membrane¶

Bindings for protocols::membrane namespace

class pyrosetta.rosetta.protocols.membrane.AddMPLigandMover¶

Bases: Mover

Add Membrane protein ligand mover

Accommodate membrane protein ligand in the membrane foldtree

apply(self: pyrosetta.rosetta.protocols.membrane.AddMPLigandMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Mover Apply Method

C++: protocols::membrane::AddMPLigandMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.AddMPLigandMover, : pyrosetta.rosetta.protocols.membrane.AddMPLigandMover) → pyrosetta.rosetta.protocols.membrane.AddMPLigandMover¶: C++: protocols::membrane::AddMPLigandMover::operator=(const class protocols::membrane::AddMPLigandMover &) –> class protocols::membrane::AddMPLigandMover &

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.membrane.AddMPLigandMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::AddMPLigandMover::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.membrane.AddMPLigandMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::AddMPLigandMover::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.membrane.AddMPLigandMover) → str¶

Show the name of this mvoer

C++: protocols::membrane::AddMPLigandMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::membrane::AddMPLigandMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.AddMPLigandMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Pase Rosetta Scripts Options for this Mover

C++: protocols::membrane::AddMPLigandMover::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::membrane::AddMPLigandMover::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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator, : pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator) → pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator¶: C++: protocols::membrane::AddMPLigandMoverCreator::operator=(const class protocols::membrane::AddMPLigandMoverCreator &) –> class protocols::membrane::AddMPLigandMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::AddMPLigandMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator) → str¶: C++: protocols::membrane::AddMPLigandMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::membrane::AddMPLigandMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.membrane.AddMembraneMover¶

Bases: Mover

Initialize the RosettaMP framework by adding representations of the membrane

add_membrane_virtual(self: pyrosetta.rosetta.protocols.membrane.AddMembraneMover, pose: pyrosetta.rosetta.core.pose.Pose) → int¶

Create and append a membrane virtual residue to the pose

C++: protocols::membrane::AddMembraneMover::add_membrane_virtual(class core::pose::Pose &) –> unsigned long

apply(self: pyrosetta.rosetta.protocols.membrane.AddMembraneMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Initialize the RosettaMP elements with this pose

C++: protocols::membrane::AddMembraneMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.AddMembraneMover, : pyrosetta.rosetta.protocols.membrane.AddMembraneMover) → pyrosetta.rosetta.protocols.membrane.AddMembraneMover¶: C++: protocols::membrane::AddMembraneMover::operator=(const class protocols::membrane::AddMembraneMover &) –> class protocols::membrane::AddMembraneMover &

static attributes_for_parse_center_normal_from_tag(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::membrane::AddMembraneMover::attributes_for_parse_center_normal_from_tag(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> 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.membrane.AddMembraneMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::AddMembraneMover::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.membrane.AddMembraneMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::AddMembraneMover::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.membrane.AddMembraneMover) → str¶: C++: protocols::membrane::AddMembraneMover::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_spanfile(self: pyrosetta.rosetta.protocols.membrane.AddMembraneMover) → str¶

Path to file with transmembrane span data

C++: protocols::membrane::AddMembraneMover::get_spanfile() const –> std::string

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::membrane::AddMembraneMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.AddMembraneMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Pase Rosetta Scripts Options for this Mover

C++: protocols::membrane::AddMembraneMover::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::membrane::AddMembraneMover::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

restore_lazaridis_IMM1_behavior(self: pyrosetta.rosetta.protocols.membrane.AddMembraneMover, restore: bool) → None¶: C++: protocols::membrane::AddMembraneMover::restore_lazaridis_IMM1_behavior(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_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

spanfile(self: pyrosetta.rosetta.protocols.membrane.AddMembraneMover, spanfile: str) → None¶

Set path to spanfile

C++: protocols::membrane::AddMembraneMover::spanfile(std::string) –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator, : pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator) → pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator¶: C++: protocols::membrane::AddMembraneMoverCreator::operator=(const class protocols::membrane::AddMembraneMoverCreator &) –> class protocols::membrane::AddMembraneMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::AddMembraneMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator) → str¶: C++: protocols::membrane::AddMembraneMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::membrane::AddMembraneMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Flip the downstream partner in the membrane

C++: protocols::membrane::AddMembraneSpanConstraint::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint, src: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint) → pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint¶

Assignment Operator

C++: protocols::membrane::AddMembraneSpanConstraint::operator=(const class protocols::membrane::AddMembraneSpanConstraint &) –> class protocols::membrane::AddMembraneSpanConstraint &

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.membrane.AddMembraneSpanConstraint) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::AddMembraneSpanConstraint::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.membrane.AddMembraneSpanConstraint) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::AddMembraneSpanConstraint::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.membrane.AddMembraneSpanConstraint) → str¶: C++: protocols::membrane::AddMembraneSpanConstraint::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::membrane::AddMembraneSpanConstraint::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Pase Rosetta Scripts Options for this Mover

C++: protocols::membrane::AddMembraneSpanConstraint::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::membrane::AddMembraneSpanConstraint::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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator, : pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator) → pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator¶: C++: protocols::membrane::AddMembraneSpanConstraintCreator::operator=(const class protocols::membrane::AddMembraneSpanConstraintCreator &) –> class protocols::membrane::AddMembraneSpanConstraintCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::AddMembraneSpanConstraintCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator) → str¶: C++: protocols::membrane::AddMembraneSpanConstraintCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::membrane::AddMembraneSpanConstraintCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Flip the downstream partner in the membrane

C++: protocols::membrane::AddMembraneSpanTermZConstraint::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint, src: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint) → pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint¶

Assignment Operator

C++: protocols::membrane::AddMembraneSpanTermZConstraint::operator=(const class protocols::membrane::AddMembraneSpanTermZConstraint &) –> class protocols::membrane::AddMembraneSpanTermZConstraint &

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.membrane.AddMembraneSpanTermZConstraint) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::AddMembraneSpanTermZConstraint::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.membrane.AddMembraneSpanTermZConstraint) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::AddMembraneSpanTermZConstraint::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.membrane.AddMembraneSpanTermZConstraint) → str¶: C++: protocols::membrane::AddMembraneSpanTermZConstraint::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::membrane::AddMembraneSpanTermZConstraint::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Pase Rosetta Scripts Options for this Mover

C++: protocols::membrane::AddMembraneSpanTermZConstraint::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::membrane::AddMembraneSpanTermZConstraint::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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator, : pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator) → pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator¶: C++: protocols::membrane::AddMembraneSpanTermZConstraintCreator::operator=(const class protocols::membrane::AddMembraneSpanTermZConstraintCreator &) –> class protocols::membrane::AddMembraneSpanTermZConstraintCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::AddMembraneSpanTermZConstraintCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator) → str¶: C++: protocols::membrane::AddMembraneSpanTermZConstraintCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::membrane::AddMembraneSpanTermZConstraintCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder¶

Bases: Mover

Compute the center, major axis and minor axis of an ellipsoidal aqueous pore

apply(self: pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::membrane::AqueousPoreFinder::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder, : pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder) → pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder¶: C++: protocols::membrane::AqueousPoreFinder::operator=(const class protocols::membrane::AqueousPoreFinder &) –> class protocols::membrane::AqueousPoreFinder &

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.membrane.AqueousPoreFinder) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::membrane::AqueousPoreFinder::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.membrane.AqueousPoreFinder) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::membrane::AqueousPoreFinder::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_dummy_rotation_matrix(self: pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder) → pyrosetta.rosetta.numeric.MathMatrix_double_t¶

Return a rotation matrix that results in no rotation

C++: protocols::membrane::AqueousPoreFinder::get_dummy_rotation_matrix() const –> class numeric::MathMatrix<double>

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder) → str¶: C++: protocols::membrane::AqueousPoreFinder::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::membrane::AqueousPoreFinder::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::membrane::AqueousPoreFinder::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::membrane::AqueousPoreFinder::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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder) -> None
show(self: pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::membrane::AqueousPoreFinder::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

update_mp_geo_pore(self: pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder, pose: pyrosetta.rosetta.core.pose.Pose, aqueous_pore: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters) → None¶: C++: protocols::membrane::AqueousPoreFinder::update_mp_geo_pore(class core::pose::Pose &, class std::shared_ptr<class core::conformation::membrane::AqueousPoreParameters>) –> void

class pyrosetta.rosetta.protocols.membrane.AqueousPoreFinderCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.membrane.AqueousPoreFinderCreator, : pyrosetta.rosetta.protocols.membrane.AqueousPoreFinderCreator) → pyrosetta.rosetta.protocols.membrane.AqueousPoreFinderCreator¶: C++: protocols::membrane::AqueousPoreFinderCreator::operator=(const class protocols::membrane::AqueousPoreFinderCreator &) –> class protocols::membrane::AqueousPoreFinderCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.AqueousPoreFinderCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::AqueousPoreFinderCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.AqueousPoreFinderCreator) → str¶: C++: protocols::membrane::AqueousPoreFinderCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.membrane.AqueousPoreFinderCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::membrane::AqueousPoreFinderCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.membrane.FlipMover¶

Bases: Mover

Takes a pose and flips the downstream partner around the axis between the COMs of the partners, projected into the membrane plane. CAUTION: THIS MOVER ONLY WORKS FOR A FIXED MEMBRANE WHERE THE MEMBRANE VIRTUAL RESIDUE IS AT THE ROOT OF THE FOLDTREE!!!

apply(self: pyrosetta.rosetta.protocols.membrane.FlipMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Flip the downstream partner in the membrane

C++: protocols::membrane::FlipMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.FlipMover, src: pyrosetta.rosetta.protocols.membrane.FlipMover) → pyrosetta.rosetta.protocols.membrane.FlipMover¶

Assignment Operator

C++: protocols::membrane::FlipMover::operator=(const class protocols::membrane::FlipMover &) –> class protocols::membrane::FlipMover &

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.membrane.FlipMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::FlipMover::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.membrane.FlipMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::FlipMover::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_angle(self: pyrosetta.rosetta.protocols.membrane.FlipMover) → float¶

get rotation angle

C++: protocols::membrane::FlipMover::get_angle() const –> double

get_axis(self: pyrosetta.rosetta.protocols.membrane.FlipMover) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

get rotation axis

C++: protocols::membrane::FlipMover::get_axis() const –> class numeric::xyzVector<double>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_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_jump_num(self: pyrosetta.rosetta.protocols.membrane.FlipMover) → int¶

get jump num

C++: protocols::membrane::FlipMover::get_jump_num() const –> unsigned long

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_max_angle_dev(self: pyrosetta.rosetta.protocols.membrane.FlipMover) → float¶

get maximum angle deviation from 180 degrees

C++: protocols::membrane::FlipMover::get_max_angle_dev() const –> double

get_name(self: pyrosetta.rosetta.protocols.membrane.FlipMover) → str¶: C++: protocols::membrane::FlipMover::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_random_angle(self: pyrosetta.rosetta.protocols.membrane.FlipMover) → bool¶

get random angle status

C++: protocols::membrane::FlipMover::get_random_angle() const –> bool

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::membrane::FlipMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.FlipMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Parse Rosetta Scripts Options for this Mover

C++: protocols::membrane::FlipMover::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¶

Provide xml schema for RosettaScripts compatibility

C++: protocols::membrane::FlipMover::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_membrane_flip_angle(self: pyrosetta.rosetta.protocols.membrane.FlipMover) → None¶

Set Random flip angle between 135 and 225 degrees to keep: protein oriented in the membrane correctly

C++: protocols::membrane::FlipMover::set_random_membrane_flip_angle() –> void

set_range(self: pyrosetta.rosetta.protocols.membrane.FlipMover, max_angle_dev: float) → None¶

Set angle range

Maximum angle deviation from 180 degrees

C++: protocols::membrane::FlipMover::set_range(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.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.FlipMoverCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.FlipMoverCreator, : pyrosetta.rosetta.protocols.membrane.FlipMoverCreator) → pyrosetta.rosetta.protocols.membrane.FlipMoverCreator¶: C++: protocols::membrane::FlipMoverCreator::operator=(const class protocols::membrane::FlipMoverCreator &) –> class protocols::membrane::FlipMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.FlipMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::FlipMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.FlipMoverCreator) → str¶: C++: protocols::membrane::FlipMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.membrane.FlipMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::membrane::FlipMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.membrane.HelixFromSequence¶

Bases: Mover

Generates a (transmembrane) helix from a fasta file containing the sequence

apply(self: pyrosetta.rosetta.protocols.membrane.HelixFromSequence, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::membrane::HelixFromSequence::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.HelixFromSequence, : pyrosetta.rosetta.protocols.membrane.HelixFromSequence) → pyrosetta.rosetta.protocols.membrane.HelixFromSequence¶: C++: protocols::membrane::HelixFromSequence::operator=(const class protocols::membrane::HelixFromSequence &) –> class protocols::membrane::HelixFromSequence &

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.membrane.HelixFromSequence) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::membrane::HelixFromSequence::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.membrane.HelixFromSequence) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::membrane::HelixFromSequence::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.membrane.HelixFromSequence) → str¶

Get the name of the Mover

C++: protocols::membrane::HelixFromSequence::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.HelixFromSequence, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.membrane.HelixFromSequence) -> None
show(self: pyrosetta.rosetta.protocols.membrane.HelixFromSequence, output: pyrosetta.rosetta.std.ostream) -> None

Show the contents of the Mover

C++: protocols::membrane::HelixFromSequence::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.HelixFromSequenceCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.membrane.HelixFromSequenceCreator, : pyrosetta.rosetta.protocols.membrane.HelixFromSequenceCreator) → pyrosetta.rosetta.protocols.membrane.HelixFromSequenceCreator¶: C++: protocols::membrane::HelixFromSequenceCreator::operator=(const class protocols::membrane::HelixFromSequenceCreator &) –> class protocols::membrane::HelixFromSequenceCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.HelixFromSequenceCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::HelixFromSequenceCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.HelixFromSequenceCreator) → str¶: C++: protocols::membrane::HelixFromSequenceCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::membrane::HelixFromSequenceCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

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

class pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility¶

Bases: Mover

Mover that computes which residues are lipid accessible and puts that information into the B-factors: 50 is lipid accessible, 0 is lipid INaccessible

apply(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover

C++: protocols::membrane::MPLipidAccessibility::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility, : pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility) → pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility¶: C++: protocols::membrane::MPLipidAccessibility::operator=(const class protocols::membrane::MPLipidAccessibility &) –> class protocols::membrane::MPLipidAccessibility &

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.membrane.MPLipidAccessibility) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::membrane::MPLipidAccessibility::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.membrane.MPLipidAccessibility) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::membrane::MPLipidAccessibility::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_angle_cutoff(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility) → float¶

get angle cutoff

C++: protocols::membrane::MPLipidAccessibility::get_angle_cutoff() const –> double

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_dist_cutoff(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility) → float¶

get dist cutoff

C++: protocols::membrane::MPLipidAccessibility::get_dist_cutoff() const –> double

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility) → str¶: C++: protocols::membrane::MPLipidAccessibility::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_shell_radius(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility) → float¶

get shell radius

C++: protocols::membrane::MPLipidAccessibility::get_shell_radius() const –> double

get_slice_width(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility) → float¶

get slice width

C++: protocols::membrane::MPLipidAccessibility::get_slice_width() const –> double

get_tm_alpha(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility) → bool¶

get tm_alpha

C++: protocols::membrane::MPLipidAccessibility::get_tm_alpha() const –> bool

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

is_alpha_helical(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility) → bool¶

Is this an alpha helical protein? (no >7 exception)

C++: protocols::membrane::MPLipidAccessibility::is_alpha_helical() const –> bool

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::membrane::MPLipidAccessibility::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::membrane::MPLipidAccessibility::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::membrane::MPLipidAccessibility::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_slice_width(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility, width: float) → None¶

Set slice width via commandline

C++: protocols::membrane::MPLipidAccessibility::set_slice_width(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.

show(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility) -> None
show(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::membrane::MPLipidAccessibility::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.MPLipidAccessibilityCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibilityCreator, : pyrosetta.rosetta.protocols.membrane.MPLipidAccessibilityCreator) → pyrosetta.rosetta.protocols.membrane.MPLipidAccessibilityCreator¶: C++: protocols::membrane::MPLipidAccessibilityCreator::operator=(const class protocols::membrane::MPLipidAccessibilityCreator &) –> class protocols::membrane::MPLipidAccessibilityCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibilityCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::MPLipidAccessibilityCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibilityCreator) → str¶: C++: protocols::membrane::MPLipidAccessibilityCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibilityCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::membrane::MPLipidAccessibilityCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Mutate residue and then quick relax the membrane protein

C++: protocols::membrane::MPMutateRelaxMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover, src: pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover) → pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover¶

Assignment Operator

C++: protocols::membrane::MPMutateRelaxMover::operator=(const class protocols::membrane::MPMutateRelaxMover &) –> class protocols::membrane::MPMutateRelaxMover &

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.membrane.MPMutateRelaxMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::MPMutateRelaxMover::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.membrane.MPMutateRelaxMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::MPMutateRelaxMover::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.membrane.MPMutateRelaxMover) → str¶

Get the name of this Mover (MPMutateRelaxMover)

C++: protocols::membrane::MPMutateRelaxMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Pase Rosetta Scripts Options for this Mover

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator, : pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator) → pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator¶: C++: protocols::membrane::MPMutateRelaxMoverCreator::operator=(const class protocols::membrane::MPMutateRelaxMoverCreator &) –> class protocols::membrane::MPMutateRelaxMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::MPMutateRelaxMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator) → str¶: C++: protocols::membrane::MPMutateRelaxMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::membrane::MPMutateRelaxMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

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

class pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover¶

Bases: Mover

add_membrane_again(self: pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover, yesno: bool) → None¶

Run AddMembraneMover before?

If you want to keep your anchor point for MEM, then pick no

C++: protocols::membrane::MPQuickRelaxMover::add_membrane_again(bool) –> void

apply(self: pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Flip the downstream partner in the membrane

C++: protocols::membrane::MPQuickRelaxMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover, src: pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover) → pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover¶

Assignment Operator

C++: protocols::membrane::MPQuickRelaxMover::operator=(const class protocols::membrane::MPQuickRelaxMover &) –> class protocols::membrane::MPQuickRelaxMover &

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.membrane.MPQuickRelaxMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::MPQuickRelaxMover::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.membrane.MPQuickRelaxMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::MPQuickRelaxMover::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.membrane.MPQuickRelaxMover) → str¶

Get the name of this Mover (MPQuickRelaxMover)

C++: protocols::membrane::MPQuickRelaxMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

membrane_from_topology(self: pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover, yesno: bool) → None¶

Run MembranePositionFromTopology again?

Will change the starting membrane position

C++: protocols::membrane::MPQuickRelaxMover::membrane_from_topology(bool) –> void

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

optimize_membrane(self: pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover, yesno: bool) → None¶

Optimize membrane position before relax?

C++: protocols::membrane::MPQuickRelaxMover::optimize_membrane(bool) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Pase Rosetta Scripts Options for this Mover

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator, : pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator) → pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator¶: C++: protocols::membrane::MPQuickRelaxMoverCreator::operator=(const class protocols::membrane::MPQuickRelaxMoverCreator &) –> class protocols::membrane::MPQuickRelaxMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::MPQuickRelaxMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator) → str¶: C++: protocols::membrane::MPQuickRelaxMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::membrane::MPQuickRelaxMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

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

class pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover¶

Bases: Mover

Compute the initial position of the membrane based upon sequence or structure

anchor_at_res1(self: pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover, truefalse: bool) → None¶

Anchor membrane at residue 1, default is true

C++: protocols::membrane::MembranePositionFromTopologyMover::anchor_at_res1(bool) –> void

apply(self: pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Update Membrane position in pose

Compute membrane posiiton based on sequence or structure and then call pose.update_membrane_position() to update the membrane position

C++: protocols::membrane::MembranePositionFromTopologyMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover, : pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover) → pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover¶: C++: protocols::membrane::MembranePositionFromTopologyMover::operator=(const class protocols::membrane::MembranePositionFromTopologyMover &) –> class protocols::membrane::MembranePositionFromTopologyMover &

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.membrane.MembranePositionFromTopologyMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::MembranePositionFromTopologyMover::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.membrane.MembranePositionFromTopologyMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::MembranePositionFromTopologyMover::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.membrane.MembranePositionFromTopologyMover) → str¶: C++: protocols::membrane::MembranePositionFromTopologyMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::membrane::MembranePositionFromTopologyMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Pase Rosetta Scripts Options for this Mover

C++: protocols::membrane::MembranePositionFromTopologyMover::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::membrane::MembranePositionFromTopologyMover::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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator, : pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator) → pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator¶: C++: protocols::membrane::MembranePositionFromTopologyMoverCreator::operator=(const class protocols::membrane::MembranePositionFromTopologyMoverCreator &) –> class protocols::membrane::MembranePositionFromTopologyMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::MembranePositionFromTopologyMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator) → str¶: C++: protocols::membrane::MembranePositionFromTopologyMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::membrane::MembranePositionFromTopologyMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Flip the downstream partner in the membrane

C++: protocols::membrane::OptimizeMembranePositionMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover, src: pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover) → pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover¶

Assignment Operator

C++: protocols::membrane::OptimizeMembranePositionMover::operator=(const class protocols::membrane::OptimizeMembranePositionMover &) –> class protocols::membrane::OptimizeMembranePositionMover &

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.membrane.OptimizeMembranePositionMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::OptimizeMembranePositionMover::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.membrane.OptimizeMembranePositionMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::OptimizeMembranePositionMover::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_best_z(self: pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover) → float¶

Get best_z for this Mover

C++: protocols::membrane::OptimizeMembranePositionMover::get_best_z() const –> double

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_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.membrane.OptimizeMembranePositionMover) → str¶

Get the name of this Mover (OptimizeMembranePositionMover)

C++: protocols::membrane::OptimizeMembranePositionMover::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_score_best(self: pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover) → float¶

Get score_best for this Mover

C++: protocols::membrane::OptimizeMembranePositionMover::get_score_best() const –> 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_sfxn(self: pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶

Get Scorefunction for this Mover

C++: protocols::membrane::OptimizeMembranePositionMover::get_sfxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

get_starting_z(self: pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover) → float¶

Get starting_z for this Mover

C++: protocols::membrane::OptimizeMembranePositionMover::get_starting_z() const –> double

get_stepsize_angle(self: pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover) → float¶

Get stepsize_angle for this Mover

C++: protocols::membrane::OptimizeMembranePositionMover::get_stepsize_angle() const –> double

get_stepsize_z(self: pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover) → float¶

Get stepsize_z for this Mover

C++: protocols::membrane::OptimizeMembranePositionMover::get_stepsize_z() 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_t¶

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Parse Rosetta Scripts Options for this Mover

C++: protocols::membrane::OptimizeMembranePositionMover::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¶

Provide xml schema for RosettaScripts compatibility

C++: protocols::membrane::OptimizeMembranePositionMover::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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator, : pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator) → pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator¶: C++: protocols::membrane::OptimizeMembranePositionMoverCreator::operator=(const class protocols::membrane::OptimizeMembranePositionMoverCreator &) –> class protocols::membrane::OptimizeMembranePositionMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::OptimizeMembranePositionMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator) → str¶: C++: protocols::membrane::OptimizeMembranePositionMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::membrane::OptimizeMembranePositionMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

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

class pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Flip the downstream partner in the membrane

C++: protocols::membrane::OptimizeProteinEmbeddingMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover, : pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover) → pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover¶: C++: protocols::membrane::OptimizeProteinEmbeddingMover::operator=(const class protocols::membrane::OptimizeProteinEmbeddingMover &) –> class protocols::membrane::OptimizeProteinEmbeddingMover &

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.membrane.OptimizeProteinEmbeddingMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::OptimizeProteinEmbeddingMover::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.membrane.OptimizeProteinEmbeddingMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::OptimizeProteinEmbeddingMover::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.membrane.OptimizeProteinEmbeddingMover) → str¶

Get the name of this Mover (OptimizeProteinEmbeddingMover)

C++: protocols::membrane::OptimizeProteinEmbeddingMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Parse Rosetta Scripts Options for this Mover

C++: protocols::membrane::OptimizeProteinEmbeddingMover::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¶

Provide xml schema for RosettaScripts compatibility

C++: protocols::membrane::OptimizeProteinEmbeddingMover::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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator, : pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator) → pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator¶: C++: protocols::membrane::OptimizeProteinEmbeddingMoverCreator::operator=(const class protocols::membrane::OptimizeProteinEmbeddingMoverCreator &) –> class protocols::membrane::OptimizeProteinEmbeddingMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::OptimizeProteinEmbeddingMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator) → str¶: C++: protocols::membrane::OptimizeProteinEmbeddingMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::membrane::OptimizeProteinEmbeddingMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

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

class pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover¶

Bases: Mover

Random Position Rotation Move

Rotate the orientation of the membrane position to a new normal position. Angle chosen randomnly - moved from current axis

apply(self: pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply Rotation

C++: protocols::membrane::RandomPositionRotationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover, src: pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover) → pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover¶

Assignment Operator

Make a deep copy of this mover object, overriding the assignment operator

C++: protocols::membrane::RandomPositionRotationMover::operator=(const class protocols::membrane::RandomPositionRotationMover &) –> class protocols::membrane::RandomPositionRotationMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

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

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover) → str¶

Get the name of this mover

C++: protocols::membrane::RandomPositionRotationMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover¶

Bases: Mover

Random Position Translation Move

apply(self: pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply Translation to membrane position

Translate membrane position to new center

C++: protocols::membrane::RandomPositionTranslationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover, src: pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover) → pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover¶

Assignment Operator

Make a deep copy of this mover object, overriding the assignment operator

C++: protocols::membrane::RandomPositionTranslationMover::operator=(const class protocols::membrane::RandomPositionTranslationMover &) –> class protocols::membrane::RandomPositionTranslationMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

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

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover) → str¶

Get the name of this mover

C++: protocols::membrane::RandomPositionTranslationMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.RotationMover¶

Bases: Mover

Rotates the pose such that a vector in the old orientation will be overlayed in the new orientation. Requires two vectors (old and new) and a point on the new vector around which the rotation takes place. The mover is a general mover but used mainly on membrane proteins. For membrane proteins, the two vectors will be the old and new normal and the point will be the new center. The default jump is going to be the membrane jump, but you can also specify your own. The rotation happens around the axis perpendicular to both vectors with an angle enclosed by both vectors.

apply(self: pyrosetta.rosetta.protocols.membrane.RotationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Rotate the pose - see above

C++: protocols::membrane::RotationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.RotationMover, : pyrosetta.rosetta.protocols.membrane.RotationMover) → pyrosetta.rosetta.protocols.membrane.RotationMover¶: C++: protocols::membrane::RotationMover::operator=(const class protocols::membrane::RotationMover &) –> class protocols::membrane::RotationMover &

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.membrane.RotationMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::RotationMover::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.membrane.RotationMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::RotationMover::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.membrane.RotationMover) → str¶

Get the name of this Mover (RotationMover)

C++: protocols::membrane::RotationMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.RotationMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Pase Rosetta Scripts Options for this Mover

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.RotationMoverCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.RotationMoverCreator, : pyrosetta.rosetta.protocols.membrane.RotationMoverCreator) → pyrosetta.rosetta.protocols.membrane.RotationMoverCreator¶: C++: protocols::membrane::RotationMoverCreator::operator=(const class protocols::membrane::RotationMoverCreator &) –> class protocols::membrane::RotationMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.RotationMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::RotationMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.RotationMoverCreator) → str¶: C++: protocols::membrane::RotationMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::membrane::RotationMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

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

class pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover¶

Bases: Mover

Membrane Position Translation Move

Translate the center of the membrane stub ot the specified position

apply(self: pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply Translation to membrane position

Translate membrane position to new center

C++: protocols::membrane::SetMembraneCenterMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover, src: pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover) → pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover¶

Assignment Operator

Make a deep copy of this mover object, overriding the assignment operator

C++: protocols::membrane::SetMembraneCenterMover::operator=(const class protocols::membrane::SetMembraneCenterMover &) –> class protocols::membrane::SetMembraneCenterMover &

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.membrane.SetMembraneCenterMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::SetMembraneCenterMover::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.membrane.SetMembraneCenterMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::SetMembraneCenterMover::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.membrane.SetMembraneCenterMover) → str¶

Get the name of this mover

C++: protocols::membrane::SetMembraneCenterMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Pase Rosetta Scripts Options for this Mover

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator¶

Bases: MoverCreator

Mover Creator for membrane translation mover

assign(self: pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator, : pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator) → pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator¶: C++: protocols::membrane::SetMembraneCenterMoverCreator::operator=(const class protocols::membrane::SetMembraneCenterMoverCreator &) –> class protocols::membrane::SetMembraneCenterMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::SetMembraneCenterMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator) → str¶: C++: protocols::membrane::SetMembraneCenterMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::membrane::SetMembraneCenterMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

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

class pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover¶

Bases: Mover

Membrane Position Rotation Move

Rotate the orientation of the membrane position to a new normal position. Applies rotation to jump

apply(self: pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply Rotation to Membrane

Rotate the membrane to the new normal position

C++: protocols::membrane::SetMembraneNormalMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover, src: pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover) → pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover¶

Assignment Operator

Make a deep copy of this mover object, overriding the assignment operator

C++: protocols::membrane::SetMembraneNormalMover::operator=(const class protocols::membrane::SetMembraneNormalMover &) –> class protocols::membrane::SetMembraneNormalMover &

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.membrane.SetMembraneNormalMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::SetMembraneNormalMover::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.membrane.SetMembraneNormalMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::SetMembraneNormalMover::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.membrane.SetMembraneNormalMover) → str¶

Get the name of this mover

C++: protocols::membrane::SetMembraneNormalMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Pase Rosetta Scripts Options for this Mover

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator¶

Bases: MoverCreator

Mover creator for membrane rotation mover

assign(self: pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator, : pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator) → pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator¶: C++: protocols::membrane::SetMembraneNormalMoverCreator::operator=(const class protocols::membrane::SetMembraneNormalMoverCreator &) –> class protocols::membrane::SetMembraneNormalMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::SetMembraneNormalMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator) → str¶: C++: protocols::membrane::SetMembraneNormalMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::membrane::SetMembraneNormalMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

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

class pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover¶

Bases: Mover

Membrane Position Translation-Rotation Mover

apply(self: pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply Rotation/Translation to Membrane

Translate the membrane position in this pose to the new center position, and rotate to new normal

C++: protocols::membrane::SetMembranePositionMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover, src: pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover) → pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover¶

Assignment Operator

Make a deep copy of this mover object, overriding the assignment operator

C++: protocols::membrane::SetMembranePositionMover::operator=(const class protocols::membrane::SetMembranePositionMover &) –> class protocols::membrane::SetMembranePositionMover &

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.membrane.SetMembranePositionMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::SetMembranePositionMover::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.membrane.SetMembranePositionMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::SetMembranePositionMover::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.membrane.SetMembranePositionMover) → str¶: C++: protocols::membrane::SetMembranePositionMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::membrane::SetMembranePositionMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Pase Rosetta Scripts Options for this Mover

C++: protocols::membrane::SetMembranePositionMover::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::membrane::SetMembranePositionMover::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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator¶

Bases: MoverCreator

Mover Creator for composed RT mover

assign(self: pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator, : pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator) → pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator¶: C++: protocols::membrane::SetMembranePositionMoverCreator::operator=(const class protocols::membrane::SetMembranePositionMoverCreator &) –> class protocols::membrane::SetMembranePositionMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::SetMembranePositionMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator) → str¶: C++: protocols::membrane::SetMembranePositionMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::membrane::SetMembranePositionMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.membrane.SpanInfo¶

Bases: pybind11_object

A utility class to store deferred parse span information

property orient¶

property start¶

property stop¶

class pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Flip the downstream partner in the membrane

C++: protocols::membrane::SpinAroundPartnerMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover, src: pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover) → pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover¶

Assignment Operator

C++: protocols::membrane::SpinAroundPartnerMover::operator=(const class protocols::membrane::SpinAroundPartnerMover &) –> class protocols::membrane::SpinAroundPartnerMover &

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.membrane.SpinAroundPartnerMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::SpinAroundPartnerMover::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.membrane.SpinAroundPartnerMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::SpinAroundPartnerMover::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_jump(self: pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover) → int¶

Get the jump number for this Mover

C++: protocols::membrane::SpinAroundPartnerMover::get_jump() const –> unsigned long

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.membrane.SpinAroundPartnerMover) → str¶

Get the name of this Mover (SpinAroundPartnerMover)

C++: protocols::membrane::SpinAroundPartnerMover::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_rand_range(self: pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover) → bool¶

Get the random range for this Mover

C++: protocols::membrane::SpinAroundPartnerMover::get_rand_range() const –> bool

get_range(self: pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover) → int¶

Get the sampling range for this Mover

C++: protocols::membrane::SpinAroundPartnerMover::get_range() const –> unsigned long

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

get_x(self: pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover) → float¶

Get the x position for this Mover

C++: protocols::membrane::SpinAroundPartnerMover::get_x() const –> double

get_y(self: pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover) → float¶

Get the y position for this Mover

C++: protocols::membrane::SpinAroundPartnerMover::get_y() const –> double

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Pase Rosetta Scripts Options for this Mover

C++: protocols::membrane::SpinAroundPartnerMover::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¶

Provide xml schema for RosettaScripts compatibility

C++: protocols::membrane::SpinAroundPartnerMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

random_range(self: pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover, yesno: bool) → None¶

Set random range

C++: protocols::membrane::SpinAroundPartnerMover::random_range(bool) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

set_x(self: pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover, x: float) → None¶

Set x position

C++: protocols::membrane::SpinAroundPartnerMover::set_x(double) –> void

set_y(self: pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover, y: float) → None¶

Set y position

C++: protocols::membrane::SpinAroundPartnerMover::set_y(double) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator, : pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator) → pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator¶: C++: protocols::membrane::SpinAroundPartnerMoverCreator::operator=(const class protocols::membrane::SpinAroundPartnerMoverCreator &) –> class protocols::membrane::SpinAroundPartnerMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::SpinAroundPartnerMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator) → str¶: C++: protocols::membrane::SpinAroundPartnerMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::membrane::SpinAroundPartnerMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

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

class pyrosetta.rosetta.protocols.membrane.TiltMover¶

Bases: Mover

Tilts the downstream partner along the axis between the COMs of the partners.

apply(self: pyrosetta.rosetta.protocols.membrane.TiltMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Flip the downstream partner in the membrane

C++: protocols::membrane::TiltMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.TiltMover, src: pyrosetta.rosetta.protocols.membrane.TiltMover) → pyrosetta.rosetta.protocols.membrane.TiltMover¶

Assignment Operator

C++: protocols::membrane::TiltMover::operator=(const class protocols::membrane::TiltMover &) –> class protocols::membrane::TiltMover &

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.membrane.TiltMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::TiltMover::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.membrane.TiltMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::TiltMover::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_angle(self: pyrosetta.rosetta.protocols.membrane.TiltMover) → int¶

Get the angle for this Mover

C++: protocols::membrane::TiltMover::get_angle() const –> int

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_jump_num(self: pyrosetta.rosetta.protocols.membrane.TiltMover) → int¶

Get the jump number for this Mover

C++: protocols::membrane::TiltMover::get_jump_num() const –> unsigned long

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.membrane.TiltMover) → str¶

Get the name of this Mover (TiltMover)

C++: protocols::membrane::TiltMover::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_random_angle(self: pyrosetta.rosetta.protocols.membrane.TiltMover) → bool¶

Get the random angle for this Mover

C++: protocols::membrane::TiltMover::get_random_angle() const –> bool

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.TiltMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Parse Rosetta Scripts Options for this Mover

C++: protocols::membrane::TiltMover::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¶

Provide xml schema for RosettaScripts compatibility

C++: protocols::membrane::TiltMover::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_membrane_tilt_angle(self: pyrosetta.rosetta.protocols.membrane.TiltMover) → None¶

Set Random tilt angle between -20 and 20 degrees to keep: protein oriented in the membrane correctly

C++: protocols::membrane::TiltMover::set_random_membrane_tilt_angle() –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.TiltMoverCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.TiltMoverCreator, : pyrosetta.rosetta.protocols.membrane.TiltMoverCreator) → pyrosetta.rosetta.protocols.membrane.TiltMoverCreator¶: C++: protocols::membrane::TiltMoverCreator::operator=(const class protocols::membrane::TiltMoverCreator &) –> class protocols::membrane::TiltMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.TiltMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::TiltMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.TiltMoverCreator) → str¶: C++: protocols::membrane::TiltMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::membrane::TiltMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

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

class pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover¶

Bases: Mover

Transform a pose into membrane coordinates based on the current embedding of the protein

apply(self: pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Move the pose into membrane coordinate frame

C++: protocols::membrane::TransformIntoMembraneMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover, : pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover) → pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover¶: C++: protocols::membrane::TransformIntoMembraneMover::operator=(const class protocols::membrane::TransformIntoMembraneMover &) –> class protocols::membrane::TransformIntoMembraneMover &

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.membrane.TransformIntoMembraneMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::TransformIntoMembraneMover::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.membrane.TransformIntoMembraneMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::TransformIntoMembraneMover::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.membrane.TransformIntoMembraneMover) → str¶: C++: protocols::membrane::TransformIntoMembraneMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::membrane::TransformIntoMembraneMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Pase Rosetta Scripts Options for this Mover

C++: protocols::membrane::TransformIntoMembraneMover::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::membrane::TransformIntoMembraneMover::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_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

use_default_membrane(self: pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover, truefalse: bool) → None¶

Use the default membrane (cntr 0,0,0 and normal 0,0,1) instead: of the membrane from the MEM coordinates stored in MembraneInfo

C++: protocols::membrane::TransformIntoMembraneMover::use_default_membrane(bool) –> void

class pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator, : pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator) → pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator¶: C++: protocols::membrane::TransformIntoMembraneMoverCreator::operator=(const class protocols::membrane::TransformIntoMembraneMoverCreator &) –> class protocols::membrane::TransformIntoMembraneMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::TransformIntoMembraneMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator) → str¶: C++: protocols::membrane::TransformIntoMembraneMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::membrane::TransformIntoMembraneMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.membrane.TranslationMover¶

Bases: Mover

Translation vector can be defined in -mp:setup center flag to translate the new pose to. The mover is a general mover but used mainly on membrane proteins, that’s why we use this flag here The default jump is going to be the membrane jump, but you can also specify your own

apply(self: pyrosetta.rosetta.protocols.membrane.TranslationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Translate the pose along the defined vector

C++: protocols::membrane::TranslationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.TranslationMover, : pyrosetta.rosetta.protocols.membrane.TranslationMover) → pyrosetta.rosetta.protocols.membrane.TranslationMover¶: C++: protocols::membrane::TranslationMover::operator=(const class protocols::membrane::TranslationMover &) –> class protocols::membrane::TranslationMover &

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.membrane.TranslationMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::TranslationMover::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.membrane.TranslationMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::TranslationMover::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.membrane.TranslationMover) → str¶

Get the name of this Mover (TranslationMover)

C++: protocols::membrane::TranslationMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.TranslationMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Pase Rosetta Scripts Options for this Mover

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator, : pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator) → pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator¶: C++: protocols::membrane::TranslationMoverCreator::operator=(const class protocols::membrane::TranslationMoverCreator &) –> class protocols::membrane::TranslationMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::TranslationMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator) → str¶: C++: protocols::membrane::TranslationMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::membrane::TranslationMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

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

class pyrosetta.rosetta.protocols.membrane.TranslationRotationMover¶

Bases: Mover

Translation and Rotation of a pose. The new position can be defined by the -mp:setup center and normal flags. The mover is a general mover, but used mainly on membrane proteins, that’s why we use this flag here. The default jump is going to be the membrane jump, but you can also specify your own. See above for the TranslationMover and the RotationMover

apply(self: pyrosetta.rosetta.protocols.membrane.TranslationRotationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Translate the pose along the defined vector

C++: protocols::membrane::TranslationRotationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.membrane.TranslationRotationMover, : pyrosetta.rosetta.protocols.membrane.TranslationRotationMover) → pyrosetta.rosetta.protocols.membrane.TranslationRotationMover¶: C++: protocols::membrane::TranslationRotationMover::operator=(const class protocols::membrane::TranslationRotationMover &) –> class protocols::membrane::TranslationRotationMover &

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.membrane.TranslationRotationMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Clone of this mover

C++: protocols::membrane::TranslationRotationMover::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.membrane.TranslationRotationMover) → pyrosetta.rosetta.protocols.moves.Mover¶

Create a Fresh Instance of this Mover

C++: protocols::membrane::TranslationRotationMover::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.membrane.TranslationRotationMover) → str¶

Get the name of this Mover (TranslationRotationMover)

C++: protocols::membrane::TranslationRotationMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

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

non-const accessor

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.membrane.TranslationRotationMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Pase Rosetta Scripts Options for this Mover

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator¶

Bases: MoverCreator

Mover Creator

assign(self: pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator, : pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator) → pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator¶: C++: protocols::membrane::TranslationRotationMoverCreator::operator=(const class protocols::membrane::TranslationRotationMoverCreator &) –> class protocols::membrane::TranslationRotationMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::membrane::TranslationRotationMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator) → str¶: C++: protocols::membrane::TranslationRotationMoverCreator::keyname() const –> std::string

static mover_name() → str¶: C++: protocols::membrane::TranslationRotationMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

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

pyrosetta.rosetta.protocols.membrane.average_antiparallel_embeddings(parts: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_membrane_geometry_EmbeddingDef_t) → pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef¶

Average EmbeddingDefs after first inverting some vectors accounting for topology

Get average center and normal from a vector of EmbeddingDefs

C++: protocols::membrane::average_antiparallel_embeddings(const class utility::vector1<class std::shared_ptr<class protocols::membrane::geometry::EmbeddingDef>, class std::allocator<class std::shared_ptr<class protocols::membrane::geometry::EmbeddingDef> > >) –> class std::shared_ptr<class protocols::membrane::geometry::EmbeddingDef>

pyrosetta.rosetta.protocols.membrane.average_embeddings(parts: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_membrane_geometry_EmbeddingDef_t) → pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef¶

Average EmbeddingDefs as they are (without vector inversion accounting for topology)

Get average center and normal from a vector of EmbeddingDefs

C++: protocols::membrane::average_embeddings(const class utility::vector1<class std::shared_ptr<class protocols::membrane::geometry::EmbeddingDef>, class std::allocator<class std::shared_ptr<class protocols::membrane::geometry::EmbeddingDef> > >) –> class std::shared_ptr<class protocols::membrane::geometry::EmbeddingDef>

pyrosetta.rosetta.protocols.membrane.calc_angle_rmsd(measured_angle: float, ref_angle: float) → float¶

Calculate the RMSD between a helix tilt angle & reference

Given a reference angle and measured angle, calculate the root mean square deviation between the two single values. Takes the measured tilt angle and reference angle (typically from experiment)

C++: protocols::membrane::calc_angle_rmsd(double, double) –> double

pyrosetta.rosetta.protocols.membrane.calc_helix_axis(pose: pyrosetta.rosetta.core.pose.Pose, span_no: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

Determine the axis used to define a single TM Helix

Using the COM of the helix start & end position, calculate a helix describing its geometry relative to the memrbane normal. Takes a pose & span number. Not a good approx for helices with kinks. TODO: CODE INSIDE SHOULD BE REPLACED WITH SPAN EMBEDDING CALCULATIONS!

THAT’S WHAT THEY ARE THERE FOR! (JKLeman)

C++: protocols::membrane::calc_helix_axis(class core::pose::Pose &, unsigned long) –> class numeric::xyzVector<double>

pyrosetta.rosetta.protocols.membrane.calc_helix_tilt_angle(pose: pyrosetta.rosetta.core.pose.Pose, span_no: int) → float¶

Calculate tilt of a TM span relative to the membrane normal

Given a transmembrane span #, calculate the angle between the axis through the helix and the membrane normal. Works for relatively straight helices but less accurate for kinks. Takes a pose & span number.

C++: protocols::membrane::calc_helix_tilt_angle(class core::pose::Pose &, unsigned long) –> double

pyrosetta.rosetta.protocols.membrane.chain_com(pose: pyrosetta.rosetta.core.pose.Pose, chain: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

Chain center-of-mass

Gets the coordinates of the chain center-of-mass

C++: protocols::membrane::chain_com(const class core::pose::Pose &, unsigned long) –> class numeric::xyzVector<double>

pyrosetta.rosetta.protocols.membrane.chain_tm_com(pose: pyrosetta.rosetta.core.pose.Pose, chain: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

Chain center-of-mass of TM regions

Gets the coordinates of the chain center-of-mass but only the TM regions

C++: protocols::membrane::chain_tm_com(const class core::pose::Pose &, unsigned long) –> class numeric::xyzVector<double>

pyrosetta.rosetta.protocols.membrane.check_orientation(pose: pyrosetta.rosetta.core.pose.Pose, span_no: int) → bool¶

Check if the orientation of the TM span matches: the orientation of the span in the pose

C++: protocols::membrane::check_orientation(class core::pose::Pose &, unsigned long) –> bool

pyrosetta.rosetta.protocols.membrane.check_vector(vector: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Check reasonable range of vector

C++: protocols::membrane::check_vector(const class numeric::xyzVector<double>) –> void

pyrosetta.rosetta.protocols.membrane.com(a: pyrosetta.rosetta.numeric.xyzVector_double_t, b: pyrosetta.rosetta.numeric.xyzVector_double_t, c: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

Calculate center of mass between 3 xyz coords

Given three xyz vectors, calculate the center of mass and return a vector. Helper method to calc_helix axis.

C++: protocols::membrane::com(class numeric::xyzVector<double>, class numeric::xyzVector<double>, class numeric::xyzVector<double>) –> class numeric::xyzVector<double>

pyrosetta.rosetta.protocols.membrane.compute_embeddings_by_chain(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.membrane.geometry.Embedding¶

Compute embeddings by chain

The embeddings can be computed either from pose and topology or they
can be optimized differently; the function correlates each EmbeddingDef object in embeddings with a span object in the pose’s topology; The bool means whether embeddings in Embedding object are antiparallel or not

C++: protocols::membrane::compute_embeddings_by_chain(const class core::pose::Pose &) –> class std::shared_ptr<class protocols::membrane::geometry::Embedding>

pyrosetta.rosetta.protocols.membrane.compute_structure_based_embedding(*args, **kwargs)¶

Overloaded function.

compute_structure_based_embedding(pose: pyrosetta.rosetta.core.pose.Pose, topology: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, center: pyrosetta.rosetta.numeric.xyzVector_double_t, normal: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Compute Membrane Center/Normal from Membrane Spanning: topology

C++: protocols::membrane::compute_structure_based_embedding(const class core::pose::Pose &, const class core::conformation::membrane::SpanningTopology &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) –> void

compute_structure_based_embedding(pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, normal: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Compute Membrane Center/Normal from Membrane Spanning: topology, uses topology from MembraneInfo

C++: protocols::membrane::compute_structure_based_embedding(const class core::pose::Pose &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) –> void

compute_structure_based_embedding(pose: pyrosetta.rosetta.core.pose.Pose, topo: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology) -> pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef

Compute Membrane Center/Normal from Membrane Spanning: topology

C++: protocols::membrane::compute_structure_based_embedding(const class core::pose::Pose &, const class core::conformation::membrane::SpanningTopology &) –> class std::shared_ptr<class protocols::membrane::geometry::EmbeddingDef>

compute_structure_based_embedding(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef

Compute Membrane Center/Normal from Membrane Spanning: topology, uses topology from MembraneInfo

C++: protocols::membrane::compute_structure_based_embedding(const class core::pose::Pose &) –> class std::shared_ptr<class protocols::membrane::geometry::EmbeddingDef>

pyrosetta.rosetta.protocols.membrane.create_membrane_docking_foldtree_from_partners(pose: pyrosetta.rosetta.core.pose.Pose, partners: str) → int¶

Create a membrane foldtree with an interface

Currently only works for two-body-docking. Both partners can have
multiple chains in any order, the anchoring happens at the TM COM of each chain

|________________ _________________ | |________ iJ ||________ | | | | || | | |

——- ——- ——- ——- ——- M=root
chain1 chain2 chain3 chain4 …

^————–^ ^———————–^

partner 1 partner 2

iJ = interface jump, will be returned from the function

C++: protocols::membrane::create_membrane_docking_foldtree_from_partners(class core::pose::Pose &, const std::string &) –> unsigned long

pyrosetta.rosetta.protocols.membrane.create_membrane_foldtree_anchor_com(pose: pyrosetta.rosetta.core.pose.Pose) → int¶

Create membrane foldtree from scratch

The foldtree is setup such that the membrane is at the root and
anchored at the first chain COM residue with jumps from the first chain COM to each chain COM; requires the membrane to be present Returns the root anchoring point, i.e. rsd nearest chain COM of chain 1

|__________________________ | |_________________ | | |________ | | | | | | | |

——- ——- ——- ——- M=root
chain1 chain2 chain3 chain4 …

C++: protocols::membrane::create_membrane_foldtree_anchor_com(class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.membrane.create_membrane_foldtree_anchor_pose_tmcom(pose: pyrosetta.rosetta.core.pose.Pose) → int¶

Create membrane foldtree from scratch

The foldtree is setup such that the membrane is at the root and
anchored at the residue closest to the pose TM COM with jumps from there to each chain TRANSMEMBRANE COM; requires the membrane to be present; Returns the root anchoring point, i.e. rsd nearest pose TM COM that can be in any chain

|_________________ | |________ | |

________| | | |

| | | |

——- ——- ——- ——- M=root
chain1 chain2 chain3 chain4 …

C++: protocols::membrane::create_membrane_foldtree_anchor_pose_tmcom(class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.membrane.create_membrane_foldtree_anchor_tmcom(pose: pyrosetta.rosetta.core.pose.Pose) → int¶

Create membrane foldtree from scratch

The foldtree is setup such that the membrane is at the root and
anchored at the first chain TRANSMEMBRANE COM residue with jumps from the first chain COM to each chain TRANSMEMBRANE COM; requires the membrane to be present Returns the root anchoring point, i.e. rsd nearest chain TM COM of chain 1

|__________________________ | |_________________ | | |________ | | | | | | | |

——- ——- ——- ——- M=root
chain1 chain2 chain3 chain4 …

C++: protocols::membrane::create_membrane_foldtree_anchor_tmcom(class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.membrane.create_membrane_foldtree_from_anchors(pose: pyrosetta.rosetta.core.pose.Pose, anchors: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶

Helper function to create membrane foldtrees

The anchors vector is a vector of anchor residues in all chains,
one per chain. This function assumes that the first entry in the vector is the root anchor point to which all other chains are connected;

|__________________________ | |_________________ | | |________ | | | | | | | |

——- ——- ——- ——- M=root
chain1 chain2 chain3 chain4 …

C++: protocols::membrane::create_membrane_foldtree_from_anchors(class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

pyrosetta.rosetta.protocols.membrane.create_membrane_multi_partner_foldtree_anchor_tmcom(pose: pyrosetta.rosetta.core.pose.Pose, partner: str) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Create foldtree for multiple docking partners

The foldtree is setup such that the membrane is at the root and
anchored at the residue closest to the TM COM of the first chain. The partner setup defines how the foldtree will look like: partners are anchored at the first chain, and multiple chains in a partner are anchored to the first chain of that partner, example below. Returns all interface jump numbers. Example: A_BCD_E

|________________________________ | | _______________ | | |_______ |_______ | | | | | | | | | |

——- ——- ——- ——- ——- M=root
chain1 chain2 chain3 chain4 chain5…

^—–^ ^———————–^ ^—–^ partner1 partner2 partner3

C++: protocols::membrane::create_membrane_multi_partner_foldtree_anchor_tmcom(class core::pose::Pose &, std::string) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.membrane.create_specific_membrane_foldtree(pose: pyrosetta.rosetta.core.pose.Pose, anchors: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) → int¶

Helper function to create a specific membrane foldtree

I am hijacking xyzVectors to hold the jumps that need to be
created in the foldtree: xyz = ( rsd1, rsd2, cutpoint ) THE JUMP NUMBERS WILL BE CONSECUTIVE, ACCORDING TO THE VECTOR1

C++: protocols::membrane::create_specific_membrane_foldtree(class core::pose::Pose &, class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >) –> unsigned long

pyrosetta.rosetta.protocols.membrane.get_anchor_points_for_tmcom(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Helper function to create membrane foldtrees

Returns the residues closest to the COMs for each chain

C++: protocols::membrane::get_anchor_points_for_tmcom(class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.membrane.get_chain_and_z(pose: pyrosetta.rosetta.core.pose.Pose) → Tuple[pyrosetta.rosetta.utility.vector1_double, pyrosetta.rosetta.utility.vector1_double]¶

Grab the z-coordinates and chainIDs from the entire pose

From the pose, grab all of the z_coords of CA atoms and chain IDs, currently used for spanning topology construction. Returns a std::pair of two vectors: the first a vector1 of z coordinates and the second a vector1 of chainIDs for CA atoms

C++: protocols::membrane::get_chain_and_z(const class core::pose::Pose &) –> struct std::pair<class utility::vector1<double, class std::allocator<double> >, class utility::vector1<double, class std::allocator<double> > >

pyrosetta.rosetta.protocols.membrane.get_secstruct(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_char¶

Get dssp defined secondary structure from the pose

Given a pose, grab a vector of characters describing the secondary structure at each residue position in the pose, defined by DSSP

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

pyrosetta.rosetta.protocols.membrane.is_membrane_fixed(pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

Determine whether the membrane is modeled as fixed

Based on the setup of the foldtree, determined whether the membrane is currently fixed, meaning it is setup as the root in the FoldTree and has no upstream children. Takes a pose.

C++: protocols::membrane::is_membrane_fixed(class core::pose::Pose &) –> bool

pyrosetta.rosetta.protocols.membrane.is_membrane_moveable_by_itself(pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

Determine whether membrane can move on its own

Based on the setup of the FoldTree, determine whether the membrane is moveable, but when moved, won’t cause anything in the protein to move (i.e. independently moveable). Takes a pose.

C++: protocols::membrane::is_membrane_moveable_by_itself(class core::pose::Pose &) –> bool

pyrosetta.rosetta.protocols.membrane.mem_all_atom_rmsd_no_super(native_pose: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

Compute all-atom RMSD between TM regions - don’t superimpose

Calculate the rmsd between all atoms in the pose in the transmembrane regions, as defined by the spanning topology object. Do not superimpose the poses. Takes a native pose & current pose

C++: protocols::membrane::mem_all_atom_rmsd_no_super(class core::pose::Pose &, class core::pose::Pose &) –> double

pyrosetta.rosetta.protocols.membrane.mem_all_atom_rmsd_with_super(native_pose: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

Compute all-atom RMSD between TM regions - do superimpose

Calculate the rmsd between all atoms in the pose in the transmembrane regions, as defined by the spanning topology object. Superimpose the poses. Takes a native pose & current pose

C++: protocols::membrane::mem_all_atom_rmsd_with_super(class core::pose::Pose &, class core::pose::Pose &) –> double

pyrosetta.rosetta.protocols.membrane.mem_bb_rmsd_no_super(native_pose: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

Compute backbone RMSD between TM regions - don’t superimpose

Calculate the rmsd between backbone atoms (N, CB, CA, O) in the transmembrane regions, as defined by the spanning topology object Do not superimpose the poses. Takes a native pose and current pose

C++: protocols::membrane::mem_bb_rmsd_no_super(class core::pose::Pose &, class core::pose::Pose &) –> double

pyrosetta.rosetta.protocols.membrane.mem_bb_rmsd_with_super(native_pose: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

Compute backbone RMSD between TM regions - do superimpose

Calculate the rmsd between backbone atoms (N, CB, CA, O) in the transmembrane regions, as defined by the spanning topology object Superimpose the poses. Takes a native pose and current pose

C++: protocols::membrane::mem_bb_rmsd_with_super(class core::pose::Pose &, class core::pose::Pose &) –> double

pyrosetta.rosetta.protocols.membrane.membrane_axis(pose: pyrosetta.rosetta.core.pose.Pose, jumpnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

Calculates translation axis lying in the membrane (= projection axis: between embedding centers)

C++: protocols::membrane::membrane_axis(class core::pose::Pose &, int) –> const class numeric::xyzVector<double>

pyrosetta.rosetta.protocols.membrane.membrane_normal_to_length_15(pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Normalize normal vector to length 15 for visualization

C++: protocols::membrane::membrane_normal_to_length_15(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.membrane.pose_tilt_angle_and_center_distance(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_double¶

Calculate tilt angle and distance from membrane center

Computes the tilt angle and distance from membrane center for the
protein embedding center and normal

C++: protocols::membrane::pose_tilt_angle_and_center_distance(class core::pose::Pose &) –> class utility::vector1<double, class std::allocator<double> >

pyrosetta.rosetta.protocols.membrane.pose_tm_com(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

Pose transmembrane center-of-mass

Gets the coordinates of the TM span center-of-mass
This only looks at the span start and end residues for calculation of the TM span COM, this should be faster than the real thing though

C++: protocols::membrane::pose_tm_com(const class core::pose::Pose &) –> class numeric::xyzVector<double>

pyrosetta.rosetta.protocols.membrane.read_center_normal_from_cmd(center: pyrosetta.rosetta.numeric.xyzVector_double_t, normal: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Read in a user provided center/normal pair from the commandline, safetly

Read the membrane setup center & normal options form the command line from mp:setup:center and mp:setup:normal. Intended to reduce IO code duplication in membrane framework movers.

C++: protocols::membrane::read_center_normal_from_cmd(class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) –> void

pyrosetta.rosetta.protocols.membrane.read_center_normal_from_tag(center: pyrosetta.rosetta.numeric.xyzVector_double_t, normal: pyrosetta.rosetta.numeric.xyzVector_double_t, tag: pyrosetta.rosetta.utility.tag.Tag) → None¶

Read in a user provided center/normal pair from RosettaScripts

Given an XML tag from a RosettaScript read in a center & normal option into two xyzVector objects. This method is intended to reduce duplication accross membrane framework movers that use the same tricks for vectors. Takes two Vector references and a Tag&

C++: protocols::membrane::read_center_normal_from_tag(class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, class std::shared_ptr<const class utility::tag::Tag>) –> void

pyrosetta.rosetta.protocols.membrane.reorder_membrane_foldtree(pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Set membrane residue to root of foldtree

Naively sets the root of the foldtree to be the membrane residue. Should perform checks before doing this!

C++: protocols::membrane::reorder_membrane_foldtree(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.membrane.rsd_closest_to_chain_com(pose: pyrosetta.rosetta.core.pose.Pose, chain: int) → int¶

Residue closest to chain center-of-mass

Gets the residue number closest to the chain center-of-mass

C++: protocols::membrane::rsd_closest_to_chain_com(const class core::pose::Pose &, unsigned long) –> unsigned long

pyrosetta.rosetta.protocols.membrane.rsd_closest_to_chain_tm_com(pose: pyrosetta.rosetta.core.pose.Pose, chainid: int) → int¶

Residue closest to chain TM center-of-mass

Gets the residue number closest to the chain TM center-of-mass

C++: protocols::membrane::rsd_closest_to_chain_tm_com(const class core::pose::Pose &, unsigned long) –> unsigned long

pyrosetta.rosetta.protocols.membrane.rsd_closest_to_pose_tm_com(pose: pyrosetta.rosetta.core.pose.Pose) → int¶

Residue closest to pose transmembrane center-of-mass

Gets the coordinates of the residue closest to TM span center-of-mass
This only looks at the span start and end residues for calculation of the TM span COM, this should be faster than the real thing though

C++: protocols::membrane::rsd_closest_to_pose_tm_com(const class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.membrane.setup_foldtree_from_anchors(pose: pyrosetta.rosetta.core.pose.Pose, anchors: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶

Helper function to setup foldtrees

The anchors vector is a vector of anchor residues in all chains,
one per chain. This function assumes that the first entry in the vector is the root anchor point to which all other chains are connected;

|_________________ | |________ | | | | | |

——- ——- ——- ——-

chain1 chain2 chain3 chain4 …
^

root anchor point

C++: protocols::membrane::setup_foldtree_from_anchors(class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

pyrosetta.rosetta.protocols.membrane.setup_foldtree_pose_com(pose: pyrosetta.rosetta.core.pose.Pose) → int¶

Setup foldtree from scratch

The foldtree is setup such that the residue closest to the
COM is at the root, with jumps from there to each chain COM; requires the membrane to be present; Returns the root anchoring point, i.e. rsd nearest pose COM that can be in any chain

|________ |

________| | |

| | |

——- ——- ——- ——-

chain1 chain2 chain3 chain4 …

^

root anchor point

C++: protocols::membrane::setup_foldtree_pose_com(class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.membrane.split_topology_by_jump(pose: pyrosetta.rosetta.core.pose.Pose, jumpnum: int, topo: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, pose_up: pyrosetta.rosetta.core.pose.Pose, pose_down: pyrosetta.rosetta.core.pose.Pose, topo_up: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, topo_down: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology) → None¶

Splits the SpanningTopology object into two objects, depending on

given jump number

This is useful for calculating an embedding for parts of the structure: this can now easily be accomplished by creating two empty topology objects, call this function, and then use both topology objects and subposes to call compute_structure_based_membrane_embedding BEWARE: this does not work for splitting topology by spans! It only works chainwise

C++: protocols::membrane::split_topology_by_jump(const class core::pose::Pose &, const unsigned long, const class core::conformation::membrane::SpanningTopology &, class core::pose::Pose &, class core::pose::Pose &, class core::conformation::membrane::SpanningTopology &, class core::conformation::membrane::SpanningTopology &) –> void

pyrosetta.rosetta.protocols.membrane.split_topology_by_jump_noshift(pose: pyrosetta.rosetta.core.pose.Pose, jumpnum: int, topo: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, topo_up: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, topo_down: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology) → None¶

Splits the SpanningTopology object into two objects, depending on

given jump number

This doesn’t shift the topology to start at 1 for each partner, it remains exactly the same as it would be for the complete pose, just split BEWARE: this does not work for splitting topology by spans! It only works chainwise

C++: protocols::membrane::split_topology_by_jump_noshift(const class core::pose::Pose &, const unsigned long, class std::shared_ptr<class core::conformation::membrane::SpanningTopology>, class std::shared_ptr<class core::conformation::membrane::SpanningTopology>, class std::shared_ptr<class core::conformation::membrane::SpanningTopology>) –> void

pyrosetta.rosetta.protocols.membrane.update_partner_embeddings(pose: pyrosetta.rosetta.core.pose.Pose, jumpnum: int, emb_up: pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef, emb_down: pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef) → None¶

Update embedding of the partners after a move

Requires the jump number between the partners, the topology will
be taken from MembraneInfo and will be split accordingly; up and down means upstream and downstream

C++: protocols::membrane::update_partner_embeddings(const class core::pose::Pose &, const unsigned long, class protocols::membrane::geometry::EmbeddingDef &, class protocols::membrane::geometry::EmbeddingDef &) –> void