cluster

Bindings for protocols::cluster namespace

class pyrosetta.rosetta.protocols.cluster.APCluster

Bases: pybind11_builtins.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: pyrosetta.rosetta.protocols.cluster.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_std_allocator_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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. 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_builtins.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: pyrosetta.rosetta.protocols.cluster.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.

  1. export_only_low(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. 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_std_allocator_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.

  1. limit_groups(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. 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.

  1. limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None

C++: protocols::cluster::ClusterBase::limit_groupsize(int) –> void

  1. 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.

  1. limit_total_structures(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. 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: pyrosetta.rosetta.protocols.cluster.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.

  1. export_only_low(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. 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_std_allocator_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.

  1. limit_groups(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. 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.

  1. limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None

C++: protocols::cluster::ClusterBase::limit_groupsize(int) –> void

  1. 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.

  1. limit_total_structures(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. 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: pyrosetta.rosetta.protocols.cluster.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.

  1. export_only_low(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. 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_std_allocator_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.

  1. limit_groups(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. 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.

  1. limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None

C++: protocols::cluster::ClusterBase::limit_groupsize(int) –> void

  1. 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.

  1. limit_total_structures(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. 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: pyrosetta.rosetta.protocols.cluster.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.

  1. export_only_low(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. 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_std_allocator_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.

  1. limit_groups(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. 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.

  1. limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. limit_groupsize(self: pyrosetta.rosetta.protocols.cluster.ClusterBase, limit: int) -> None

C++: protocols::cluster::ClusterBase::limit_groupsize(int) –> void

  1. 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.

  1. limit_total_structures(self: pyrosetta.rosetta.protocols.cluster.ClusterBase) -> None

  2. 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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. 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_builtins.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: pyrosetta.rosetta.protocols.cluster.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_std_allocator_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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. 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: pyrosetta.rosetta.protocols.cluster.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_std_allocator_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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. 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_builtins.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: pyrosetta.rosetta.protocols.moves.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_std_allocator_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.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. 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.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &