cluster¶
Bindings for protocols::cluster namespace
- class pyrosetta.rosetta.protocols.cluster.APCluster¶
Bases:
pybind11_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).
- assign(self: pyrosetta.rosetta.protocols.cluster.APCluster, : pyrosetta.rosetta.protocols.cluster.APCluster) pyrosetta.rosetta.protocols.cluster.APCluster ¶
C++: protocols::cluster::APCluster::operator=(const class protocols::cluster::APCluster &) –> class protocols::cluster::APCluster &
- cluster(self: pyrosetta.rosetta.protocols.cluster.APCluster, maxits: int, convits: int, lambda: float) bool ¶
Run the actual clustering algorithm.
C++: protocols::cluster::APCluster::cluster(unsigned long, unsigned long, double) –> bool
- get_all_exemplars(self: pyrosetta.rosetta.protocols.cluster.APCluster, exemplars: pyrosetta.rosetta.utility.vector1_unsigned_long) None ¶
Return the indices of data points chosen as exemplars (cluster centers).
C++: protocols::cluster::APCluster::get_all_exemplars(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void
- get_cluster_for(self: pyrosetta.rosetta.protocols.cluster.APCluster, k: int, cluster: pyrosetta.rosetta.utility.vector1_unsigned_long) None ¶
- 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().
C++: protocols::cluster::APCluster::get_cluster_for(unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void
- get_exemplar_for(self: pyrosetta.rosetta.protocols.cluster.APCluster, i: int) int ¶
Return the index of the point that is the exemplar for point i.
C++: protocols::cluster::APCluster::get_exemplar_for(unsigned long) const –> unsigned long
- get_net_sim(self: pyrosetta.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.
C++: protocols::cluster::APCluster::get_net_sim() const –> double
- get_num_exemplars(self: pyrosetta.rosetta.protocols.cluster.APCluster) int ¶
- The number of exemplars selected (number of clusters).
Monotonically related to the self-preferences s(k,k).
C++: protocols::cluster::APCluster::get_num_exemplars() const –> unsigned long
- load_binary(self: pyrosetta.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).
C++: protocols::cluster::APCluster::load_binary(const std::string &) –> bool
- num_pts(self: pyrosetta.rosetta.protocols.cluster.APCluster) int ¶
C++: protocols::cluster::APCluster::num_pts() const –> unsigned long
- save_binary(self: pyrosetta.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).
C++: protocols::cluster::APCluster::save_binary(const std::string &) const –> bool
- set_sim(self: pyrosetta.rosetta.protocols.cluster.APCluster, i: int, k: int, sim: float) None ¶
How appropriate is k as an exemplar for i?
C++: protocols::cluster::APCluster::set_sim(unsigned long, unsigned long, double) –> void
- class pyrosetta.rosetta.protocols.cluster.AssignToClustersMover¶
Bases:
GatherPosesMover
- apply(self: pyrosetta.rosetta.protocols.cluster.AssignToClustersMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::AssignToClustersMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.cluster.AssignToClustersMover, : pyrosetta.rosetta.protocols.cluster.AssignToClustersMover) pyrosetta.rosetta.protocols.cluster.AssignToClustersMover ¶
C++: protocols::cluster::AssignToClustersMover::operator=(const class protocols::cluster::AssignToClustersMover &) –> class protocols::cluster::AssignToClustersMover &
- check_tag(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, query_tag: str) bool ¶
C++: protocols::cluster::GatherPosesMover::check_tag(const std::string &) –> bool
- clear(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) None ¶
C++: protocols::cluster::GatherPosesMover::clear() –> void
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.cluster.AssignToClustersMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::cluster::AssignToClustersMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob ¶
C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>
- get_current_tag(self: pyrosetta.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.
C++: protocols::moves::Mover::get_current_tag() const –> std::string
- get_distance_measure(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::cluster::GatherPosesMover::get_distance_measure(const class core::pose::Pose &, const class core::pose::Pose &) const –> double
- get_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) float ¶
C++: protocols::cluster::GatherPosesMover::get_filter() const –> double
- get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.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.
C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus
- get_name(self: pyrosetta.rosetta.protocols.cluster.AssignToClustersMover) str ¶
C++: protocols::cluster::AssignToClustersMover::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_pose_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_core_pose_Pose ¶
C++: protocols::cluster::GatherPosesMover::get_pose_list() –> class std::vector<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_tag_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_std_string ¶
C++: protocols::cluster::GatherPosesMover::get_tag_list() const –> const class std::vector<std::string, class std::allocator<std::string > > &
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nposes(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) int ¶
- Return the number of poses gathered by this mover
This is the post-filtered number of poses.
C++: protocols::cluster::GatherPosesMover::nposes() const –> unsigned long
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- push_back(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::GatherPosesMover::push_back(const class core::pose::Pose &) –> void
- static register_options() None ¶
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.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.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).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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.
