membrane

Classes:

Functions:

    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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    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.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

    1. show(self: pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder) -> None

    2. 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.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

    1. show(self: pyrosetta.rosetta.protocols.membrane.HelixFromSequence) -> None

    2. 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.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

    1. show(self: pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility) -> None

    2. 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.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

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

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

    Outputs details about the Mover, including current settings.

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

    test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None
    : Unit test support function. Apply one move to a given pose.

    Allows extra test specific functions to be called before applying

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

    type(*args, **kwargs)

    Overloaded function.

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

    Set the ‘type’ string

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

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

    Get the set ‘type’ string

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

    class pyrosetta.rosetta.protocols.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.

    1. 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

    1. 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

    1. 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>

    1. 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

    ——- ——- ——- ——- ——- 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