stateless

Bindings for protocols::docking::stateless namespace

class pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol

Bases: DockingProtocol

add_additional_low_resolution_step(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, additional_low_resolution_mover: pyrosetta.rosetta.protocols.moves.Mover) → None

C++: protocols::docking::DockingProtocol::add_additional_low_resolution_step(class std::shared_ptr<class protocols::moves::Mover>) –> void

add_additional_task_operaration(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, task_operation: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) → None

C++: protocols::docking::DockingProtocol::add_additional_task_operaration(class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void

add_jump(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, jump_number: int) → None

C++: protocols::docking::DockingProtocol::add_jump(const unsigned long) –> void

apply(self: pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::docking::stateless::SaneDockingProtocol::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol, : pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol) → pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol

C++: protocols::docking::stateless::SaneDockingProtocol::operator=(const class protocols::docking::stateless::SaneDockingProtocol &) –> class protocols::docking::stateless::SaneDockingProtocol &

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.docking.DockingProtocol) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::DockingProtocol::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>

docking_highres_mover(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.protocols.docking.DockingHighRes

C++: protocols::docking::DockingProtocol::docking_highres_mover() const –> class std::shared_ptr<const class protocols::docking::DockingHighRes>

docking_lowres_mover(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.protocols.docking.DockingLowRes

C++: protocols::docking::DockingProtocol::docking_lowres_mover() const –> class std::shared_ptr<const class protocols::docking::DockingLowRes>

fresh_instance(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::DockingProtocol::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_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t

C++: protocols::docking::DockingProtocol::get_additional_task_operarations() –> class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >

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_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::docking::DockingProtocol::get_highres_scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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.docking.stateless.SaneDockingProtocol) → str

C++: protocols::docking::stateless::SaneDockingProtocol::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

movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.utility.vector1_int

returns ref to the jumps vector for docking

C++: protocols::docking::DockingProtocol::movable_jumps() –> class utility::vector1<int, class std::allocator<int> > &

static mover_name() → str

C++: protocols::docking::DockingProtocol::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::docking::DockingProtocol::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

partners(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → str

returns the docking partners chain identifiers

C++: protocols::docking::DockingProtocol::partners() const –> std::string

perturber(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation

C++: protocols::docking::DockingProtocol::perturber() const –> class std::shared_ptr<const class protocols::docking::DockingInitialPerturbation>

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 provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::docking::DockingProtocol::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Associates relevant options with the DockingProtocol class

C++: protocols::docking::DockingProtocol::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.docking.DockingProtocol) → bool

This mover retains state such that a fresh version is needed if the input Pose is about to change

C++: protocols::docking::DockingProtocol::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_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) → None

C++: protocols::docking::DockingProtocol::set_additional_task_operarations(class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > >) –> void

set_autofoldtree(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, autofoldtree: bool) → None

C++: protocols::docking::DockingProtocol::set_autofoldtree(const bool) –> void

set_cst_weight(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, cst_weight: float) → None

C++: protocols::docking::DockingProtocol::set_cst_weight(const 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_default(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → None

Assigns default values to primitive members

C++: protocols::docking::DockingProtocol::set_default() –> void

set_design(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, design: bool) → None

C++: protocols::docking::DockingProtocol::set_design(const bool) –> void

set_dock_min(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, dock_min: bool) → None

C++: protocols::docking::DockingProtocol::set_dock_min(const bool) –> void

set_docking_highres_mover(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_highres_mover: pyrosetta.rosetta.protocols.docking.DockingHighRes) → None

C++: protocols::docking::DockingProtocol::set_docking_highres_mover(class std::shared_ptr<class protocols::docking::DockingHighRes>) –> void

set_docking_local_refine(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_local_refine: bool) → None

C++: protocols::docking::DockingProtocol::set_docking_local_refine(const bool) –> void

set_ensemble1(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, ensemble1: str) → None

C++: protocols::docking::DockingProtocol::set_ensemble1(const std::string &) –> void

set_ensemble2(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, ensemble2: str) → None

C++: protocols::docking::DockingProtocol::set_ensemble2(const std::string &) –> void

set_highres_scorefxn(*args, **kwargs)

Overloaded function.