C++: protocols::moves::Mover::reset_status() –> void
- set_cluster_by_all_atom(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_all_atom(const bool &) –> void
- set_cluster_by_protein_backbone(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_protein_backbone(const bool &) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, filter: float) None ¶
C++: protocols::cluster::GatherPosesMover::set_filter(double) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_score_function(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::cluster::GatherPosesMover::set_score_function(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.cluster.Cluster¶
Bases:
pybind11_object
- add_member(self: pyrosetta.rosetta.protocols.cluster.Cluster, new_member: int) None ¶
C++: protocols::cluster::Cluster::add_member(int) –> void
- add_member_front(self: pyrosetta.rosetta.protocols.cluster.Cluster, new_member: int) None ¶
C++: protocols::cluster::Cluster::add_member_front(int) –> void
- clear(self: pyrosetta.rosetta.protocols.cluster.Cluster) None ¶
C++: protocols::cluster::Cluster::clear() –> void
- property cluster_center_¶
- erase(self: pyrosetta.rosetta.protocols.cluster.Cluster, j: int) None ¶
C++: protocols::cluster::Cluster::erase(unsigned long) –> void
- get_cluster_center(self: pyrosetta.rosetta.protocols.cluster.Cluster) int ¶
C++: protocols::cluster::Cluster::get_cluster_center() const –> int
- group_size(self: pyrosetta.rosetta.protocols.cluster.Cluster) int ¶
C++: protocols::cluster::Cluster::group_size() –> unsigned long
- property group_size_¶
- property member¶
- push_back(self: pyrosetta.rosetta.protocols.cluster.Cluster, new_member: int) None ¶
C++: protocols::cluster::Cluster::push_back(int) –> void
- push_front(self: pyrosetta.rosetta.protocols.cluster.Cluster, new_member: int) None ¶
C++: protocols::cluster::Cluster::push_front(int) –> void
- remove_member(self: pyrosetta.rosetta.protocols.cluster.Cluster, old_member: int) None ¶
C++: protocols::cluster::Cluster::remove_member(int) –> void
- shuffle(self: pyrosetta.rosetta.protocols.cluster.Cluster) None ¶
C++: protocols::cluster::Cluster::shuffle() –> void
- size(self: pyrosetta.rosetta.protocols.cluster.Cluster) int ¶
C++: protocols::cluster::Cluster::size() const –> unsigned long
- class pyrosetta.rosetta.protocols.cluster.ClusterBase¶
Bases:
GatherPosesMover
- add_structure(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::ClusterBase::add_structure(class core::pose::Pose &) –> void
- apply(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::GatherPosesMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, : pyrosetta.rosetta.protocols.cluster.ClusterBase) pyrosetta.rosetta.protocols.cluster.ClusterBase ¶
C++: protocols::cluster::ClusterBase::operator=(const class protocols::cluster::ClusterBase &) –> class protocols::cluster::ClusterBase &
- calculate_distance_matrix(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::calculate_distance_matrix() –> void
- check_tag(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, query_tag: str) bool ¶
C++: protocols::cluster::GatherPosesMover::check_tag(const std::string &) –> bool
- clean_pose_store(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::clean_pose_store() –> void
- clear(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) None ¶
C++: protocols::cluster::GatherPosesMover::clear() –> void
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- create_constraints(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, prefix: str, constraint_maker: pyrosetta.rosetta.protocols.cluster.EnsembleConstraints) None ¶
C++: protocols::cluster::ClusterBase::create_constraints(std::string, class protocols::cluster::EnsembleConstraints &) –> void
- export_only_low(*args, **kwargs)¶
Overloaded function.
export_only_low(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
export_only_low(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, value: bool) -> None
C++: protocols::cluster::ClusterBase::export_only_low(bool) –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_cluster_list(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) pyrosetta.rosetta.std.vector_protocols_cluster_Cluster ¶
C++: protocols::cluster::ClusterBase::get_cluster_list() const –> const class std::vector<struct protocols::cluster::Cluster, class std::allocator<struct protocols::cluster::Cluster> > &
- get_cluster_radius(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) float ¶
C++: protocols::cluster::ClusterBase::get_cluster_radius() –> double
- get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob ¶
C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>
- get_current_tag(self: pyrosetta.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.
C++: protocols::moves::Mover::get_current_tag() const –> std::string
- get_distance_measure(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::cluster::GatherPosesMover::get_distance_measure(const class core::pose::Pose &, const class core::pose::Pose &) const –> double
- get_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) float ¶
C++: protocols::cluster::GatherPosesMover::get_filter() const –> double
- get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.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.
