...) from builtins.PyCapsule limit_groups(*args, **kwargs) Overloaded function.   1. limit_groups(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. limit_groups(self : rosetta.protocols.cluster.ClusterBase, limit : int) -> NoneType limit_groupsize(...) from builtins.PyCapsule limit_groupsize(*args, **kwargs) Overloaded function.   1. limit_groupsize(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. limit_groupsize(self : rosetta.protocols.cluster.ClusterBase, limit : int) -> NoneType   3. limit_groupsize(self : rosetta.protocols.cluster.ClusterBase, percent_limit : float) -> NoneType limit_total_structures(...) from builtins.PyCapsule limit_total_structures(*args, **kwargs) Overloaded function.   1. limit_total_structures(rosetta.protocols.cluster.ClusterBase) -> NoneType   2. limit_total_structures(self : rosetta.protocols.cluster.ClusterBase, limit : int) -> NoneType print_cluster_PDBs(...) from builtins.PyCapsule print_cluster_PDBs(self : rosetta.protocols.cluster.ClusterBase, prefix : str) -> NoneType print_cluster_assignment(...) from builtins.PyCapsule print_cluster_assignment(rosetta.protocols.cluster.ClusterBase) -> NoneType print_clusters_silentfile(...) from builtins.PyCapsule print_clusters_silentfile(self : rosetta.protocols.cluster.ClusterBase, prefix : str) -> NoneType print_raw_numbers(...) from builtins.PyCapsule print_raw_numbers(rosetta.protocols.cluster.ClusterBase) -> NoneType print_summary(...) from builtins.PyCapsule print_summary(rosetta.protocols.cluster.ClusterBase) -> NoneType random_limit_groupsize(...) from builtins.PyCapsule random_limit_groupsize(self : rosetta.protocols.cluster.ClusterBase, percent_limit : float) -> NoneType remove_highest_energy_member_of_each_group(...) from builtins.PyCapsule remove_highest_energy_member_of_each_group(rosetta.protocols.cluster.ClusterBase) -> NoneType remove_singletons(...) from builtins.PyCapsule remove_singletons(rosetta.protocols.cluster.ClusterBase) -> NoneType return_lowest_poses_in_clusters(...) from builtins.PyCapsule return_lowest_poses_in_clusters(rosetta.protocols.cluster.ClusterBase) -> rosetta.std.vector_std_shared_ptr_core_pose_Pose_t return_top_poses_in_clusters(...) from builtins.PyCapsule return_top_poses_in_clusters(self : rosetta.protocols.cluster.ClusterBase, count : int) -> rosetta.std.vector_std_shared_ptr_core_pose_Pose_t set_cluster_radius(...) from builtins.PyCapsule set_cluster_radius(self : rosetta.protocols.cluster.ClusterBase, cluster_radius : float) -> NoneType set_population_weight(...) from builtins.PyCapsule set_population_weight(self : rosetta.protocols.cluster.ClusterBase, population_weight : float) -> NoneType sort_each_group_by_energy(...) from builtins.PyCapsule sort_each_group_by_energy(rosetta.protocols.cluster.ClusterBase) -> NoneType sort_groups_by_energy(...) from builtins.PyCapsule sort_groups_by_energy(rosetta.protocols.cluster.ClusterBase) -> NoneType Methods inherited from GatherPosesMover: apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.cluster.GatherPosesMover, pose : rosetta.core.pose.Pose) -> NoneType check_tag(...) from builtins.PyCapsule check_tag(self : rosetta.protocols.cluster.GatherPosesMover, query_tag : str) -> bool clear(...) from builtins.PyCapsule clear(rosetta.protocols.cluster.GatherPosesMover) -> NoneType get_filter(...) from builtins.PyCapsule get_filter(rosetta.protocols.cluster.GatherPosesMover) -> float get_pose_list(...) from builtins.PyCapsule get_pose_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_core_pose_Pose get_tag_list(...) from builtins.PyCapsule get_tag_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_std_string nposes(...) from builtins.PyCapsule nposes(rosetta.protocols.cluster.GatherPosesMover) -> int   Return the number of poses gathered by this mover  This is the post-filtered number of poses. push_back(...) from builtins.PyCapsule push_back(self : rosetta.protocols.cluster.GatherPosesMover, pose : rosetta.core.pose.Pose) -> NoneType set_cluster_by_all_atom(...) from builtins.PyCapsule set_cluster_by_all_atom(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_cluster_by_protein_backbone(...) from builtins.PyCapsule set_cluster_by_protein_backbone(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_filter(...) from builtins.PyCapsule set_filter(self : rosetta.protocols.cluster.GatherPosesMover, filter : float) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.protocols.cluster.GatherPosesMover, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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   class DataPoint(builtins.object)     Data structure for one input data point for affinity propagation clustering.     There should be one instance of this class for each input point. Fields are public because it's a glorified struct -- clients shouldn't use this directly.