docking

Bindings for protocols::docking namespace

class pyrosetta.rosetta.protocols.docking.ConformerSwitchMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

this mover does the conformer swap in RosettaDock’s ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction.

apply(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, pose: pyrosetta.rosetta.core.pose.Pose) None

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

assign(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, : pyrosetta.rosetta.protocols.docking.ConformerSwitchMover) pyrosetta.rosetta.protocols.docking.ConformerSwitchMover

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

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_ensemble(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover) protocols::docking::DockingEnsemble

C++: protocols::docking::ConformerSwitchMover::get_ensemble() –> class std::shared_ptr<class protocols::docking::DockingEnsemble>

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.ConformerSwitchMover) str

C++: protocols::docking::ConformerSwitchMover::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_temperature(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover) float

C++: protocols::docking::ConformerSwitchMover::get_temperature() const –> double

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 mover_name() str

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

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

C++: protocols::docking::ConformerSwitchMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> 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_random_confomer(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, rand: bool) None

C++: protocols::docking::ConformerSwitchMover::set_random_confomer(bool) –> void

set_specific_conformer(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, conformer_num_in: int) None

C++: protocols::docking::ConformerSwitchMover::set_specific_conformer(unsigned long) –> void

set_temperature(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, temp_in: float) None

C++: protocols::docking::ConformerSwitchMover::set_temperature(double) –> 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.docking.ConformerSwitchMover) -> None

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

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

switch_conformer(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover, pose: pyrosetta.rosetta.core.pose.Pose, conf_num: int) None

C++: protocols::docking::ConformerSwitchMover::switch_conformer(class core::pose::Pose &, unsigned long) –> 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 &

use_random_conformer(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMover) bool

C++: protocols::docking::ConformerSwitchMover::use_random_conformer() const –> bool

class pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator, : pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator) pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator

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

create_mover(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator) str

C++: protocols::docking::ConformerSwitchMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.docking.DHR_Type

Bases: pybind11_builtins.pybind11_object

Members:

DockingHighResLegacy

DockingPrepackProtocol

DockMCMProtocol

DockMinMover

SnugDock

DockMCMProtocol = <DHR_Type.DockMCMProtocol: 2>
DockMinMover = <DHR_Type.DockMinMover: 3>
DockingHighResLegacy = <DHR_Type.DockingHighResLegacy: 0>
DockingPrepackProtocol = <DHR_Type.DockingPrepackProtocol: 1>
SnugDock = <DHR_Type.SnugDock: 4>
property name
class pyrosetta.rosetta.protocols.docking.DockMCMCycle

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, pose: pyrosetta.rosetta.core.pose.Pose) None

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

assign(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, : pyrosetta.rosetta.protocols.docking.DockMCMCycle) pyrosetta.rosetta.protocols.docking.DockMCMCycle

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

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.DockMCMCycle) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::DockMCMCycle::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_mc(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle) pyrosetta.rosetta.protocols.moves.MonteCarlo

C++: protocols::docking::DockMCMCycle::get_mc() –> class std::shared_ptr<class protocols::moves::MonteCarlo>

get_name(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle) str

C++: protocols::docking::DockMCMCycle::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_std_allocator_std_string_t

non-const accessor

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

init_mc(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockMCMCycle::init_mc(class core::pose::Pose &) –> void

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.DockMCMCycle) pyrosetta.rosetta.utility.vector1_int

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

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_cycle_index(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle) None

C++: protocols::docking::DockMCMCycle::reset_cycle_index() –> 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

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.DockMCMCycle) None

Sets the default values for all members

C++: protocols::docking::DockMCMCycle::set_default() –> 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_min_type(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, min_type: str) None

C++: protocols::docking::DockMCMCycle::set_min_type(std::string) –> void

set_move_map(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::docking::DockMCMCycle::set_move_map(class std::shared_ptr<class core::kinematics::MoveMap>) –> 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_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, value: float) None

C++: protocols::docking::DockMCMCycle::set_rot_magnitude(double) –> void

set_rtmin(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, setting: bool) None

C++: protocols::docking::DockMCMCycle::set_rtmin(bool) –> void

set_scmin(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, setting: bool) None

C++: protocols::docking::DockMCMCycle::set_scmin(bool) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockMCMCycle, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::docking::DockMCMCycle::set_task_factory(class std::shared_ptr<const 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

show(*args, **kwargs)

Overloaded function.

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

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

C++: protocols::docking::DockMCMCycle::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.docking.DockMCMProtocol

Bases: pyrosetta.rosetta.protocols.docking.DockingHighRes

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

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

apply(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None

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

assign(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol, : pyrosetta.rosetta.protocols.docking.DockMCMProtocol) pyrosetta.rosetta.protocols.docking.DockMCMProtocol

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

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.DockMCMProtocol) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::DockMCMProtocol::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_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t

C++: protocols::docking::DockingHighRes::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_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.DockMCMProtocol) str

C++: protocols::docking::DockMCMProtocol::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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str

C++: protocols::docking::DockingHighRes::get_partners() const –> std::string

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

ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::ignore_default_task() –> bool

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 > > &

init(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol) None

Performs the setup specific to this subclass of DockingHighRes (sets up filters).

C++: protocols::docking::DockMCMProtocol::init() –> void

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.DockingHighRes) pyrosetta.rosetta.utility.vector1_int

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

static mover_name() str

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

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

partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str

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

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::DockMCMProtocol::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> 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

rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::rt_min() –> bool

sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::sc_min() –> bool

scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction

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

scorefxn_docking(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol) pyrosetta.rosetta.core.scoring.ScoreFunction

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

scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction

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

scorefxn_packing(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol) pyrosetta.rosetta.core.scoring.ScoreFunction

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

set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None

C++: protocols::docking::DockingHighRes::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_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.docking.DockMCMProtocol, filter: pyrosetta.rosetta.protocols.docking.DockingHighResFilter) None

C++: protocols::docking::DockMCMProtocol::set_filter(class std::shared_ptr<class protocols::docking::DockingHighResFilter>) –> void

set_first_cycle(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol, num: int) None

C++: protocols::docking::DockMCMProtocol::set_first_cycle(const unsigned long &) –> void

set_ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, ignore_default_task: bool) None

C++: protocols::docking::DockingHighRes::set_ignore_default_task(bool) –> 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.DockingHighRes, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None

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

set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None

C++: protocols::docking::DockingHighRes::set_movable_jumps(class utility::vector1<int, class std::allocator<int> >) –> void

set_move_map(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::docking::DockMCMProtocol::set_move_map(class std::shared_ptr<class core::kinematics::MoveMap>) –> 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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) None

C++: protocols::docking::DockingHighRes::set_partners(std::string) –> void

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

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

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

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

set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

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

set_scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) None

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

set_second_cycle(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocol, num: int) None

C++: protocols::docking::DockMCMProtocol::set_second_cycle(const unsigned long &) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::docking::DockingHighRes::set_task_factory(class std::shared_ptr<const 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

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

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

C++: protocols::docking::DockingHighRes::task_factory() –> class std::shared_ptr<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

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.docking.DockMCMProtocolCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator, : pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator) pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator

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

create_mover(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator) str

C++: protocols::docking::DockMCMProtocolCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.docking.DockMinMover

Bases: pyrosetta.rosetta.protocols.docking.DockingHighRes

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

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

apply(self: pyrosetta.rosetta.protocols.docking.DockMinMover, : pyrosetta.rosetta.core.pose.Pose) None

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

assign(self: pyrosetta.rosetta.protocols.docking.DockMinMover, : pyrosetta.rosetta.protocols.docking.DockMinMover) pyrosetta.rosetta.protocols.docking.DockMinMover

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

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_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t

C++: protocols::docking::DockingHighRes::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_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.DockMinMover) str

C++: protocols::docking::DockMinMover::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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str

C++: protocols::docking::DockingHighRes::get_partners() const –> std::string

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

ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::ignore_default_task() –> bool

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

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

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

static mover_name() str

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

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

partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str

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

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::DockMinMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> 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

rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::rt_min() –> bool

sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::sc_min() –> bool

scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction

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

scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction

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

set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None

C++: protocols::docking::DockingHighRes::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_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.DockMinMover) None

Sets up the default values for the obejct including the movemap and minimization type.

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

set_ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, ignore_default_task: bool) None

C++: protocols::docking::DockingHighRes::set_ignore_default_task(bool) –> 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.DockingHighRes, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None

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

set_min_tolerance(self: pyrosetta.rosetta.protocols.docking.DockMinMover, min_tolerance: float) None

C++: protocols::docking::DockMinMover::set_min_tolerance(double) –> void

set_min_type(self: pyrosetta.rosetta.protocols.docking.DockMinMover, min_type: str) None

setters for member variables

C++: protocols::docking::DockMinMover::set_min_type(std::string) –> void

set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None

C++: protocols::docking::DockingHighRes::set_movable_jumps(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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) None

C++: protocols::docking::DockingHighRes::set_partners(std::string) –> void

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

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

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

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

set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

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

set_scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) None

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

set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::docking::DockingHighRes::set_task_factory(class std::shared_ptr<const 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

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

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

C++: protocols::docking::DockingHighRes::task_factory() –> class std::shared_ptr<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

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.docking.DockMinMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.docking.DockMinMoverCreator, : pyrosetta.rosetta.protocols.docking.DockMinMoverCreator) pyrosetta.rosetta.protocols.docking.DockMinMoverCreator

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

create_mover(self: pyrosetta.rosetta.protocols.docking.DockMinMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.docking.DockMinMoverCreator) str

C++: protocols::docking::DockMinMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.docking.DockMinMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.docking.DockSetupMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

allows docking using simulated or parallel tempering

apply(self: pyrosetta.rosetta.protocols.docking.DockSetupMover, pose: pyrosetta.rosetta.core.pose.Pose) None

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

assign(self: pyrosetta.rosetta.protocols.docking.DockSetupMover, rhs: pyrosetta.rosetta.protocols.docking.DockSetupMover) pyrosetta.rosetta.protocols.docking.DockSetupMover

assignment operator

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

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.DockSetupMover) pyrosetta.rosetta.protocols.moves.Mover

clone

C++: protocols::docking::DockSetupMover::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.docking.DockSetupMover) str

C++: protocols::docking::DockSetupMover::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_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 mover_name() str

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

static name() str

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

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

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

partners(self: pyrosetta.rosetta.protocols.docking.DockSetupMover) str

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

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::DockSetupMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> 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_defaults(self: pyrosetta.rosetta.protocols.docking.DockSetupMover) None

Assigns default values to primitive members

C++: protocols::docking::DockSetupMover::set_defaults() –> 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_partners(self: pyrosetta.rosetta.protocols.docking.DockSetupMover, setting: str) None

C++: protocols::docking::DockSetupMover::set_partners(const std::string &) –> 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.docking.DockSetupMover) -> None

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

C++: protocols::docking::DockSetupMover::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.docking.DockSetupMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator, : pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator) pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator

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

create_mover(self: pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator) str

C++: protocols::docking::DockSetupMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.docking.DockTaskFactory

Bases: pybind11_builtins.pybind11_object

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

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

assign(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, : pyrosetta.rosetta.protocols.docking.DockTaskFactory) pyrosetta.rosetta.protocols.docking.DockTaskFactory

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

create_and_attach_task_factory(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, docker: pyrosetta.rosetta.protocols.docking.DockingHighRes, pose: pyrosetta.rosetta.core.pose.Pose) None
Creates an appropriate TaskFactory based on command line options and attach it to a DockingHighResOP

Two arguments: DockingHighResOP and a pose.

C++: protocols::docking::DockTaskFactory::create_and_attach_task_factory(class protocols::docking::DockingHighRes *, const class core::pose::Pose &) const –> void

get_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t

C++: protocols::docking::DockTaskFactory::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_norepack1(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory) bool

C++: protocols::docking::DockTaskFactory::get_norepack1() const –> bool

get_norepack2(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory) bool

C++: protocols::docking::DockTaskFactory::get_norepack2() const –> bool

init_from_options(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory) None

Assigns user specified values to members using command line options

C++: protocols::docking::DockTaskFactory::init_from_options() –> void

register_options(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory) None

Associates relevant options with the DockTaskFactory class

C++: protocols::docking::DockTaskFactory::register_options() –> void

set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None

C++: protocols::docking::DockTaskFactory::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_default(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory) None

Sets booleans to default values

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

set_design_chains(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, design_chains: pyrosetta.rosetta.utility.vector1_char) None

C++: protocols::docking::DockTaskFactory::set_design_chains(class utility::vector1<char, class std::allocator<char> >) –> void

set_interface_definition_task_operation(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None

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

set_norepack1(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, norepack1: bool) None

C++: protocols::docking::DockTaskFactory::set_norepack1(bool) –> void

set_norepack2(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, norepack2: bool) None

C++: protocols::docking::DockTaskFactory::set_norepack2(bool) –> void

set_prepack_only(self: pyrosetta.rosetta.protocols.docking.DockTaskFactory, prepack_only: bool) None

C++: protocols::docking::DockTaskFactory::set_prepack_only(bool) –> void

class pyrosetta.rosetta.protocols.docking.DockingEnsemble

Bases: pybind11_builtins.pybind11_object

this mover does the conformer swap in RosettaDock’s ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction.

assign(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, : pyrosetta.rosetta.protocols.docking.DockingEnsemble) pyrosetta.rosetta.protocols.docking.DockingEnsemble

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

calculate_highres_ref_energy(*args, **kwargs)

Overloaded function.

  1. calculate_highres_ref_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) -> None

C++: protocols::docking::DockingEnsemble::calculate_highres_ref_energy(unsigned long) –> void

  1. calculate_highres_ref_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, pose: pyrosetta.rosetta.core.pose.Pose, partner_num: str) -> None

C++: protocols::docking::DockingEnsemble::calculate_highres_ref_energy(class core::pose::Pose &, std::string) –> void

calculate_lowres_ref_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockingEnsemble::calculate_lowres_ref_energy(class core::pose::Pose &) –> void

conf_size(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) int

C++: protocols::docking::DockingEnsemble::conf_size() –> unsigned long

end_res(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) int

C++: protocols::docking::DockingEnsemble::end_res() –> unsigned long

get_conformer(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) pyrosetta.rosetta.core.pose.Pose

C++: protocols::docking::DockingEnsemble::get_conformer(unsigned long) –> class core::pose::Pose &

get_conformer_cen(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) pyrosetta.rosetta.core.pose.Pose

C++: protocols::docking::DockingEnsemble::get_conformer_cen(unsigned long) –> class core::pose::Pose &

get_current_confnum(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) int

C++: protocols::docking::DockingEnsemble::get_current_confnum() –> unsigned long

highres_reference_energy(*args, **kwargs)

Overloaded function.

  1. highres_reference_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) -> float

C++: protocols::docking::DockingEnsemble::highres_reference_energy(unsigned long) –> double

  1. highres_reference_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) -> float

C++: protocols::docking::DockingEnsemble::highres_reference_energy() –> double

jump_id(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) int

C++: protocols::docking::DockingEnsemble::jump_id() –> unsigned long

lowres_reference_energy(*args, **kwargs)

Overloaded function.

  1. lowres_reference_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) -> float

C++: protocols::docking::DockingEnsemble::lowres_reference_energy(unsigned long) –> double

  1. lowres_reference_energy(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) -> float

C++: protocols::docking::DockingEnsemble::lowres_reference_energy() –> double

partner(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) str

C++: protocols::docking::DockingEnsemble::partner() –> std::string

recover_and_pack_conformer_sidechains(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockingEnsemble::recover_and_pack_conformer_sidechains(class core::pose::Pose &) –> void

scorefxn_low(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) pyrosetta.rosetta.core.scoring.ScoreFunction

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

set_current_confnum(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, conf_num: int) None

C++: protocols::docking::DockingEnsemble::set_current_confnum(unsigned long) –> void

set_packer(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, packer: protocols::moves::SequenceMover) None

C++: protocols::docking::DockingEnsemble::set_packer(class std::shared_ptr<class protocols::moves::SequenceMover>) –> void

size(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) int

C++: protocols::docking::DockingEnsemble::size() –> unsigned long

start_res(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble) int

C++: protocols::docking::DockingEnsemble::start_res() –> unsigned long

update_pdblist_file(self: pyrosetta.rosetta.protocols.docking.DockingEnsemble, partner_num: str) None

C++: protocols::docking::DockingEnsemble::update_pdblist_file(std::string) –> void

class pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol

Bases: pyrosetta.rosetta.protocols.docking.DockingHighRes

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

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

apply(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol, : pyrosetta.rosetta.core.pose.Pose) None

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

assign(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol, : pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol) pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol

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

check_ensemble_member_compatibility(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol) None

Ensures all members of either ensemble are compatible with one another

C++: protocols::docking::DockingEnsemblePrepackProtocol::check_ensemble_member_compatibility() –> 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_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t

C++: protocols::docking::DockingHighRes::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_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.DockingEnsemblePrepackProtocol) str

C++: protocols::docking::DockingEnsemblePrepackProtocol::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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str

C++: protocols::docking::DockingHighRes::get_partners() const –> std::string

get_pose_chains(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol, : pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_char

Returns a vector1 of the pdb chains in a pose, in order

C++: protocols::docking::DockingEnsemblePrepackProtocol::get_pose_chains(class core::pose::Pose &) –> class utility::vector1<char, class std::allocator<char> >

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

ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::ignore_default_task() –> bool

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

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

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

move_away(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockingEnsemblePrepackProtocol::move_away(class core::pose::Pose &) –> void

move_back(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockingEnsemblePrepackProtocol::move_back(class core::pose::Pose &) –> void

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

partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str

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

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

rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::rt_min() –> bool

sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::sc_min() –> bool

scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction

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

scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction

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

set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None

C++: protocols::docking::DockingHighRes::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_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_ensemble1(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol, ensemble1: str) None

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

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

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

set_ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, ignore_default_task: bool) None

C++: protocols::docking::DockingHighRes::set_ignore_default_task(bool) –> 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.DockingHighRes, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None

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

set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None

C++: protocols::docking::DockingHighRes::set_movable_jumps(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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) None

C++: protocols::docking::DockingHighRes::set_partners(std::string) –> void

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

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

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

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

set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

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

set_scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) None

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

set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::docking::DockingHighRes::set_task_factory(class std::shared_ptr<const 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

setup_defaults(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol) None

Assigns default values to members

C++: protocols::docking::DockingEnsemblePrepackProtocol::setup_defaults() –> void

setup_pack_operation_movers(self: pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol) None

Instantiates and configures movers used by DockingEnsemblePrepackProtocol

C++: protocols::docking::DockingEnsemblePrepackProtocol::setup_pack_operation_movers() –> 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

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

C++: protocols::docking::DockingHighRes::task_factory() –> class std::shared_ptr<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

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.docking.DockingHighRes

Bases: pyrosetta.rosetta.protocols.moves.Mover

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

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

apply(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, pose: pyrosetta.rosetta.core.pose.Pose) None

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

assign(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, : pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.protocols.docking.DockingHighRes

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

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_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t

C++: protocols::docking::DockingHighRes::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_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.DockingHighRes) str

C++: protocols::docking::DockingHighRes::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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str

C++: protocols::docking::DockingHighRes::get_partners() const –> std::string

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

ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::ignore_default_task() –> bool

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

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

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

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

partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str

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

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

rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::rt_min() –> bool

sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::sc_min() –> bool

scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction

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

scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction

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

set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None

C++: protocols::docking::DockingHighRes::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_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_ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, ignore_default_task: bool) None

C++: protocols::docking::DockingHighRes::set_ignore_default_task(bool) –> 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.DockingHighRes, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None

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

set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None

C++: protocols::docking::DockingHighRes::set_movable_jumps(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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) None

C++: protocols::docking::DockingHighRes::set_partners(std::string) –> void

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

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

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

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

set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

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

set_scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) None

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

set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::docking::DockingHighRes::set_task_factory(class std::shared_ptr<const 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

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

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

C++: protocols::docking::DockingHighRes::task_factory() –> class std::shared_ptr<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

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.docking.DockingHighResFactory

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_docking_DockingHighResFactory_t

DockingHighResFactory uses the MoverFactory to create instances of DockingHighRes

create_docking_high_res_mover(self: pyrosetta.rosetta.protocols.docking.DockingHighResFactory, type_name: pyrosetta.rosetta.protocols.docking.DHR_Type) pyrosetta.rosetta.protocols.docking.DockingHighRes

Create the specified DockingHighRes

C++: protocols::docking::DockingHighResFactory::create_docking_high_res_mover(const enum protocols::docking::DHR_Type &) –> class std::shared_ptr<class protocols::docking::DockingHighRes>

static get_instance() protocols::docking::DockingHighResFactory

C++: utility::SingletonBase<protocols::docking::DockingHighResFactory>::get_instance() –> class protocols::docking::DockingHighResFactory *

class pyrosetta.rosetta.protocols.docking.DockingHighResFilter

Bases: pyrosetta.rosetta.protocols.filters.Filter

High-resolution (all-atom) filter for docking. Checks (1) total_score beats the cutoff given

  1. interface_score must be negative

/// ++ had: 1-score filter 2-fa_rep filter 3-interfaceE filter 4-chainbreak filter TTD: add these other filters

apply(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::docking::DockingHighResFilter::apply(const class core::pose::Pose &) const –> bool

clear(self: pyrosetta.rosetta.protocols.filters.Filter) None

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter) pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::docking::DockingHighResFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter) pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::docking::DockingHighResFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) str

C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) str

C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.filters.Filter) str

C++: protocols::filters::Filter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

Called by FilterFactory when constructing new Filter. Takes care of the specific mover’s parsing.

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

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : 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 filters wishing to provide citation information.

C++: protocols::filters::Filter::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

report(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::filters::Filter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::filters::Filter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_moveable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None

C++: protocols::docking::DockingHighResFilter::set_moveable_jumps(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_score_cutoff(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, new_cutoff: float) None

C++: protocols::docking::DockingHighResFilter::set_score_cutoff(double) –> void

set_score_margin(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, new_score_margin: float) None

C++: protocols::docking::DockingHighResFilter::set_score_margin(double) –> void

set_scorefunction(self: pyrosetta.rosetta.protocols.docking.DockingHighResFilter, scorefunction: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::docking::DockingHighResFilter::set_scorefunction(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) None

C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

class pyrosetta.rosetta.protocols.docking.DockingHighResLegacy

Bases: pyrosetta.rosetta.protocols.docking.DockingHighRes

this mover does the high resolution refinement stage of the RosettaDock algorithm

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

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

apply(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose) None

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

assign(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, : pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) pyrosetta.rosetta.protocols.docking.DockingHighResLegacy

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

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.DockingHighResLegacy) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::DockingHighResLegacy::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>

define_loops(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose, loop_set: pyrosetta.rosetta.protocols.loops.Loops, interface_dist: float) None

C++: protocols::docking::DockingHighResLegacy::define_loops(const class core::pose::Pose &, class std::shared_ptr<class protocols::loops::Loops>, double &) –> void

design(*args, **kwargs)

Overloaded function.

  1. design(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, des: bool) -> None

C++: protocols::docking::DockingHighResLegacy::design(const bool) –> void

  1. design(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) -> bool

C++: protocols::docking::DockingHighResLegacy::design() const –> bool

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_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t

C++: protocols::docking::DockingHighRes::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_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_mc(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) pyrosetta.rosetta.protocols.moves.MonteCarlo

C++: protocols::docking::DockingHighResLegacy::get_mc() –> class std::shared_ptr<class protocols::moves::MonteCarlo>

get_name(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) str

C++: protocols::docking::DockingHighResLegacy::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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str

C++: protocols::docking::DockingHighRes::get_partners() const –> std::string

get_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) float

C++: protocols::docking::DockingHighResLegacy::get_rot_magnitude() –> double

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_trans_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) float

C++: protocols::docking::DockingHighResLegacy::get_trans_magnitude() –> double

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::ignore_default_task() –> bool

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

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

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

static mover_name() str

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

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

partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str

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

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::DockingHighResLegacy::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> 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

rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) bool

C++: protocols::docking::DockingHighResLegacy::rt_min() –> bool

sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) bool

C++: protocols::docking::DockingHighResLegacy::sc_min() –> bool

scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction

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

scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction

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

set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None

C++: protocols::docking::DockingHighRes::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_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.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockingHighResLegacy::set_default(class core::pose::Pose &) –> void

set_dock_mcm_protocol(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(class core::pose::Pose &) –> void

set_dock_min_protocol(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy) None

C++: protocols::docking::DockingHighResLegacy::set_dock_min_protocol() –> void

set_dock_ppk_protocol(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockingHighResLegacy::set_dock_ppk_protocol(class core::pose::Pose &) –> void

set_ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, ignore_default_task: bool) None

C++: protocols::docking::DockingHighRes::set_ignore_default_task(bool) –> 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.DockingHighRes, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None

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

set_min_type(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, min_type_in: str) None

C++: protocols::docking::DockingHighResLegacy::set_min_type(std::string) –> void

set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None

C++: protocols::docking::DockingHighRes::set_movable_jumps(class utility::vector1<int, class std::allocator<int> >) –> void

set_move_map(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, movemap_in: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::docking::DockingHighResLegacy::set_move_map(class std::shared_ptr<class core::kinematics::MoveMap>) –> 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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) None

C++: protocols::docking::DockingHighRes::set_partners(std::string) –> void

set_protocol(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockingHighResLegacy::set_protocol(class core::pose::Pose &) –> void

set_repack(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, repack_switch: bool) None

C++: protocols::docking::DockingHighResLegacy::set_repack(bool) –> void

set_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, rot_magnitude: float) None

C++: protocols::docking::DockingHighResLegacy::set_rot_magnitude(double) –> void

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

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

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

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

set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

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

set_scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) None

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

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

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

set_trans_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacy, trans_magnitude: float) None

C++: protocols::docking::DockingHighResLegacy::set_trans_magnitude(double) –> 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

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

C++: protocols::docking::DockingHighRes::task_factory() –> class std::shared_ptr<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

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.docking.DockingHighResLegacyCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator, : pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator) pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator

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

create_mover(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator) str

C++: protocols::docking::DockingHighResLegacyCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation

Bases: pyrosetta.rosetta.protocols.moves.Mover

this mover carries out the initial perturbation phase of the RosettaDock algorithm based on user-inputted command line options

apply(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, pose: pyrosetta.rosetta.core.pose.Pose) None

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

apply_body(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, pose: pyrosetta.rosetta.core.pose.Pose, jump_number: int) None

C++: protocols::docking::DockingInitialPerturbation::apply_body(class core::pose::Pose &, unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, : pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation) pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation

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

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.DockingInitialPerturbation) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::DockingInitialPerturbation::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.docking.DockingInitialPerturbation) str

C++: protocols::docking::DockingInitialPerturbation::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_std_allocator_std_string_t

non-const accessor

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

init(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation) None

Calls set_dault, register_from_options and init_from_options

C++: protocols::docking::DockingInitialPerturbation::init() –> void

init_from_options(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation) None

Assigns user specified values to primitive members using command line options

C++: protocols::docking::DockingInitialPerturbation::init_from_options() –> void

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

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

static mover_name() str

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

static name() str

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

or_randomize2(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, randomize2: bool) None

C++: protocols::docking::DockingInitialPerturbation::or_randomize2(bool) –> void

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

zhe for rosetta_scripts

C++: protocols::docking::DockingInitialPerturbation::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 provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

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

static register_options() None

Associates relevant options with the DockingInitialPerturbation class

C++: protocols::docking::DockingInitialPerturbation::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_center(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, center: bool) None

C++: protocols::docking::DockingInitialPerturbation::set_center(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_default(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation) None

Sets members to default values

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

set_dock_pert(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, dock_pert: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::docking::DockingInitialPerturbation::set_dock_pert(const class utility::vector1<double, class std::allocator<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_randomize1(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, randomize1: bool) None

set functions

C++: protocols::docking::DockingInitialPerturbation::set_randomize1(bool) –> void

set_randomize2(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, randomize2: bool) None

C++: protocols::docking::DockingInitialPerturbation::set_randomize2(bool) –> void

set_spin(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, spin: bool) None

C++: protocols::docking::DockingInitialPerturbation::set_spin(bool) –> void

set_tilt(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, tilt: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::docking::DockingInitialPerturbation::set_tilt(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_tilt1_center(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, tilt_center: str) None

C++: protocols::docking::DockingInitialPerturbation::set_tilt1_center(const std::string &) –> void

set_tilt2_center(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, tilt_center: str) None

C++: protocols::docking::DockingInitialPerturbation::set_tilt2_center(const std::string &) –> 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_uniform_trans(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, uniform_trans: float) None

C++: protocols::docking::DockingInitialPerturbation::set_uniform_trans(double) –> void

set_use_ellipsoidal_randomization(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation, use_ellipsoidal_randomization: bool) None

C++: protocols::docking::DockingInitialPerturbation::set_use_ellipsoidal_randomization(bool) –> 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.docking.DockingInitialPerturbationCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator, : pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator) pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator

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

create_mover(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator) str

C++: protocols::docking::DockingInitialPerturbationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.docking.DockingLowRes

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None

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

assign(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, : pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.protocols.docking.DockingLowRes

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

calc_accept_rate(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None

C++: protocols::docking::DockingLowRes::calc_accept_rate() –> 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.docking.DockingLowRes) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::DockingLowRes::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>

property first_apply_with_current_setup_
property flags_and_objects_are_in_sync_
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_accept_rate(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float

C++: protocols::docking::DockingLowRes::get_accept_rate() –> double

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_conformer_ensemble1(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) int

C++: protocols::docking::DockingLowRes::get_current_conformer_ensemble1() –> unsigned long

get_current_conformer_ensemble2(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) int

C++: protocols::docking::DockingLowRes::get_current_conformer_ensemble2() –> unsigned long

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_inner_cycles(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) int

C++: protocols::docking::DockingLowRes::get_inner_cycles() –> unsigned long

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_mc(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.protocols.moves.MonteCarlo

C++: protocols::docking::DockingLowRes::get_mc() –> class std::shared_ptr<class protocols::moves::MonteCarlo>

get_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.utility.vector1_int

C++: protocols::docking::DockingLowRes::get_movable_jumps() –> class utility::vector1<int, class std::allocator<int> >

get_name(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) str

C++: protocols::docking::DockingLowRes::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_outer_cycles(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) int

C++: protocols::docking::DockingLowRes::get_outer_cycles() –> unsigned long

get_pymol_mover(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) protocols::moves::PyMOLMover

C++: protocols::docking::DockingLowRes::get_pymol_mover() –> class std::shared_ptr<class protocols::moves::PyMOLMover>

get_rb_mover(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover

C++: protocols::docking::DockingLowRes::get_rb_mover() –> class std::shared_ptr<class protocols::rigid::RigidBodyPerturbNoCenterMover>

get_rb_seq(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.protocols.moves.SequenceMover

C++: protocols::docking::DockingLowRes::get_rb_seq() –> class std::shared_ptr<class protocols::moves::SequenceMover>

get_rb_trial(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) protocols::moves::TrialMover

C++: protocols::docking::DockingLowRes::get_rb_trial() –> class std::shared_ptr<class protocols::moves::TrialMover>

get_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float

C++: protocols::docking::DockingLowRes::get_rot_magnitude() –> double

get_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.core.scoring.ScoreFunction

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

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_temperature(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float

C++: protocols::docking::DockingLowRes::get_temperature() –> double

get_trans_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float

Option getters - added by SSRB

C++: protocols::docking::DockingLowRes::get_trans_magnitude() –> double

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

get_view_in_pymol(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) bool

C++: protocols::docking::DockingLowRes::get_view_in_pymol() –> bool

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

lowres_inner_cycle(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockingLowRes::lowres_inner_cycle(class core::pose::Pose &) –> void

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

pymol_color_change(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockingLowRes::pymol_color_change(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_rb_trial_counters(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None

C++: protocols::docking::DockingLowRes::reset_rb_trial_counters() –> 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

rigid_body_trial(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None

Perform a cycle of rigid-body Monte Carlo moves

C++: protocols::docking::DockingLowRes::rigid_body_trial(class core::pose::Pose &) –> 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.DockingLowRes) None

Assigns default values to primitive members

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

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

C++: protocols::docking::DockingLowRes::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_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_outer_cycles(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, outer_cycles: int) None

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

set_rb_trial(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, rb_trial_in: protocols::moves::TrialMover) None

C++: protocols::docking::DockingLowRes::set_rb_trial(class std::shared_ptr<class protocols::moves::TrialMover>) –> void

set_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, rot_magnitude: float) None

C++: protocols::docking::DockingLowRes::set_rot_magnitude(double) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::docking::DockingLowRes::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_trans_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, trans_magnitude: float) None

C++: protocols::docking::DockingLowRes::set_trans_magnitude(double) –> 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.docking.DockingLowRes) -> None

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

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

sync_magnitudes_with_flags(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None

C++: protocols::docking::DockingLowRes::sync_magnitudes_with_flags() –> void

sync_objects_with_flags(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None

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

C++: protocols::docking::DockingLowRes::sync_objects_with_flags() –> 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.docking.DockingLowResEnsemble

Bases: pyrosetta.rosetta.protocols.docking.DockingLowRes

adaptive_inner_cycle(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockingLowResEnsemble::adaptive_inner_cycle(class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None

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

assign(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble, : pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble) pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble

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

calc_accept_rate(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None

C++: protocols::docking::DockingLowRes::calc_accept_rate() –> void

calc_ensemble_accept_rate_(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble) None

C++: protocols::docking::DockingLowResEnsemble::calc_ensemble_accept_rate_() –> 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.docking.DockingLowResEnsemble) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::docking::DockingLowResEnsemble::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>

ensemble_defaults(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble) None

C++: protocols::docking::DockingLowResEnsemble::ensemble_defaults() –> void

property first_apply_with_current_setup_
property flags_and_objects_are_in_sync_
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_accept_rate(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float

C++: protocols::docking::DockingLowRes::get_accept_rate() –> double

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_conformer_ensemble1(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble) int

C++: protocols::docking::DockingLowResEnsemble::get_current_conformer_ensemble1() –> unsigned long

get_current_conformer_ensemble2(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble) int

C++: protocols::docking::DockingLowResEnsemble::get_current_conformer_ensemble2() –> unsigned long

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_inner_cycles(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) int

C++: protocols::docking::DockingLowRes::get_inner_cycles() –> unsigned long

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_mc(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.protocols.moves.MonteCarlo

C++: protocols::docking::DockingLowRes::get_mc() –> class std::shared_ptr<class protocols::moves::MonteCarlo>

get_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.utility.vector1_int

C++: protocols::docking::DockingLowRes::get_movable_jumps() –> class utility::vector1<int, class std::allocator<int> >

get_name(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) str

C++: protocols::docking::DockingLowRes::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_outer_cycles(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) int

C++: protocols::docking::DockingLowRes::get_outer_cycles() –> unsigned long

get_pymol_mover(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) protocols::moves::PyMOLMover

C++: protocols::docking::DockingLowRes::get_pymol_mover() –> class std::shared_ptr<class protocols::moves::PyMOLMover>

get_rb_mover(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover

C++: protocols::docking::DockingLowRes::get_rb_mover() –> class std::shared_ptr<class protocols::rigid::RigidBodyPerturbNoCenterMover>

get_rb_seq(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.protocols.moves.SequenceMover

C++: protocols::docking::DockingLowRes::get_rb_seq() –> class std::shared_ptr<class protocols::moves::SequenceMover>

get_rb_trial(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) protocols::moves::TrialMover

C++: protocols::docking::DockingLowRes::get_rb_trial() –> class std::shared_ptr<class protocols::moves::TrialMover>

get_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float

C++: protocols::docking::DockingLowRes::get_rot_magnitude() –> double

get_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) pyrosetta.rosetta.core.scoring.ScoreFunction

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

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_temperature(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float

C++: protocols::docking::DockingLowRes::get_temperature() –> double

get_trans_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) float

Option getters - added by SSRB

C++: protocols::docking::DockingLowRes::get_trans_magnitude() –> double

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

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

get_view_in_pymol(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) bool

C++: protocols::docking::DockingLowRes::get_view_in_pymol() –> bool

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 > > &

initialize_movers(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble) None

C++: protocols::docking::DockingLowResEnsemble::initialize_movers() –> void

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

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

lowres_inner_cycle(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockingLowResEnsemble::lowres_inner_cycle(class core::pose::Pose &) –> void

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

pymol_color_change(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockingLowRes::pymol_color_change(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_ensemble_trial_counters(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble) None

C++: protocols::docking::DockingLowResEnsemble::reset_ensemble_trial_counters() –> void

reset_rb_trial_counters(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None

C++: protocols::docking::DockingLowRes::reset_rb_trial_counters() –> 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

rigid_body_trial(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None

Perform a cycle of rigid-body Monte Carlo moves

C++: protocols::docking::DockingLowRes::rigid_body_trial(class core::pose::Pose &) –> 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.DockingLowRes) None

Assigns default values to primitive members

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

set_ensemble1(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble, ensemble1: pyrosetta.rosetta.protocols.docking.DockingEnsemble) None

C++: protocols::docking::DockingLowResEnsemble::set_ensemble1(class std::shared_ptr<class protocols::docking::DockingEnsemble>) –> void

set_ensemble2(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble, ensemble2: pyrosetta.rosetta.protocols.docking.DockingEnsemble) None

C++: protocols::docking::DockingLowResEnsemble::set_ensemble2(class std::shared_ptr<class protocols::docking::DockingEnsemble>) –> void

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

C++: protocols::docking::DockingLowRes::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_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_outer_cycles(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, outer_cycles: int) None

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

set_rb_trial(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, rb_trial_in: protocols::moves::TrialMover) None

C++: protocols::docking::DockingLowRes::set_rb_trial(class std::shared_ptr<class protocols::moves::TrialMover>) –> void

set_rot_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, rot_magnitude: float) None

C++: protocols::docking::DockingLowRes::set_rot_magnitude(double) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::docking::DockingLowRes::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_trans_magnitude(self: pyrosetta.rosetta.protocols.docking.DockingLowRes, trans_magnitude: float) None

C++: protocols::docking::DockingLowRes::set_trans_magnitude(double) –> 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.docking.DockingLowResEnsemble) -> None

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

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

sync_magnitudes_with_flags(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None

C++: protocols::docking::DockingLowRes::sync_magnitudes_with_flags() –> void

sync_objects_with_flags(self: pyrosetta.rosetta.protocols.docking.DockingLowRes) None

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

C++: protocols::docking::DockingLowRes::sync_objects_with_flags() –> 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

try_all_conformers(self: pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockingLowResEnsemble::try_all_conformers(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.docking.DockingLowResFilter

Bases: pyrosetta.rosetta.protocols.filters.Filter

Low-resolution (centroid-mode) filter for docking. Checks (1) at least some contact is being made between docking partners,

  1. clashes are limited so partners are not overlapping

and (3) constraints, if present, are met

apply(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool

add docking constraints

C++: protocols::docking::DockingLowResFilter::apply(const class core::pose::Pose &) const –> bool

clear(self: pyrosetta.rosetta.protocols.filters.Filter) None

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter) pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::docking::DockingLowResFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter) pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::docking::DockingLowResFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) str

C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) str

C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.filters.Filter) str

C++: protocols::filters::Filter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

Called by FilterFactory when constructing new Filter. Takes care of the specific mover’s parsing.

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

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : 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 filters wishing to provide citation information.

C++: protocols::filters::Filter::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

report(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::docking::DockingLowResFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::filters::Filter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_use_constraints(*args, **kwargs)

Overloaded function.

  1. set_use_constraints(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter, flag: bool) -> None

  2. set_use_constraints(self: pyrosetta.rosetta.protocols.docking.DockingLowResFilter, flag: bool, cutoff: float) -> None

C++: protocols::docking::DockingLowResFilter::set_use_constraints(bool, double) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) None

C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

class pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol

Bases: pyrosetta.rosetta.protocols.docking.DockingHighRes

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

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

apply(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol, : pyrosetta.rosetta.core.pose.Pose) None

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

assign(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol, : pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol) pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol

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

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_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t

C++: protocols::docking::DockingHighRes::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_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.DockingPrepackProtocol) str

C++: protocols::docking::DockingPrepackProtocol::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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str

C++: protocols::docking::DockingHighRes::get_partners() const –> std::string

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

ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::ignore_default_task() –> bool

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

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

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

static mover_name() str

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

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

partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) str

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

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::DockingPrepackProtocol::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> 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

rt_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::rt_min() –> bool

sc_min(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) bool

C++: protocols::docking::DockingHighRes::sc_min() –> bool

score_and_output(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol, filename: str, : pyrosetta.rosetta.core.pose.Pose) None

Scores and outputs the pose - jd2 compatible.

C++: protocols::docking::DockingPrepackProtocol::score_and_output(std::string, class core::pose::Pose &) –> void

scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction

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

scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes) pyrosetta.rosetta.core.scoring.ScoreFunction

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

set_additional_task_operarations(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, additional_task_operations: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None

C++: protocols::docking::DockingHighRes::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_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_dock_ppk(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol, dock_ppk: bool) None

C++: protocols::docking::DockingPrepackProtocol::set_dock_ppk(bool) –> void

set_ignore_default_task(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, ignore_default_task: bool) None

C++: protocols::docking::DockingHighRes::set_ignore_default_task(bool) –> 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.DockingHighRes, interface_definition: protocols::simple_task_operations::InterfaceTaskOperation) None

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

set_movable_jumps(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, movable_jumps: pyrosetta.rosetta.utility.vector1_int) None

C++: protocols::docking::DockingHighRes::set_movable_jumps(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_partners(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, partners: str) None

C++: protocols::docking::DockingHighRes::set_partners(std::string) –> void

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

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

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

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

set_scorefxn(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

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

set_scorefxn_pack(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, scorefxn_pack: pyrosetta.rosetta.core.scoring.ScoreFunction) None

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

set_task_factory(self: pyrosetta.rosetta.protocols.docking.DockingHighRes, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::docking::DockingHighRes::set_task_factory(class std::shared_ptr<const 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

setup_defaults(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol) None

Assigns default values to members

C++: protocols::docking::DockingPrepackProtocol::setup_defaults() –> void

setup_pack_operation_movers(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol) None

Instantiates and configures movers used by DockingPrepackProtocol

C++: protocols::docking::DockingPrepackProtocol::setup_pack_operation_movers() –> 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

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

C++: protocols::docking::DockingHighRes::task_factory() –> class std::shared_ptr<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

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.docking.DockingPrepackProtocolCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator, : pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator) pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator

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

create_mover(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator) str

C++: protocols::docking::DockingPrepackProtocolCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.docking.DockingProtocol

Bases: pyrosetta.rosetta.protocols.moves.Mover

This is the standard RosettaDock protocol

RosettaDock protocol based on [refs…Gray2003, Wang2005, Chaudhury 2007 … ]

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.DockingProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None

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

assign(self: pyrosetta.rosetta.protocols.docking.DockingProtocol, rhs: pyrosetta.rosetta.protocols.docking.DockingProtocol) pyrosetta.rosetta.protocols.docking.DockingProtocol

assignment operator

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

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.DockingProtocol) str

C++: protocols::docking::DockingProtocol::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_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

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</