C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus
- get_median_rms(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) float ¶
C++: protocols::cluster::ClusterBase::get_median_rms() –> double
- get_name(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) str ¶
C++: protocols::cluster::ClusterBase::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_pose_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_core_pose_Pose ¶
C++: protocols::cluster::GatherPosesMover::get_pose_list() –> class std::vector<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_tag_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_std_string ¶
C++: protocols::cluster::GatherPosesMover::get_tag_list() const –> const class std::vector<std::string, class std::allocator<std::string > > &
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- limit_groups(*args, **kwargs)¶
Overloaded function.
limit_groups(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
limit_groups(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None
C++: protocols::cluster::ClusterBase::limit_groups(int) –> void
- limit_groupsize(*args, **kwargs)¶
Overloaded function.
limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None
C++: protocols::cluster::ClusterBase::limit_groupsize(int) –> void
limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, percent_limit: float) -> None
C++: protocols::cluster::ClusterBase::limit_groupsize(double) –> void
- limit_total_structures(*args, **kwargs)¶
Overloaded function.
limit_total_structures(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
limit_total_structures(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None
C++: protocols::cluster::ClusterBase::limit_total_structures(int) –> void
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nposes(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) int ¶
- Return the number of poses gathered by this mover
This is the post-filtered number of poses.
C++: protocols::cluster::GatherPosesMover::nposes() const –> unsigned long
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- print_cluster_PDBs(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, prefix: str) None ¶
C++: protocols::cluster::ClusterBase::print_cluster_PDBs(std::string) –> void
- print_cluster_assignment(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::print_cluster_assignment() –> void
- print_clusters_silentfile(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, prefix: str) None ¶
C++: protocols::cluster::ClusterBase::print_clusters_silentfile(std::string) –> void
- print_raw_numbers(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::print_raw_numbers() –> void
- print_summary(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::print_summary() –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- push_back(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::GatherPosesMover::push_back(const class core::pose::Pose &) –> void
- random_limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, percent_limit: float) None ¶
C++: protocols::cluster::ClusterBase::random_limit_groupsize(double) –> void
- static register_options() None ¶
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.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.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).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- remove_highest_energy_member_of_each_group(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::remove_highest_energy_member_of_each_group() –> void
- remove_singletons(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::remove_singletons() –> void
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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.
C++: protocols::moves::Mover::reset_status() –> void
- return_lowest_poses_in_clusters(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t ¶
C++: protocols::cluster::ClusterBase::return_lowest_poses_in_clusters() –> class std::vector<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >
- return_top_poses_in_clusters(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, count: int) pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t ¶
C++: protocols::cluster::ClusterBase::return_top_poses_in_clusters(unsigned long) –> class std::vector<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >
- set_cluster_by_all_atom(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_all_atom(const bool &) –> void
- set_cluster_by_protein_backbone(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_protein_backbone(const bool &) –> void
- set_cluster_radius(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, cluster_radius: float) None ¶
C++: protocols::cluster::ClusterBase::set_cluster_radius(double) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, filter: float) None ¶
C++: protocols::cluster::GatherPosesMover::set_filter(double) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_population_weight(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, population_weight: float) None ¶
C++: protocols::cluster::ClusterBase::set_population_weight(double) –> void
- set_score_function(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::cluster::GatherPosesMover::set_score_function(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- sort_each_group_by_energy(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::sort_each_group_by_energy() –> void
- sort_groups_by_energy(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::sort_groups_by_energy() –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle¶
Bases:
ClusterBase
- add_structure(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::ClusterBase::add_structure(class core::pose::Pose &) –> void
- apply(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::GatherPosesMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle, : pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle) pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle ¶
C++: protocols::cluster::ClusterPhilStyle::operator=(const class protocols::cluster::ClusterPhilStyle &) –> class protocols::cluster::ClusterPhilStyle &
- calculate_distance_matrix(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::calculate_distance_matrix() –> void
- check_tag(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, query_tag: str) bool ¶
C++: protocols::cluster::GatherPosesMover::check_tag(const std::string &) –> bool
- clean_pose_store(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::clean_pose_store() –> void
- clear(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) None ¶
C++: protocols::cluster::GatherPosesMover::clear() –> void
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::cluster::ClusterPhilStyle::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- create_constraints(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, prefix: str, constraint_maker: pyrosetta.rosetta.protocols.cluster.EnsembleConstraints) None ¶
C++: protocols::cluster::ClusterBase::create_constraints(std::string, class protocols::cluster::EnsembleConstraints &) –> void
- do_clustering(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle, max_total_cluster: int) None ¶
C++: protocols::cluster::ClusterPhilStyle::do_clustering(unsigned long) –> void
- do_redistribution(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle) None ¶
C++: protocols::cluster::ClusterPhilStyle::do_redistribution() –> void
- export_only_low(*args, **kwargs)¶
Overloaded function.
export_only_low(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
export_only_low(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, value: bool) -> None
C++: protocols::cluster::ClusterBase::export_only_low(bool) –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_cluster_list(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) pyrosetta.rosetta.std.vector_protocols_cluster_Cluster ¶
C++: protocols::cluster::ClusterBase::get_cluster_list() const –> const class std::vector<struct protocols::cluster::Cluster, class std::allocator<struct protocols::cluster::Cluster> > &
- get_cluster_radius(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) float ¶
C++: protocols::cluster::ClusterBase::get_cluster_radius() –> double
- get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob ¶
C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>
- get_current_tag(self: pyrosetta.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.
C++: protocols::moves::Mover::get_current_tag() const –> std::string
- get_distance_measure(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::cluster::GatherPosesMover::get_distance_measure(const class core::pose::Pose &, const class core::pose::Pose &) const –> double
- get_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) float ¶
C++: protocols::cluster::GatherPosesMover::get_filter() const –> double
- get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.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.
C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus
- get_median_rms(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) float ¶
C++: protocols::cluster::ClusterBase::get_median_rms() –> double
- get_name(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle) str ¶
C++: protocols::cluster::ClusterPhilStyle::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_pose_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_core_pose_Pose ¶
C++: protocols::cluster::GatherPosesMover::get_pose_list() –> class std::vector<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_tag_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_std_string ¶
C++: protocols::cluster::GatherPosesMover::get_tag_list() const –> const class std::vector<std::string, class std::allocator<std::string > > &
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- limit_groups(*args, **kwargs)¶
Overloaded function.
limit_groups(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
limit_groups(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None
C++: protocols::cluster::ClusterBase::limit_groups(int) –> void
- limit_groupsize(*args, **kwargs)¶
Overloaded function.
limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None
C++: protocols::cluster::ClusterBase::limit_groupsize(int) –> void
limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, percent_limit: float) -> None
C++: protocols::cluster::ClusterBase::limit_groupsize(double) –> void
- limit_total_structures(*args, **kwargs)¶
Overloaded function.
limit_total_structures(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
limit_total_structures(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None
C++: protocols::cluster::ClusterBase::limit_total_structures(int) –> void
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nposes(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) int ¶
- Return the number of poses gathered by this mover
This is the post-filtered number of poses.
C++: protocols::cluster::GatherPosesMover::nposes() const –> unsigned long
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- print_cluster_PDBs(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, prefix: str) None ¶
C++: protocols::cluster::ClusterBase::print_cluster_PDBs(std::string) –> void
- print_cluster_assignment(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::print_cluster_assignment() –> void
- print_clusters_silentfile(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, prefix: str) None ¶
C++: protocols::cluster::ClusterBase::print_clusters_silentfile(std::string) –> void
- print_raw_numbers(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::print_raw_numbers() –> void
- print_summary(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::print_summary() –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- push_back(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::GatherPosesMover::push_back(const class core::pose::Pose &) –> void
- random_limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, percent_limit: float) None ¶
C++: protocols::cluster::ClusterBase::random_limit_groupsize(double) –> void
- static register_options() None ¶
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.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.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).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- remove_highest_energy_member_of_each_group(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::remove_highest_energy_member_of_each_group() –> void
- remove_singletons(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::remove_singletons() –> void
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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.
C++: protocols::moves::Mover::reset_status() –> void
- return_lowest_poses_in_clusters(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t ¶
C++: protocols::cluster::ClusterBase::return_lowest_poses_in_clusters() –> class std::vector<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >
- return_top_poses_in_clusters(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, count: int) pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t ¶
C++: protocols::cluster::ClusterBase::return_top_poses_in_clusters(unsigned long) –> class std::vector<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >
- set_cluster_by_all_atom(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_all_atom(const bool &) –> void
- set_cluster_by_protein_backbone(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_protein_backbone(const bool &) –> void
- set_cluster_radius(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, cluster_radius: float) None ¶
C++: protocols::cluster::ClusterBase::set_cluster_radius(double) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, filter: float) None ¶
C++: protocols::cluster::GatherPosesMover::set_filter(double) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_population_weight(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, population_weight: float) None ¶
C++: protocols::cluster::ClusterBase::set_population_weight(double) –> void
- set_score_function(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::cluster::GatherPosesMover::set_score_function(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- sort_each_group_by_energy(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::sort_each_group_by_energy() –> void
- sort_groups_by_energy(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::sort_groups_by_energy() –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop¶
Bases:
ClusterPhilStyle
- add_structure(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::ClusterBase::add_structure(class core::pose::Pose &) –> void
- apply(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::GatherPosesMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop, : pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop) pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop ¶
C++: protocols::cluster::ClusterPhilStyle_Loop::operator=(const class protocols::cluster::ClusterPhilStyle_Loop &) –> class protocols::cluster::ClusterPhilStyle_Loop &
- calculate_distance_matrix(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::calculate_distance_matrix() –> void
- check_tag(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, query_tag: str) bool ¶
C++: protocols::cluster::GatherPosesMover::check_tag(const std::string &) –> bool
- clean_pose_store(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::clean_pose_store() –> void
- clear(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) None ¶
C++: protocols::cluster::GatherPosesMover::clear() –> void
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::cluster::ClusterPhilStyle_Loop::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- create_constraints(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, prefix: str, constraint_maker: pyrosetta.rosetta.protocols.cluster.EnsembleConstraints) None ¶
C++: protocols::cluster::ClusterBase::create_constraints(std::string, class protocols::cluster::EnsembleConstraints &) –> void
- do_clustering(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle, max_total_cluster: int) None ¶
C++: protocols::cluster::ClusterPhilStyle::do_clustering(unsigned long) –> void
- do_redistribution(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle) None ¶
C++: protocols::cluster::ClusterPhilStyle::do_redistribution() –> void
- export_only_low(*args, **kwargs)¶
Overloaded function.
export_only_low(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
export_only_low(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, value: bool) -> None
C++: protocols::cluster::ClusterBase::export_only_low(bool) –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_cluster_list(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) pyrosetta.rosetta.std.vector_protocols_cluster_Cluster ¶
C++: protocols::cluster::ClusterBase::get_cluster_list() const –> const class std::vector<struct protocols::cluster::Cluster, class std::allocator<struct protocols::cluster::Cluster> > &
- get_cluster_radius(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) float ¶
C++: protocols::cluster::ClusterBase::get_cluster_radius() –> double
- get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob ¶
C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>
- get_current_tag(self: pyrosetta.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.
C++: protocols::moves::Mover::get_current_tag() const –> std::string
- get_distance_measure(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::cluster::ClusterPhilStyle_Loop::get_distance_measure(const class core::pose::Pose &, const class core::pose::Pose &) const –> double
- get_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) float ¶
C++: protocols::cluster::GatherPosesMover::get_filter() const –> double
- get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.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.
C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus
- get_median_rms(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) float ¶
C++: protocols::cluster::ClusterBase::get_median_rms() –> double
- get_name(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop) str ¶
C++: protocols::cluster::ClusterPhilStyle_Loop::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_pose_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_core_pose_Pose ¶
C++: protocols::cluster::GatherPosesMover::get_pose_list() –> class std::vector<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_tag_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_std_string ¶
C++: protocols::cluster::GatherPosesMover::get_tag_list() const –> const class std::vector<std::string, class std::allocator<std::string > > &
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- limit_groups(*args, **kwargs)¶
Overloaded function.
limit_groups(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
limit_groups(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None
C++: protocols::cluster::ClusterBase::limit_groups(int) –> void
- limit_groupsize(*args, **kwargs)¶
Overloaded function.
limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None
C++: protocols::cluster::ClusterBase::limit_groupsize(int) –> void
limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, percent_limit: float) -> None
C++: protocols::cluster::ClusterBase::limit_groupsize(double) –> void
- limit_total_structures(*args, **kwargs)¶
Overloaded function.
limit_total_structures(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
limit_total_structures(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None
C++: protocols::cluster::ClusterBase::limit_total_structures(int) –> void
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nposes(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) int ¶
- Return the number of poses gathered by this mover
This is the post-filtered number of poses.
C++: protocols::cluster::GatherPosesMover::nposes() const –> unsigned long
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- print_cluster_PDBs(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, prefix: str) None ¶
C++: protocols::cluster::ClusterBase::print_cluster_PDBs(std::string) –> void
- print_cluster_assignment(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::print_cluster_assignment() –> void
- print_clusters_silentfile(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, prefix: str) None ¶
C++: protocols::cluster::ClusterBase::print_clusters_silentfile(std::string) –> void
- print_raw_numbers(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::print_raw_numbers() –> void
- print_summary(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::print_summary() –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- push_back(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::GatherPosesMover::push_back(const class core::pose::Pose &) –> void
- random_limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, percent_limit: float) None ¶
C++: protocols::cluster::ClusterBase::random_limit_groupsize(double) –> void
- static register_options() None ¶
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.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.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).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- remove_highest_energy_member_of_each_group(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::remove_highest_energy_member_of_each_group() –> void
- remove_singletons(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::remove_singletons() –> void
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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.
C++: protocols::moves::Mover::reset_status() –> void
- return_lowest_poses_in_clusters(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t ¶
C++: protocols::cluster::ClusterBase::return_lowest_poses_in_clusters() –> class std::vector<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >
- return_top_poses_in_clusters(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, count: int) pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t ¶
C++: protocols::cluster::ClusterBase::return_top_poses_in_clusters(unsigned long) –> class std::vector<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >
- set_cluster_by_all_atom(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_all_atom(const bool &) –> void
- set_cluster_by_protein_backbone(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_protein_backbone(const bool &) –> void
- set_cluster_radius(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, cluster_radius: float) None ¶
C++: protocols::cluster::ClusterBase::set_cluster_radius(double) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, filter: float) None ¶
C++: protocols::cluster::GatherPosesMover::set_filter(double) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_population_weight(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, population_weight: float) None ¶
C++: protocols::cluster::ClusterBase::set_population_weight(double) –> void
- set_score_function(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::cluster::GatherPosesMover::set_score_function(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- sort_each_group_by_energy(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::sort_each_group_by_energy() –> void
- sort_groups_by_energy(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::sort_groups_by_energy() –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter¶
Bases:
ClusterPhilStyle
- add_structure(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::ClusterBase::add_structure(class core::pose::Pose &) –> void
- apply(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::GatherPosesMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter, : pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter) pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter ¶
C++: protocols::cluster::ClusterPhilStyle_PoseReporter::operator=(const class protocols::cluster::ClusterPhilStyle_PoseReporter &) –> class protocols::cluster::ClusterPhilStyle_PoseReporter &
- calculate_distance_matrix(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::calculate_distance_matrix() –> void
- check_tag(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, query_tag: str) bool ¶
C++: protocols::cluster::GatherPosesMover::check_tag(const std::string &) –> bool
- clean_pose_store(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::clean_pose_store() –> void
- clear(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) None ¶
C++: protocols::cluster::GatherPosesMover::clear() –> void
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::cluster::ClusterPhilStyle_PoseReporter::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- create_constraints(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, prefix: str, constraint_maker: pyrosetta.rosetta.protocols.cluster.EnsembleConstraints) None ¶
C++: protocols::cluster::ClusterBase::create_constraints(std::string, class protocols::cluster::EnsembleConstraints &) –> void
- do_clustering(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle, max_total_cluster: int) None ¶
C++: protocols::cluster::ClusterPhilStyle::do_clustering(unsigned long) –> void
- do_redistribution(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle) None ¶
C++: protocols::cluster::ClusterPhilStyle::do_redistribution() –> void
- export_only_low(*args, **kwargs)¶
Overloaded function.
export_only_low(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
export_only_low(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, value: bool) -> None
C++: protocols::cluster::ClusterBase::export_only_low(bool) –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_cluster_list(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) pyrosetta.rosetta.std.vector_protocols_cluster_Cluster ¶
C++: protocols::cluster::ClusterBase::get_cluster_list() const –> const class std::vector<struct protocols::cluster::Cluster, class std::allocator<struct protocols::cluster::Cluster> > &
- get_cluster_radius(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) float ¶
C++: protocols::cluster::ClusterBase::get_cluster_radius() –> double
- get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob ¶
C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>
- get_current_tag(self: pyrosetta.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.
C++: protocols::moves::Mover::get_current_tag() const –> std::string
- get_distance_measure(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::cluster::ClusterPhilStyle_PoseReporter::get_distance_measure(const class core::pose::Pose &, const class core::pose::Pose &) const –> double
- get_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) float ¶
C++: protocols::cluster::GatherPosesMover::get_filter() const –> double
- get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.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.
C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus
- get_median_rms(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) float ¶
C++: protocols::cluster::ClusterBase::get_median_rms() –> double
- get_name(self: pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter) str ¶
C++: protocols::cluster::ClusterPhilStyle_PoseReporter::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_pose_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_core_pose_Pose ¶
C++: protocols::cluster::GatherPosesMover::get_pose_list() –> class std::vector<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_tag_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_std_string ¶
C++: protocols::cluster::GatherPosesMover::get_tag_list() const –> const class std::vector<std::string, class std::allocator<std::string > > &
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- limit_groups(*args, **kwargs)¶
Overloaded function.
limit_groups(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
limit_groups(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None
C++: protocols::cluster::ClusterBase::limit_groups(int) –> void
- limit_groupsize(*args, **kwargs)¶
Overloaded function.
limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None
C++: protocols::cluster::ClusterBase::limit_groupsize(int) –> void
limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, percent_limit: float) -> None
C++: protocols::cluster::ClusterBase::limit_groupsize(double) –> void
- limit_total_structures(*args, **kwargs)¶
Overloaded function.
limit_total_structures(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None
limit_total_structures(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None
C++: protocols::cluster::ClusterBase::limit_total_structures(int) –> void
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nposes(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) int ¶
- Return the number of poses gathered by this mover
This is the post-filtered number of poses.
C++: protocols::cluster::GatherPosesMover::nposes() const –> unsigned long
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- print_cluster_PDBs(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, prefix: str) None ¶
C++: protocols::cluster::ClusterBase::print_cluster_PDBs(std::string) –> void
- print_cluster_assignment(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::print_cluster_assignment() –> void
- print_clusters_silentfile(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, prefix: str) None ¶
C++: protocols::cluster::ClusterBase::print_clusters_silentfile(std::string) –> void
- print_raw_numbers(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::print_raw_numbers() –> void
- print_summary(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::print_summary() –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- push_back(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::GatherPosesMover::push_back(const class core::pose::Pose &) –> void
- random_limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, percent_limit: float) None ¶
C++: protocols::cluster::ClusterBase::random_limit_groupsize(double) –> void
- static register_options() None ¶
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.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.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).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- remove_highest_energy_member_of_each_group(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::remove_highest_energy_member_of_each_group() –> void
- remove_singletons(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::remove_singletons() –> void
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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.