1. set_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Sets the score function that will be used in the high-resolution phase.

The same score function will be used for evaluating moves, packing and discriminating

C++: protocols::docking::DockingProtocol::set_highres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

2. set_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Sets the score function that will be used in the high-resolution phase.

The first scorefunction will be used for evaluating moves and discriminating, the second will be used for packing

C++: protocols::docking::DockingProtocol::set_highres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

3. set_highres_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_scorefxn_high: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_scorefxn_output: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Sets the score function that will be used in the high-resolution phase.

The first scorefunction will be used for evaluating moves, the second will be used for packing and the third for discriminating

C++: protocols::docking::DockingProtocol::set_highres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_ignore_default_docking_task(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, ignore_default_docking_task: bool) → None

C++: protocols::docking::DockingProtocol::set_ignore_default_docking_task(const bool) –> void

set_inner_cycles(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, inner_cycles: int) → None

C++: protocols::docking::DockingProtocol::set_inner_cycles(unsigned long) –> 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_interface_definition_task_operation(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) → None

C++: protocols::docking::DockingProtocol::set_interface_definition_task_operation(class std::shared_ptr<class protocols::simple_task_operations::InterfaceTaskOperation>) –> void

set_low_res_protocol_only(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, low_res_protocol_only: bool) → None

C++: protocols::docking::DockingProtocol::set_low_res_protocol_only(const bool) –> void

set_lowres_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, docking_scorefxn_low: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Sets the score function that will be used in the low-resolution phase

C++: protocols::docking::DockingProtocol::set_lowres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, jump_numbers: pyrosetta.rosetta.utility.vector1_int) → None

C++: protocols::docking::DockingProtocol::set_movable_jumps(const class utility::vector1<int, class std::allocator<int> >) –> 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_no_filters(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, no_filters: bool) → None

C++: protocols::docking::DockingProtocol::set_no_filters(bool) –> void

set_outer_cycles(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, outer_cycles: int) → None

C++: protocols::docking::DockingProtocol::set_outer_cycles(unsigned long) –> void

set_partners(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, partners: str) → None

C++: protocols::docking::DockingProtocol::set_partners(const std::string &) –> void

set_recover_sidechains_filename(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, file: str) → None

C++: protocols::docking::DockingProtocol::set_recover_sidechains_filename(const std::string &) –> void

set_reporting(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, report: bool) → None

C++: protocols::docking::DockingProtocol::set_reporting(bool) –> void

set_rt_min(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, rt_min: bool) → None

C++: protocols::docking::DockingProtocol::set_rt_min(bool) –> void

set_sc_min(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, sc_min: bool) → None

C++: protocols::docking::DockingProtocol::set_sc_min(bool) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

C++: protocols::docking::DockingProtocol::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> 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

set_use_constraints(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, use_csts: bool) → None

C++: protocols::docking::DockingProtocol::set_use_constraints(const bool) –> void

set_use_legacy_protocol(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, use_legacy_protocol: bool) → None

C++: protocols::docking::DockingProtocol::set_use_legacy_protocol(const bool) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) -> None

2. show(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, out: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::docking::DockingProtocol::show(std::ostream &) const –> void

sync_objects_with_flags(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → None

Instantiates non-primitive members based on the value of the primitive members

C++: protocols::docking::DockingProtocol::sync_objects_with_flags() –> void

task_factory(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::docking::DockingProtocol::task_factory() –> const class core::pack::task::TaskFactory &

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

to_all_atom(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::DockingProtocol::to_all_atom() const –> class std::shared_ptr<const class protocols::moves::Mover>

to_centroid(self: pyrosetta.rosetta.protocols.docking.DockingProtocol) → protocols::simple_moves::SwitchResidueTypeSetMover

C++: protocols::docking::DockingProtocol::to_centroid() const –> class std::shared_ptr<const class protocols::simple_moves::SwitchResidueTypeSetMover>

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 &