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.protocols.cluster.DataPoint, i_in : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_similarity(...) from builtins.PyCapsule add_similarity(self : rosetta.protocols.cluster.DataPoint, k : int, s_ik : float, max_sims : int) -> NoneType   Set similarity s(i,k), the suitability of point k to be an exemplar for this point. is_set_s_kk(...) from builtins.PyCapsule is_set_s_kk(rosetta.protocols.cluster.DataPoint) -> bool Data descriptors defined here: a_kk best_exemplar candidate_for candidates curr_exemplar i r_kk s_kk sum   class EnsembleConstraints(GatherPosesMover)       Method resolution order: EnsembleConstraints GatherPosesMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __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.cluster.EnsembleConstraints,  : rosetta.protocols.cluster.EnsembleConstraints) -> rosetta.protocols.cluster.EnsembleConstraints get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.cluster.EnsembleConstraints) -> str Methods inherited from GatherPosesMover: apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.cluster.GatherPosesMover, pose : rosetta.core.pose.Pose) -> NoneType check_tag(...) from builtins.PyCapsule check_tag(self : rosetta.protocols.cluster.GatherPosesMover, query_tag : str) -> bool clear(...) from builtins.PyCapsule clear(rosetta.protocols.cluster.GatherPosesMover) -> NoneType get_distance_measure(...) from builtins.PyCapsule get_distance_measure(self : rosetta.protocols.cluster.GatherPosesMover, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> float get_filter(...) from builtins.PyCapsule get_filter(rosetta.protocols.cluster.GatherPosesMover) -> float get_pose_list(...) from builtins.PyCapsule get_pose_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_core_pose_Pose get_tag_list(...) from builtins.PyCapsule get_tag_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_std_string nposes(...) from builtins.PyCapsule nposes(rosetta.protocols.cluster.GatherPosesMover) -> int   Return the number of poses gathered by this mover  This is the post-filtered number of poses. push_back(...) from builtins.PyCapsule push_back(self : rosetta.protocols.cluster.GatherPosesMover, pose : rosetta.core.pose.Pose) -> NoneType set_cluster_by_all_atom(...) from builtins.PyCapsule set_cluster_by_all_atom(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_cluster_by_protein_backbone(...) from builtins.PyCapsule set_cluster_by_protein_backbone(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_filter(...) from builtins.PyCapsule set_filter(self : rosetta.protocols.cluster.GatherPosesMover, filter : float) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.protocols.cluster.GatherPosesMover, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType   class EnsembleConstraints_Simple(EnsembleConstraints)       Method resolution order: EnsembleConstraints_Simple EnsembleConstraints GatherPosesMover rosetta.protocols.moves.Mover builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   doc   2. __init__(self : handle, minimum_width : float) -> NoneType   3. __init__(handle, rosetta.protocols.cluster.EnsembleConstraints_Simple) -> 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.cluster.EnsembleConstraints_Simple,  : rosetta.protocols.cluster.EnsembleConstraints_Simple) -> rosetta.protocols.cluster.EnsembleConstraints_Simple clone(...) from builtins.PyCapsule clone(rosetta.protocols.cluster.EnsembleConstraints_Simple) -> rosetta.protocols.moves.Mover get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.cluster.EnsembleConstraints_Simple) -> str Methods inherited from GatherPosesMover: apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.cluster.GatherPosesMover, pose : rosetta.core.pose.Pose) -> NoneType check_tag(...) from builtins.PyCapsule check_tag(self : rosetta.protocols.cluster.GatherPosesMover, query_tag : str) -> bool clear(...) from builtins.PyCapsule clear(rosetta.protocols.cluster.GatherPosesMover) -> NoneType get_distance_measure(...) from builtins.PyCapsule get_distance_measure(self : rosetta.protocols.cluster.GatherPosesMover, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> float get_filter(...) from builtins.PyCapsule get_filter(rosetta.protocols.cluster.GatherPosesMover) -> float get_pose_list(...) from builtins.PyCapsule get_pose_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_core_pose_Pose get_tag_list(...) from builtins.PyCapsule get_tag_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_std_string nposes(...) from builtins.PyCapsule nposes(rosetta.protocols.cluster.GatherPosesMover) -> int   Return the number of poses gathered by this mover  This is the post-filtered number of poses. push_back(...) from builtins.PyCapsule push_back(self : rosetta.protocols.cluster.GatherPosesMover, pose : rosetta.core.pose.Pose) -> NoneType set_cluster_by_all_atom(...) from builtins.PyCapsule set_cluster_by_all_atom(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_cluster_by_protein_backbone(...) from builtins.PyCapsule set_cluster_by_protein_backbone(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_filter(...) from builtins.PyCapsule set_filter(self : rosetta.protocols.cluster.GatherPosesMover, filter : float) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.protocols.cluster.GatherPosesMover, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply 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   class Exemplar(builtins.object)     Data structure for one similarity measurement (s_ik) for affinity propagation clustering.     There will be one instance of this class for each (finite) similarity between two input points, up to a maximum of N*N instances if the similarity matrix is fully populated.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.protocols.cluster.Exemplar, k_in : int, s_ik_in : float) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. min_heap(...) from builtins.PyCapsule min_heap(a : rosetta.protocols.cluster.Exemplar, b : rosetta.protocols.cluster.Exemplar) -> bool   "Less than" (actually greater than) comparator for making a heap of exemplars Data descriptors defined here: a_ik k r_ik s_ik   class GatherPosesMover(rosetta.protocols.moves.Mover)       Method resolution order: GatherPosesMover 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.cluster.GatherPosesMover) -> 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.cluster.GatherPosesMover, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.cluster.GatherPosesMover,  : rosetta.protocols.cluster.GatherPosesMover) -> rosetta.protocols.cluster.GatherPosesMover check_tag(...) from builtins.PyCapsule check_tag(self : rosetta.protocols.cluster.GatherPosesMover, query_tag : str) -> bool clear(...) from builtins.PyCapsule clear(rosetta.protocols.cluster.GatherPosesMover) -> NoneType get_distance_measure(...) from builtins.PyCapsule get_distance_measure(self : rosetta.protocols.cluster.GatherPosesMover, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> float get_filter(...) from builtins.PyCapsule get_filter(rosetta.protocols.cluster.GatherPosesMover) -> float get_name(...) from builtins.PyCapsule get_name(rosetta.protocols.cluster.GatherPosesMover) -> str get_pose_list(...) from builtins.PyCapsule get_pose_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_core_pose_Pose get_tag_list(...) from builtins.PyCapsule get_tag_list(rosetta.protocols.cluster.GatherPosesMover) -> rosetta.std.vector_std_string nposes(...) from builtins.PyCapsule nposes(rosetta.protocols.cluster.GatherPosesMover) -> int   Return the number of poses gathered by this mover  This is the post-filtered number of poses. push_back(...) from builtins.PyCapsule push_back(self : rosetta.protocols.cluster.GatherPosesMover, pose : rosetta.core.pose.Pose) -> NoneType set_cluster_by_all_atom(...) from builtins.PyCapsule set_cluster_by_all_atom(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_cluster_by_protein_backbone(...) from builtins.PyCapsule set_cluster_by_protein_backbone(self : rosetta.protocols.cluster.GatherPosesMover, setting : bool) -> NoneType set_filter(...) from builtins.PyCapsule set_filter(self : rosetta.protocols.cluster.GatherPosesMover, filter : float) -> NoneType set_score_function(...) from builtins.PyCapsule set_score_function(self : rosetta.protocols.cluster.GatherPosesMover, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType Methods inherited from rosetta.protocols.moves.Mover: clear_info(...) from builtins.PyCapsule clear_info(rosetta.protocols.moves.Mover) -> NoneType   Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.      clear_info is called by jd2 before calling apply clone(...) from builtins.PyCapsule clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Return a clone of the Mover object. create(...) from builtins.PyCapsule create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover fresh_instance(...) from builtins.PyCapsule fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   Generates a new Mover object freshly created with the default ctor. get_additional_output(...) from builtins.PyCapsule get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose   fpd      Mechanism by which a mover may return multiple output poses from a single input pose. get_current_job(...) from builtins.PyCapsule get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob get_current_tag(...) from builtins.PyCapsule get_current_tag(rosetta.protocols.moves.Mover) -> str   A tag is a unique identifier used to identify structures produced  by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )  sets the tag.  This functionality is not intended for use with the 2008 job distributor. get_input_pose(...) from builtins.PyCapsule get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_last_move_status(...) from builtins.PyCapsule get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus   returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return. get_native_pose(...) from builtins.PyCapsule get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover   2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t   2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t get_type(...) from builtins.PyCapsule get_type(rosetta.protocols.moves.Mover) -> str info(...) from builtins.PyCapsule info(*args, **kwargs) Overloaded function.   1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   non-const accessor   2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t   const accessor last_proposal_density_ratio(...) from builtins.PyCapsule last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float name(...) from builtins.PyCapsule name() -> str register_options(...) from builtins.PyCapsule register_options(*args, **kwargs) Overloaded function.   1. register_options() -> NoneType   Overload this static method if you access options within the mover.      These options will end up in -help of your application if users of this mover call register_options.  Do this recursively!  If you use movers within your mover, call their register_options in your register_options() method.   2. register_options() -> NoneType   3. register_options() -> NoneType   4. register_options() -> NoneType   5. register_options() -> NoneType   6. register_options() -> NoneType   7. register_options() -> NoneType   8. register_options() -> NoneType   9. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   10. register_options() -> NoneType   Associates relevant options with the AntibodyModeler class   11. register_options() -> NoneType   Associates relevant options with the SnugDock class   12. register_options() -> NoneType   Associates relevant options with the SnugDockProtocol class   13. register_options() -> NoneType   Register the options used by this mover with the global options  system.   14. register_options() -> NoneType   15. register_options() -> NoneType   Associate relevant options with the TemperedDocking class.   16. register_options() -> NoneType   17. register_options() -> NoneType   18. register_options() -> NoneType   Associates relevant options with the TemperedDocking class.   19. register_options() -> NoneType   20. register_options() -> NoneType   Associates relevant options with the ConstraintSetMover class   21. register_options() -> NoneType   22. register_options() -> NoneType   Associates relevant options with the DockingInitialPerturbation class   23. register_options() -> NoneType   Associates relevant options with the DockingProtocol class   24. register_options() -> NoneType   Associates relevant options with the TemperedDocking class   25. register_options() -> NoneType   26. register_options() -> NoneType   27. register_options() -> NoneType   28. register_options() -> NoneType   register options   29. register_options() -> NoneType   30. register_options() -> NoneType   Registers applicable options   31. register_options() -> NoneType   Register options with the option system.   32. register_options() -> NoneType   33. register_options() -> NoneType   34. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   35. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycleContainer class   36. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   37. register_options() -> NoneType   Associates relevant options with the LoopRefineInnerCycle class   38. register_options() -> NoneType   39. register_options() -> NoneType   Register options with the option system.   40. register_options() -> NoneType reinitialize_for_each_job(...) from builtins.PyCapsule reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on  each use. reinitialize_for_new_input(...) from builtins.PyCapsule reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool   Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input  pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for  that one input pose). reset_status(...) from builtins.PyCapsule reset_status(rosetta.protocols.moves.Mover) -> NoneType   resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. set_current_job(...) from builtins.PyCapsule set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType   ////////////////////////////end Job Distributor interface//////////////////////////////////////// set_current_tag(...) from builtins.PyCapsule set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType set_input_pose(...) from builtins.PyCapsule set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for poses contained for rms set_native_pose(...) from builtins.PyCapsule set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe set_type(...) from builtins.PyCapsule set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType test_move(...) from builtins.PyCapsule test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType   : Unit test support function.  Apply one move to a given pose.       Allows extra test specific functions to be called before applying type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.protocols.moves.Mover) -> str   2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType