network

Bindings for protocols::network namespace

pyrosetta.rosetta.protocols.network.AddUIObserver(p: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.network.UIObserver

Helper function that create UIObserver Object and add it to the give Pose.

This is the most likely the only function that you need to call…

C++: protocols::network::AddUIObserver(class core::pose::Pose &) –> class std::shared_ptr<class protocols::network::UIObserver>

pyrosetta.rosetta.protocols.network.AddUIObserver_to_conformation(p: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.network.UIObserver

Helper function that create UIObserver Object and add it to the give Pose conformation object so pymol only updates on conformation changes.

C++: protocols::network::AddUIObserver_to_conformation(class core::pose::Pose &) –> class std::shared_ptr<class protocols::network::UIObserver>

pyrosetta.rosetta.protocols.network.AddUIObserver_to_energies(p: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.network.UIObserver

Helper function that create UIObserver Object and add it to the give Pose energies object so pymol only updates on energy changes.

C++: protocols::network::AddUIObserver_to_energies(class core::pose::Pose &) –> class std::shared_ptr<class protocols::network::UIObserver>

class pyrosetta.rosetta.protocols.network.UIMover

Bases: Mover

Mover to send in-progress data to UI client Note: you will need to build Rosetta with extra=zmq for this Mover to do any real work

apply(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.network.UIMover, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::network::UIMover::apply(class core::pose::Pose &) –> void

2. apply(self: pyrosetta.rosetta.protocols.network.UIMover, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::network::UIMover::apply(const class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.network.UIMover, other: pyrosetta.rosetta.protocols.network.UIMover) → pyrosetta.rosetta.protocols.network.UIMover

C++: protocols::network::UIMover::operator=(const class protocols::network::UIMover &) –> class protocols::network::UIMover &

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_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.network.UIMover) → str

C++: protocols::network::UIMover::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_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_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str

C++: protocols::moves::Mover::name() –> std::string

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

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_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_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_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

2. 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.network.UIObserver

Bases: CacheableObserver

Special Observer which apply UIObserver if Pose is changed

class ObserverType

Bases: pybind11_object

Members:

general

energy

conformation

none

conformation = <ObserverType.conformation: 4>

energy = <ObserverType.energy: 2>

general = <ObserverType.general: 1>

property name

none = <ObserverType.none: 0>

property value

add_type(self: pyrosetta.rosetta.protocols.network.UIObserver, setting: pyrosetta.rosetta.protocols.network.UIObserver.ObserverType) → None

C++: protocols::network::UIObserver::add_type(enum protocols::network::UIObserver::ObserverType) –> void

assign(self: pyrosetta.rosetta.protocols.network.UIObserver, : pyrosetta.rosetta.protocols.network.UIObserver) → pyrosetta.rosetta.protocols.network.UIObserver

C++: protocols::network::UIObserver::operator=(const class protocols::network::UIObserver &) –> class protocols::network::UIObserver &

attach(self: pyrosetta.rosetta.protocols.network.UIObserver, p: pyrosetta.rosetta.core.pose.Pose) → None

Attach observer to the pose object

C++: protocols::network::UIObserver::attach(class core::pose::Pose &) –> void

attach_to(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver, pose: pyrosetta.rosetta.core.pose.Pose) → None

attach to Pose/Conformation

Derived classes do not overload this method – see attach_impl() instead.

C++: core::pose::datacache::CacheableObserver::attach_to(class core::pose::Pose &) –> void

clone(self: pyrosetta.rosetta.protocols.network.UIObserver) → pyrosetta.rosetta.core.pose.datacache.CacheableObserver

C++: protocols::network::UIObserver::clone() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

conformationEvent(self: pyrosetta.rosetta.protocols.network.UIObserver, ev: pyrosetta.rosetta.core.pose.signals.ConformationEvent) → None

C++: protocols::network::UIObserver::conformationEvent(const struct core::pose::signals::ConformationEvent &) –> void

create(self: pyrosetta.rosetta.protocols.network.UIObserver) → pyrosetta.rosetta.core.pose.datacache.CacheableObserver

C++: protocols::network::UIObserver::create() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

detach(self: pyrosetta.rosetta.protocols.network.UIObserver, p: pyrosetta.rosetta.core.pose.Pose) → None

Detach observer from the pose object

C++: protocols::network::UIObserver::detach(class core::pose::Pose &) –> void

detach_from(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver) → None

detach from Pose/Conformation

Derived classes do not overload this method – see

detach_impl() instead.

C++: core::pose::datacache::CacheableObserver::detach_from() –> void

energyEvent(self: pyrosetta.rosetta.protocols.network.UIObserver, ev: pyrosetta.rosetta.core.pose.signals.EnergyEvent) → None

C++: protocols::network::UIObserver::energyEvent(const struct core::pose::signals::EnergyEvent &) –> void

generalEvent(self: pyrosetta.rosetta.protocols.network.UIObserver, ev: pyrosetta.rosetta.core.pose.signals.GeneralEvent) → None

C++: protocols::network::UIObserver::generalEvent(const struct core::pose::signals::GeneralEvent &) –> void

get_type(self: pyrosetta.rosetta.protocols.network.UIObserver) → pyrosetta.rosetta.protocols.network.UIObserver.ObserverType

C++: protocols::network::UIObserver::get_type() const –> enum protocols::network::UIObserver::ObserverType

is_attached(self: pyrosetta.rosetta.protocols.network.UIObserver) → bool

C++: protocols::network::UIObserver::is_attached() const –> bool

set_type(self: pyrosetta.rosetta.protocols.network.UIObserver, setting: pyrosetta.rosetta.protocols.network.UIObserver.ObserverType) → None

C++: protocols::network::UIObserver::set_type(enum protocols::network::UIObserver::ObserverType) –> void

ui_mover(self: pyrosetta.rosetta.protocols.network.UIObserver) → pyrosetta.rosetta.protocols.network.UIMover

C++: protocols::network::UIObserver::ui_mover() –> class protocols::network::UIMover &

pyrosetta.rosetta.protocols.network.get_ui_observer(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.network.UIObserver

(Internal) helper function to create a UIObserver and add it to the given pose

NOTE: You NEED to adjust the observer type and call attach() on the return - by default a new UIObserver isn’t attached/observing.

C++: protocols::network::get_ui_observer(class core::pose::Pose &) –> class std::shared_ptr<class protocols::network::UIObserver>

pyrosetta.rosetta.protocols.network.has_observer_of_type(flag: pyrosetta.rosetta.protocols.network.UIObserver.ObserverType, observer: pyrosetta.rosetta.protocols.network.UIObserver.ObserverType) → bool

C++: protocols::network::has_observer_of_type(enum protocols::network::UIObserver::ObserverType, enum protocols::network::UIObserver::ObserverType) –> bool

pyrosetta.rosetta.protocols.network.post_decoy(*args, **kwargs)

Overloaded function.

1. post_decoy(file_name: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::network::post_decoy(const std::string &, const class core::pose::Pose &) –> void

2. post_decoy(pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::network::post_decoy(const class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.network.post_file(*args, **kwargs)

Overloaded function.

1. post_file(file_name: str, data: str) -> None

2. post_file(file_name: str, data: str, append: bool) -> None

C++: protocols::network::post_file(const std::string &, const std::string &, bool) –> void