C++: protocols::moves::Mover::reset_status() –> void
- return_lowest_poses_in_clusters(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t ¶
C++: protocols::cluster::ClusterBase::return_lowest_poses_in_clusters() –> class std::vector<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >
- return_top_poses_in_clusters(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, count: int) pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t ¶
C++: protocols::cluster::ClusterBase::return_top_poses_in_clusters(unsigned long) –> class std::vector<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >
- set_cluster_by_all_atom(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_all_atom(const bool &) –> void
- set_cluster_by_protein_backbone(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_protein_backbone(const bool &) –> void
- set_cluster_radius(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, cluster_radius: float) None ¶
C++: protocols::cluster::ClusterBase::set_cluster_radius(double) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, filter: float) None ¶
C++: protocols::cluster::GatherPosesMover::set_filter(double) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_population_weight(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, population_weight: float) None ¶
C++: protocols::cluster::ClusterBase::set_population_weight(double) –> void
- set_score_function(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::cluster::GatherPosesMover::set_score_function(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- sort_each_group_by_energy(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::sort_each_group_by_energy() –> void
- sort_groups_by_energy(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) None ¶
C++: protocols::cluster::ClusterBase::sort_groups_by_energy() –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.cluster.DataPoint¶
Bases:
pybind11_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.
- property a_kk¶
- add_similarity(self: pyrosetta.rosetta.protocols.cluster.DataPoint, k: int, s_ik: float, max_sims: int) None ¶
Set similarity s(i,k), the suitability of point k to be an exemplar for this point.
C++: protocols::cluster::DataPoint::add_similarity(unsigned long, double, unsigned long) –> void
- property best_exemplar¶
- property candidate_for¶
- property candidates¶
- property curr_exemplar¶
- property i¶
- is_set_s_kk(self: pyrosetta.rosetta.protocols.cluster.DataPoint) bool ¶
C++: protocols::cluster::DataPoint::is_set_s_kk() const –> bool
- property r_kk¶
- property s_kk¶
- property sum¶
- class pyrosetta.rosetta.protocols.cluster.EnsembleConstraints¶
Bases:
GatherPosesMover
- apply(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::GatherPosesMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.cluster.EnsembleConstraints, : pyrosetta.rosetta.protocols.cluster.EnsembleConstraints) pyrosetta.rosetta.protocols.cluster.EnsembleConstraints ¶
C++: protocols::cluster::EnsembleConstraints::operator=(const class protocols::cluster::EnsembleConstraints &) –> class protocols::cluster::EnsembleConstraints &
- check_tag(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, query_tag: str) bool ¶
C++: protocols::cluster::GatherPosesMover::check_tag(const std::string &) –> bool
- clear(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) None ¶
C++: protocols::cluster::GatherPosesMover::clear() –> void
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- createConstraints(self: pyrosetta.rosetta.protocols.cluster.EnsembleConstraints, out: pyrosetta.rosetta.std.ostream) None ¶
C++: protocols::cluster::EnsembleConstraints::createConstraints(std::ostream &) –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob ¶
C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>
- get_current_tag(self: pyrosetta.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.
C++: protocols::moves::Mover::get_current_tag() const –> std::string
- get_distance_measure(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::cluster::GatherPosesMover::get_distance_measure(const class core::pose::Pose &, const class core::pose::Pose &) const –> double
- get_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) float ¶
C++: protocols::cluster::GatherPosesMover::get_filter() const –> double
- get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.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.
C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus
- get_name(self: pyrosetta.rosetta.protocols.cluster.EnsembleConstraints) str ¶
C++: protocols::cluster::EnsembleConstraints::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_pose_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_core_pose_Pose ¶
C++: protocols::cluster::GatherPosesMover::get_pose_list() –> class std::vector<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_tag_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_std_string ¶
C++: protocols::cluster::GatherPosesMover::get_tag_list() const –> const class std::vector<std::string, class std::allocator<std::string > > &
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nposes(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) int ¶
- Return the number of poses gathered by this mover
This is the post-filtered number of poses.
C++: protocols::cluster::GatherPosesMover::nposes() const –> unsigned long
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- push_back(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::GatherPosesMover::push_back(const class core::pose::Pose &) –> void
- static register_options() None ¶
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.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.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).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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.
C++: protocols::moves::Mover::reset_status() –> void
- set_cluster_by_all_atom(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_all_atom(const bool &) –> void
- set_cluster_by_protein_backbone(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_protein_backbone(const bool &) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, filter: float) None ¶
C++: protocols::cluster::GatherPosesMover::set_filter(double) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_score_function(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::cluster::GatherPosesMover::set_score_function(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple¶
Bases:
EnsembleConstraints
- apply(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::GatherPosesMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple, : pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple) pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple ¶
C++: protocols::cluster::EnsembleConstraints_Simple::operator=(const class protocols::cluster::EnsembleConstraints_Simple &) –> class protocols::cluster::EnsembleConstraints_Simple &
- check_tag(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, query_tag: str) bool ¶
C++: protocols::cluster::GatherPosesMover::check_tag(const std::string &) –> bool
- clear(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) None ¶
C++: protocols::cluster::GatherPosesMover::clear() –> void
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::cluster::EnsembleConstraints_Simple::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- createConstraints(self: pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple, out: pyrosetta.rosetta.std.ostream) None ¶
C++: protocols::cluster::EnsembleConstraints_Simple::createConstraints(std::ostream &) –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob ¶
C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>
- get_current_tag(self: pyrosetta.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.
C++: protocols::moves::Mover::get_current_tag() const –> std::string
- get_distance_measure(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::cluster::GatherPosesMover::get_distance_measure(const class core::pose::Pose &, const class core::pose::Pose &) const –> double
- get_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) float ¶
C++: protocols::cluster::GatherPosesMover::get_filter() const –> double
- get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.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.
C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus
- get_name(self: pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple) str ¶
C++: protocols::cluster::EnsembleConstraints_Simple::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_pose_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_core_pose_Pose ¶
C++: protocols::cluster::GatherPosesMover::get_pose_list() –> class std::vector<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_tag_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_std_string ¶
C++: protocols::cluster::GatherPosesMover::get_tag_list() const –> const class std::vector<std::string, class std::allocator<std::string > > &
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nposes(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) int ¶
- Return the number of poses gathered by this mover
This is the post-filtered number of poses.
C++: protocols::cluster::GatherPosesMover::nposes() const –> unsigned long
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- push_back(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::GatherPosesMover::push_back(const class core::pose::Pose &) –> void
- static register_options() None ¶
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.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.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).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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.
C++: protocols::moves::Mover::reset_status() –> void
- set_cluster_by_all_atom(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_all_atom(const bool &) –> void
- set_cluster_by_protein_backbone(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_protein_backbone(const bool &) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, filter: float) None ¶
C++: protocols::cluster::GatherPosesMover::set_filter(double) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_score_function(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::cluster::GatherPosesMover::set_score_function(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.cluster.Exemplar¶
Bases:
pybind11_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.
- property a_ik¶
- property k¶
- static min_heap(a: pyrosetta.rosetta.protocols.cluster.Exemplar, b: pyrosetta.rosetta.protocols.cluster.Exemplar) bool ¶
“Less than” (actually greater than) comparator for making a heap of exemplars
C++: protocols::cluster::Exemplar::min_heap(class protocols::cluster::Exemplar, class protocols::cluster::Exemplar) –> bool
- property r_ik¶
- property s_ik¶
- class pyrosetta.rosetta.protocols.cluster.GatherPosesMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::GatherPosesMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, : pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.protocols.cluster.GatherPosesMover ¶
C++: protocols::cluster::GatherPosesMover::operator=(const class protocols::cluster::GatherPosesMover &) –> class protocols::cluster::GatherPosesMover &
- check_tag(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, query_tag: str) bool ¶
C++: protocols::cluster::GatherPosesMover::check_tag(const std::string &) –> bool
- clear(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) None ¶
C++: protocols::cluster::GatherPosesMover::clear() –> void
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Return a clone of the Mover object.
C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
Generates a new Mover object freshly created with the default ctor.
C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.
C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>
- get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob ¶
C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>
- get_current_tag(self: pyrosetta.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.
C++: protocols::moves::Mover::get_current_tag() const –> std::string
- get_distance_measure(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::cluster::GatherPosesMover::get_distance_measure(const class core::pose::Pose &, const class core::pose::Pose &) const –> double
- get_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) float ¶
C++: protocols::cluster::GatherPosesMover::get_filter() const –> double
- get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.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.
C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus
- get_name(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) str ¶
C++: protocols::cluster::GatherPosesMover::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_pose_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_core_pose_Pose ¶
C++: protocols::cluster::GatherPosesMover::get_pose_list() –> class std::vector<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_tag_list(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) pyrosetta.rosetta.std.vector_std_string ¶
C++: protocols::cluster::GatherPosesMover::get_tag_list() const –> const class std::vector<std::string, class std::allocator<std::string > > &
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- nposes(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover) int ¶
- Return the number of poses gathered by this mover
This is the post-filtered number of poses.
C++: protocols::cluster::GatherPosesMover::nposes() const –> unsigned long
- parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.
C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- push_back(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::cluster::GatherPosesMover::push_back(const class core::pose::Pose &) –> void
- static register_options() None ¶
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.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.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).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
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.
C++: protocols::moves::Mover::reset_status() –> void
- set_cluster_by_all_atom(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_all_atom(const bool &) –> void
- set_cluster_by_protein_backbone(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, setting: bool) None ¶
C++: protocols::cluster::GatherPosesMover::set_cluster_by_protein_backbone(const bool &) –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_filter(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, filter: float) None ¶
C++: protocols::cluster::GatherPosesMover::set_filter(double) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_score_function(self: pyrosetta.rosetta.protocols.cluster.GatherPosesMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::cluster::GatherPosesMover::set_score_function(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &