splice

Bindings for protocols::splice namespace

class pyrosetta.rosetta.protocols.splice.AlignEndsMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

N_terminal_count(*args, **kwargs)

Overloaded function.

  1. N_terminal_count(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover) -> int

C++: protocols::splice::AlignEndsMover::N_terminal_count() const –> unsigned long

  1. N_terminal_count(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, n: int) -> None

C++: protocols::splice::AlignEndsMover::N_terminal_count(unsigned long) –> void

apply(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::AlignEndsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, : pyrosetta.rosetta.protocols.splice.AlignEndsMover) pyrosetta.rosetta.protocols.splice.AlignEndsMover

C++: protocols::splice::AlignEndsMover::operator=(const class protocols::splice::AlignEndsMover &) –> class protocols::splice::AlignEndsMover &

chain(*args, **kwargs)

Overloaded function.

  1. chain(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, c: int) -> None

C++: protocols::splice::AlignEndsMover::chain(const unsigned long) –> void

  1. chain(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover) -> int

C++: protocols::splice::AlignEndsMover::chain() const –> unsigned long

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.splice.AlignEndsMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::splice::AlignEndsMover::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>

distance_threshold(*args, **kwargs)

Overloaded function.

  1. distance_threshold(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover) -> float

C++: protocols::splice::AlignEndsMover::distance_threshold() const –> double

  1. distance_threshold(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, r: float) -> None

C++: protocols::splice::AlignEndsMover::distance_threshold(const double) –> void

even(*args, **kwargs)

Overloaded function.

  1. even(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover) -> bool

C++: protocols::splice::AlignEndsMover::even() const –> bool

  1. even(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, b: bool) -> None

C++: protocols::splice::AlignEndsMover::even(const bool) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::splice::AlignEndsMover::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.splice.AlignEndsMover) str

C++: protocols::splice::AlignEndsMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

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

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

non-const accessor

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

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

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

max_strands(*args, **kwargs)

Overloaded function.

  1. max_strands(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover) -> int

C++: protocols::splice::AlignEndsMover::max_strands() const –> unsigned long

  1. max_strands(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, m: int) -> None

C++: protocols::splice::AlignEndsMover::max_strands(const unsigned long) –> void

static mover_name() str

C++: protocols::splice::AlignEndsMover::mover_name() –> std::string

static name() str

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

neighbors(*args, **kwargs)

Overloaded function.

  1. neighbors(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover) -> int

C++: protocols::splice::AlignEndsMover::neighbors() const –> unsigned long

  1. neighbors(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, n: int) -> None

C++: protocols::splice::AlignEndsMover::neighbors(unsigned long) –> void

odd(*args, **kwargs)

Overloaded function.

  1. odd(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover) -> bool

C++: protocols::splice::AlignEndsMover::odd() const –> bool

  1. odd(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, b: bool) -> None

C++: protocols::splice::AlignEndsMover::odd(const bool) –> void

parallel(*args, **kwargs)

Overloaded function.

  1. parallel(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover) -> bool

C++: protocols::splice::AlignEndsMover::parallel() const –> bool

  1. parallel(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, p: bool) -> None

C++: protocols::splice::AlignEndsMover::parallel(const bool) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::AlignEndsMover::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::splice::AlignEndsMover::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

residues_to_align_on_pose(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, r: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: protocols::splice::AlignEndsMover::residues_to_align_on_pose(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

residues_to_align_on_template(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, r: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: protocols::splice::AlignEndsMover::residues_to_align_on_template(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

sequence_separation(*args, **kwargs)

Overloaded function.

  1. sequence_separation(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, c: int) -> None

C++: protocols::splice::AlignEndsMover::sequence_separation(const unsigned long) –> void

  1. sequence_separation(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover) -> int

C++: protocols::splice::AlignEndsMover::sequence_separation() const –> unsigned long

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

stagger(*args, **kwargs)

Overloaded function.

  1. stagger(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover) -> int

C++: protocols::splice::AlignEndsMover::stagger() const –> unsigned long

  1. stagger(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, s: int) -> None

C++: protocols::splice::AlignEndsMover::stagger(const unsigned long) –> void

strand_length(*args, **kwargs)

Overloaded function.

  1. strand_length(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover) -> int

C++: protocols::splice::AlignEndsMover::strand_length() const –> unsigned long

  1. strand_length(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, s: int) -> None

C++: protocols::splice::AlignEndsMover::strand_length(const unsigned long) –> void

template_pose(*args, **kwargs)

Overloaded function.

  1. template_pose(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::splice::AlignEndsMover::template_pose() const –> class std::shared_ptr<class core::pose::Pose>

  1. template_pose(self: pyrosetta.rosetta.protocols.splice.AlignEndsMover, p: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::splice::AlignEndsMover::template_pose(class std::shared_ptr<class core::pose::Pose>) –> 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.splice.AlignEndsMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.splice.AlignEndsMoverCreator, : pyrosetta.rosetta.protocols.splice.AlignEndsMoverCreator) pyrosetta.rosetta.protocols.splice.AlignEndsMoverCreator

C++: protocols::splice::AlignEndsMoverCreator::operator=(const class protocols::splice::AlignEndsMoverCreator &) –> class protocols::splice::AlignEndsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.splice.AlignEndsMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.splice.AlignEndsMoverCreator) str

C++: protocols::splice::AlignEndsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.splice.AlignEndsMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.splice.BBDofs

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.splice.BBDofs, : pyrosetta.rosetta.protocols.splice.BBDofs) pyrosetta.rosetta.protocols.splice.BBDofs

C++: protocols::splice::BBDofs::operator=(const class protocols::splice::BBDofs &) –> class protocols::splice::BBDofs &

omega(*args, **kwargs)

Overloaded function.

  1. omega(self: pyrosetta.rosetta.protocols.splice.BBDofs) -> float

C++: protocols::splice::BBDofs::omega() const –> double

  1. omega(self: pyrosetta.rosetta.protocols.splice.BBDofs, o: float) -> None

C++: protocols::splice::BBDofs::omega(const double) –> void

phi(*args, **kwargs)

Overloaded function.

  1. phi(self: pyrosetta.rosetta.protocols.splice.BBDofs) -> float

C++: protocols::splice::BBDofs::phi() const –> double

  1. phi(self: pyrosetta.rosetta.protocols.splice.BBDofs, p: float) -> None

C++: protocols::splice::BBDofs::phi(const double) –> void

psi(*args, **kwargs)

Overloaded function.

  1. psi(self: pyrosetta.rosetta.protocols.splice.BBDofs) -> float

C++: protocols::splice::BBDofs::psi() const –> double

  1. psi(self: pyrosetta.rosetta.protocols.splice.BBDofs, p: float) -> None

C++: protocols::splice::BBDofs::psi(const double) –> void

resid(*args, **kwargs)

Overloaded function.

  1. resid(self: pyrosetta.rosetta.protocols.splice.BBDofs) -> int

C++: protocols::splice::BBDofs::resid() const –> unsigned long

  1. resid(self: pyrosetta.rosetta.protocols.splice.BBDofs, r: int) -> None

C++: protocols::splice::BBDofs::resid(const unsigned long) –> void

resn(*args, **kwargs)

Overloaded function.

  1. resn(self: pyrosetta.rosetta.protocols.splice.BBDofs) -> str

C++: protocols::splice::BBDofs::resn() const –> std::string

  1. resn(self: pyrosetta.rosetta.protocols.splice.BBDofs, r: str) -> None

C++: protocols::splice::BBDofs::resn(const std::string &) –> void

class pyrosetta.rosetta.protocols.splice.BBMatching

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.splice.BBMatching, : pyrosetta.rosetta.protocols.splice.BBMatching) pyrosetta.rosetta.protocols.splice.BBMatching

C++: protocols::splice::BBMatching::operator=(const class protocols::splice::BBMatching &) –> class protocols::splice::BBMatching &

pdb_to_next_allowed_partners(self: pyrosetta.rosetta.protocols.splice.BBMatching) pyrosetta.rosetta.std.map_std_string_std_vector_std_string_std_allocator_std_string_t

C++: protocols::splice::BBMatching::pdb_to_next_allowed_partners() –> class std::map<std::string, class std::vector<std::string, class std::allocator<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::vector<std::string, class std::allocator<std::string > > > > >

pdb_to_prev_allowed_partners(self: pyrosetta.rosetta.protocols.splice.BBMatching) pyrosetta.rosetta.std.map_std_string_std_vector_std_string_std_allocator_std_string_t

C++: protocols::splice::BBMatching::pdb_to_prev_allowed_partners() –> class std::map<std::string, class std::vector<std::string, class std::allocator<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::vector<std::string, class std::allocator<std::string > > > > >

read_partners_from_file(self: pyrosetta.rosetta.protocols.splice.BBMatching, pdb_name: str, file_name: str) None

C++: protocols::splice::BBMatching::read_partners_from_file(const std::string &, const std::string &) –> void

show(self: pyrosetta.rosetta.protocols.splice.BBMatching) str

C++: protocols::splice::BBMatching::show() –> std::string

size(self: pyrosetta.rosetta.protocols.splice.BBMatching) int

C++: protocols::splice::BBMatching::size() –> unsigned long

class pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation

Bases: pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase

this class is a TaskOperation to prevent repacking of residues not near an interface.

apply(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) None

C++: protocols::splice::DesignInterfacesOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation, : pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation) pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation

C++: protocols::splice::DesignInterfacesOperation::operator=(const class protocols::splice::DesignInterfacesOperation &) –> class protocols::splice::DesignInterfacesOperation &

clone(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation) pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: protocols::splice::DesignInterfacesOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

design_shell(*args, **kwargs)

Overloaded function.

  1. design_shell(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation, radius: float) -> None

C++: protocols::splice::DesignInterfacesOperation::design_shell(const double) –> void

  1. design_shell(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation) -> float

C++: protocols::splice::DesignInterfacesOperation::design_shell() const –> double

static keyname() str

C++: protocols::splice::DesignInterfacesOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::DesignInterfacesOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::splice::DesignInterfacesOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

repack_shell(*args, **kwargs)

Overloaded function.

  1. repack_shell(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation, repack_shell: float) -> None

C++: protocols::splice::DesignInterfacesOperation::repack_shell(const double) –> void

  1. repack_shell(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation) -> float

C++: protocols::splice::DesignInterfacesOperation::repack_shell() const –> double

restrict_to_repacking_chain1(*args, **kwargs)

Overloaded function.

  1. restrict_to_repacking_chain1(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation) -> bool

C++: protocols::splice::DesignInterfacesOperation::restrict_to_repacking_chain1() const –> bool

  1. restrict_to_repacking_chain1(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation, c: bool) -> None

C++: protocols::splice::DesignInterfacesOperation::restrict_to_repacking_chain1(const bool) –> void

restrict_to_repacking_chain2(*args, **kwargs)

Overloaded function.

  1. restrict_to_repacking_chain2(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation) -> bool

C++: protocols::splice::DesignInterfacesOperation::restrict_to_repacking_chain2() const –> bool

  1. restrict_to_repacking_chain2(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation, c: bool) -> None

C++: protocols::splice::DesignInterfacesOperation::restrict_to_repacking_chain2(const bool) –> void

class pyrosetta.rosetta.protocols.splice.DesignInterfacesOperationCreator

Bases: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperationCreator, : pyrosetta.rosetta.protocols.splice.DesignInterfacesOperationCreator) pyrosetta.rosetta.protocols.splice.DesignInterfacesOperationCreator

C++: protocols::splice::DesignInterfacesOperationCreator::operator=(const class protocols::splice::DesignInterfacesOperationCreator &) –> class protocols::splice::DesignInterfacesOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperationCreator) pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: protocols::splice::DesignInterfacesOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperationCreator) str

C++: protocols::splice::DesignInterfacesOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.splice.DesignInterfacesOperationCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.splice.FindEndpointsOperation

Bases: pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase

Find the endpoints on a beta barrel

Cterm_offset(*args, **kwargs)

Overloaded function.

  1. Cterm_offset(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation) -> int

C++: protocols::splice::FindEndpointsOperation::Cterm_offset() const –> unsigned long

  1. Cterm_offset(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation, c: int) -> None

C++: protocols::splice::FindEndpointsOperation::Cterm_offset(const unsigned long) –> void

Nterm_offset(*args, **kwargs)

Overloaded function.

  1. Nterm_offset(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation) -> int

C++: protocols::splice::FindEndpointsOperation::Nterm_offset() const –> unsigned long

  1. Nterm_offset(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation, n: int) -> None

C++: protocols::splice::FindEndpointsOperation::Nterm_offset(const unsigned long) –> void

apply(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) None

C++: protocols::splice::FindEndpointsOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation, : pyrosetta.rosetta.protocols.splice.FindEndpointsOperation) pyrosetta.rosetta.protocols.splice.FindEndpointsOperation

C++: protocols::splice::FindEndpointsOperation::operator=(const class protocols::splice::FindEndpointsOperation &) –> class protocols::splice::FindEndpointsOperation &

clone(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation) pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: protocols::splice::FindEndpointsOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

distance_cutoff(*args, **kwargs)

Overloaded function.

  1. distance_cutoff(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation) -> float

C++: protocols::splice::FindEndpointsOperation::distance_cutoff() const –> double

  1. distance_cutoff(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation, d: float) -> None

C++: protocols::splice::FindEndpointsOperation::distance_cutoff(const double) –> void

even(*args, **kwargs)

Overloaded function.

  1. even(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation) -> bool

C++: protocols::splice::FindEndpointsOperation::even() const –> bool

  1. even(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation, b: bool) -> None

C++: protocols::splice::FindEndpointsOperation::even(const bool) –> void

static keyname() str

C++: protocols::splice::FindEndpointsOperation::keyname() –> std::string

neighbors(*args, **kwargs)

Overloaded function.

  1. neighbors(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation) -> int

C++: protocols::splice::FindEndpointsOperation::neighbors() const –> unsigned long

  1. neighbors(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation, s: int) -> None

C++: protocols::splice::FindEndpointsOperation::neighbors(const unsigned long) –> void

odd(*args, **kwargs)

Overloaded function.

  1. odd(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation) -> bool

C++: protocols::splice::FindEndpointsOperation::odd() const –> bool

  1. odd(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation, b: bool) -> None

C++: protocols::splice::FindEndpointsOperation::odd(const bool) –> void

parse_tag(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::FindEndpointsOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

point_inside(*args, **kwargs)

Overloaded function.

  1. point_inside(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation) -> bool

C++: protocols::splice::FindEndpointsOperation::point_inside() const –> bool

  1. point_inside(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation, b: bool) -> None

C++: protocols::splice::FindEndpointsOperation::point_inside(const bool) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::splice::FindEndpointsOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

sequence_separation(*args, **kwargs)

Overloaded function.

  1. sequence_separation(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation) -> int

C++: protocols::splice::FindEndpointsOperation::sequence_separation() const –> unsigned long

  1. sequence_separation(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperation, s: int) -> None

C++: protocols::splice::FindEndpointsOperation::sequence_separation(const unsigned long) –> void

class pyrosetta.rosetta.protocols.splice.FindEndpointsOperationCreator

Bases: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperationCreator, : pyrosetta.rosetta.protocols.splice.FindEndpointsOperationCreator) pyrosetta.rosetta.protocols.splice.FindEndpointsOperationCreator

C++: protocols::splice::FindEndpointsOperationCreator::operator=(const class protocols::splice::FindEndpointsOperationCreator &) –> class protocols::splice::FindEndpointsOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperationCreator) pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: protocols::splice::FindEndpointsOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperationCreator) str

C++: protocols::splice::FindEndpointsOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.splice.FindEndpointsOperationCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.splice.RBInMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

RBDatabase_fname(*args, **kwargs)

Overloaded function.

  1. RBDatabase_fname(self: pyrosetta.rosetta.protocols.splice.RBInMover) -> str

C++: protocols::splice::RBInMover::RBDatabase_fname() const –> std::string

  1. RBDatabase_fname(self: pyrosetta.rosetta.protocols.splice.RBInMover, s: str) -> None

C++: protocols::splice::RBInMover::RBDatabase_fname(const std::string &) –> void

RB_dbase(*args, **kwargs)

Overloaded function.

  1. RB_dbase(self: pyrosetta.rosetta.protocols.splice.RBInMover, s: str) -> None

C++: protocols::splice::RBInMover::RB_dbase(const std::string &) –> void

  1. RB_dbase(self: pyrosetta.rosetta.protocols.splice.RBInMover) -> str

C++: protocols::splice::RBInMover::RB_dbase() const –> std::string

apply(self: pyrosetta.rosetta.protocols.splice.RBInMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::RBInMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.splice.RBInMover, : pyrosetta.rosetta.protocols.splice.RBInMover) pyrosetta.rosetta.protocols.splice.RBInMover

C++: protocols::splice::RBInMover::operator=(const class protocols::splice::RBInMover &) –> class protocols::splice::RBInMover &

checkpointing_file(*args, **kwargs)

Overloaded function.

  1. checkpointing_file(self: pyrosetta.rosetta.protocols.splice.RBInMover, s: str) -> None

C++: protocols::splice::RBInMover::checkpointing_file(const std::string &) –> void

  1. checkpointing_file(self: pyrosetta.rosetta.protocols.splice.RBInMover) -> str

C++: protocols::splice::RBInMover::checkpointing_file() const –> std::string

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.splice.RBInMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::splice::RBInMover::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>

db_entry(*args, **kwargs)

Overloaded function.

  1. db_entry(self: pyrosetta.rosetta.protocols.splice.RBInMover, s: str) -> None

C++: protocols::splice::RBInMover::db_entry(std::string) –> void

  1. db_entry(self: pyrosetta.rosetta.protocols.splice.RBInMover) -> str

C++: protocols::splice::RBInMover::db_entry() –> std::string

find_disulfide_postions(self: pyrosetta.rosetta.protocols.splice.RBInMover, pose: pyrosetta.rosetta.core.pose.Pose, cys_pos: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: protocols::splice::RBInMover::find_disulfide_postions(const class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

find_vl_vh_cut(self: pyrosetta.rosetta.protocols.splice.RBInMover, pose: pyrosetta.rosetta.core.pose.Pose) int

C++: protocols::splice::RBInMover::find_vl_vh_cut(class core::pose::Pose) const –> unsigned long

fresh_instance(self: pyrosetta.rosetta.protocols.splice.RBInMover) pyrosetta.rosetta.protocols.moves.Mover

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

from_entry(*args, **kwargs)

Overloaded function.

  1. from_entry(self: pyrosetta.rosetta.protocols.splice.RBInMover) -> int

C++: protocols::splice::RBInMover::from_entry() const –> unsigned long

  1. from_entry(self: pyrosetta.rosetta.protocols.splice.RBInMover, s: int) -> None

C++: protocols::splice::RBInMover::from_entry(const unsigned long) –> void

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.splice.RBInMover) str

C++: protocols::splice::RBInMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

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

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

non-const accessor

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

jump_library(*args, **kwargs)

Overloaded function.

  1. jump_library(self: pyrosetta.rosetta.protocols.splice.RBInMover) -> pyrosetta.rosetta.utility.vector1_std_pair_std_string_core_kinematics_Jump_t

C++: protocols::splice::RBInMover::jump_library() const –> class utility::vector1<struct std::pair<std::string, class core::kinematics::Jump>, class std::allocator<struct std::pair<std::string, class core::kinematics::Jump> > >

  1. jump_library(self: pyrosetta.rosetta.protocols.splice.RBInMover, j: pyrosetta.rosetta.utility.vector1_std_pair_std_string_core_kinematics_Jump_t) -> None

C++: protocols::splice::RBInMover::jump_library(class utility::vector1<struct std::pair<std::string, class core::kinematics::Jump>, class std::allocator<struct std::pair<std::string, class core::kinematics::Jump> > >) –> void

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

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

modify_foldtree(*args, **kwargs)

Overloaded function.

  1. modify_foldtree(self: pyrosetta.rosetta.protocols.splice.RBInMover, m: bool) -> None

C++: protocols::splice::RBInMover::modify_foldtree(const bool) –> void

  1. modify_foldtree(self: pyrosetta.rosetta.protocols.splice.RBInMover) -> bool

C++: protocols::splice::RBInMover::modify_foldtree() const –> bool

static mover_name() str

C++: protocols::splice::RBInMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.splice.RBInMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::RBInMover::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::splice::RBInMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize(*args, **kwargs)

Overloaded function.

  1. randomize(self: pyrosetta.rosetta.protocols.splice.RBInMover) -> bool

C++: protocols::splice::RBInMover::randomize() const –> bool

  1. randomize(self: pyrosetta.rosetta.protocols.splice.RBInMover, b: bool) -> None

C++: protocols::splice::RBInMover::randomize(const 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

select_entry_by_name(self: pyrosetta.rosetta.protocols.splice.RBInMover) None

C++: protocols::splice::RBInMover::select_entry_by_name() –> 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_fold_tree(self: pyrosetta.rosetta.protocols.splice.RBInMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::RBInMover::set_fold_tree(class core::pose::Pose &) –> void

set_fold_tree_nodes(self: pyrosetta.rosetta.protocols.splice.RBInMover, pose: pyrosetta.rosetta.core.pose.Pose, cys_pos: pyrosetta.rosetta.utility.vector1_unsigned_long, vl_vh_cut: int) pyrosetta.rosetta.utility.vector1_std_array_int_3_t

C++: protocols::splice::RBInMover::set_fold_tree_nodes(const class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, unsigned long) –> class utility::vector1<struct std::array<int, 3>, class std::allocator<struct std::array<int, 3> > >

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

to_entry(*args, **kwargs)

Overloaded function.

  1. to_entry(self: pyrosetta.rosetta.protocols.splice.RBInMover, s: int) -> None

C++: protocols::splice::RBInMover::to_entry(const unsigned long) –> void

  1. to_entry(self: pyrosetta.rosetta.protocols.splice.RBInMover) -> int

C++: protocols::splice::RBInMover::to_entry() const –> unsigned long

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.splice.RBInMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.splice.RBInMoverCreator, : pyrosetta.rosetta.protocols.splice.RBInMoverCreator) pyrosetta.rosetta.protocols.splice.RBInMoverCreator

C++: protocols::splice::RBInMoverCreator::operator=(const class protocols::splice::RBInMoverCreator &) –> class protocols::splice::RBInMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.splice.RBInMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.splice.RBInMoverCreator) str

C++: protocols::splice::RBInMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.splice.RBInMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.splice.RBOutMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.splice.RBOutMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::RBOutMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.splice.RBOutMover, : pyrosetta.rosetta.protocols.splice.RBOutMover) pyrosetta.rosetta.protocols.splice.RBOutMover

C++: protocols::splice::RBOutMover::operator=(const class protocols::splice::RBOutMover &) –> class protocols::splice::RBOutMover &

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.splice.RBOutMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::splice::RBOutMover::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>

debug(*args, **kwargs)

Overloaded function.

  1. debug(self: pyrosetta.rosetta.protocols.splice.RBOutMover) -> bool

C++: protocols::splice::RBOutMover::debug() –> bool

  1. debug(self: pyrosetta.rosetta.protocols.splice.RBOutMover, b: bool) -> None

C++: protocols::splice::RBOutMover::debug(bool) –> void

find_disulfide_postions(self: pyrosetta.rosetta.protocols.splice.RBOutMover, pose: pyrosetta.rosetta.core.pose.Pose, cys_pos: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: protocols::splice::RBOutMover::find_disulfide_postions(const class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

find_vl_vh_cut(self: pyrosetta.rosetta.protocols.splice.RBOutMover, pose: pyrosetta.rosetta.core.pose.Pose) int

C++: protocols::splice::RBOutMover::find_vl_vh_cut(class core::pose::Pose) –> unsigned long

fresh_instance(self: pyrosetta.rosetta.protocols.splice.RBOutMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::splice::RBOutMover::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_disulf_jump(self: pyrosetta.rosetta.protocols.splice.RBOutMover, pose: pyrosetta.rosetta.core.pose.Pose, template_pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.kinematics.Jump

C++: protocols::splice::RBOutMover::get_disulf_jump(class core::pose::Pose &, class core::pose::Pose &) –> class core::kinematics::Jump

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.splice.RBOutMover) str

C++: protocols::splice::RBOutMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

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

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

non-const accessor

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

jump_dbase_fname(*args, **kwargs)

Overloaded function.

  1. jump_dbase_fname(self: pyrosetta.rosetta.protocols.splice.RBOutMover, s: str) -> None

C++: protocols::splice::RBOutMover::jump_dbase_fname(const std::string &) –> void

  1. jump_dbase_fname(self: pyrosetta.rosetta.protocols.splice.RBOutMover) -> str

C++: protocols::splice::RBOutMover::jump_dbase_fname() const –> std::string

jump_from_foldtree(*args, **kwargs)

Overloaded function.

  1. jump_from_foldtree(self: pyrosetta.rosetta.protocols.splice.RBOutMover) -> bool

C++: protocols::splice::RBOutMover::jump_from_foldtree() const –> bool

  1. jump_from_foldtree(self: pyrosetta.rosetta.protocols.splice.RBOutMover, jfft: bool) -> None

C++: protocols::splice::RBOutMover::jump_from_foldtree(const bool) –> void

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

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

static mover_name() str

C++: protocols::splice::RBOutMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.splice.RBOutMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::RBOutMover::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::splice::RBOutMover::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_fold_tree_nodes(self: pyrosetta.rosetta.protocols.splice.RBOutMover, pose: pyrosetta.rosetta.core.pose.Pose, cys_pos: pyrosetta.rosetta.utility.vector1_unsigned_long, vl_vh_cut: int) pyrosetta.rosetta.utility.vector1_std_array_int_3_t

C++: protocols::splice::RBOutMover::set_fold_tree_nodes(const class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, unsigned long) –> class utility::vector1<struct std::array<int, 3>, class std::allocator<struct std::array<int, 3> > >

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

superimpose_source_on_pose(self: pyrosetta.rosetta.protocols.splice.RBOutMover, target_pose: pyrosetta.rosetta.core.pose.Pose, target_from_res: int, target_to_res: int, template_pose: pyrosetta.rosetta.core.pose.Pose, template_from_res: int, template_to_res: int) None

C++: protocols::splice::RBOutMover::superimpose_source_on_pose(const class core::pose::Pose &, unsigned long, unsigned long, class core::pose::Pose &, unsigned long, unsigned long) –> void

template_pdb_fname(*args, **kwargs)

Overloaded function.

  1. template_pdb_fname(self: pyrosetta.rosetta.protocols.splice.RBOutMover) -> str

C++: protocols::splice::RBOutMover::template_pdb_fname() const –> std::string

  1. template_pdb_fname(self: pyrosetta.rosetta.protocols.splice.RBOutMover, s: str) -> None

C++: protocols::splice::RBOutMover::template_pdb_fname(const 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.splice.RBOutMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.splice.RBOutMoverCreator, : pyrosetta.rosetta.protocols.splice.RBOutMoverCreator) pyrosetta.rosetta.protocols.splice.RBOutMoverCreator

C++: protocols::splice::RBOutMoverCreator::operator=(const class protocols::splice::RBOutMoverCreator &) –> class protocols::splice::RBOutMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.splice.RBOutMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.splice.RBOutMoverCreator) str

C++: protocols::splice::RBOutMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.splice.RBOutMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.splice.ROT

Bases: pybind11_builtins.pybind11_object

property AA
assign(self: pyrosetta.rosetta.protocols.splice.ROT, : pyrosetta.rosetta.protocols.splice.ROT) pyrosetta.rosetta.protocols.splice.ROT

C++: protocols::splice::ROT::operator=(const struct protocols::splice::ROT &) –> struct protocols::splice::ROT &

property chi_vec
class pyrosetta.rosetta.protocols.splice.ResidueBBDofs

Bases: pybind11_builtins.pybind11_object

aa_sequence(*args, **kwargs)

Overloaded function.

  1. aa_sequence(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs, s: str) -> None

C++: protocols::splice::ResidueBBDofs::aa_sequence(const std::string &) –> void

  1. aa_sequence(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs) -> str

C++: protocols::splice::ResidueBBDofs::aa_sequence() const –> std::string

assign(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs, : pyrosetta.rosetta.protocols.splice.ResidueBBDofs) pyrosetta.rosetta.protocols.splice.ResidueBBDofs

C++: protocols::splice::ResidueBBDofs::operator=(const class protocols::splice::ResidueBBDofs &) –> class protocols::splice::ResidueBBDofs &

bbdofs(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs) pyrosetta.rosetta.utility.vector1_protocols_splice_BBDofs

C++: protocols::splice::ResidueBBDofs::bbdofs() –> class utility::vector1<class protocols::splice::BBDofs, class std::allocator<class protocols::splice::BBDofs> >

begin(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs) __gnu_cxx::__normal_iterator<protocols::splice::BBDofs*, std::vector<protocols::splice::BBDofs, std::allocator<protocols::splice::BBDofs> > >

C++: protocols::splice::ResidueBBDofs::begin() –> class __gnu_cxx::__normal_iterator<class protocols::splice::BBDofs *, class std::vector<class protocols::splice::BBDofs, class std::allocator<class protocols::splice::BBDofs> > >

clear(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs) None

C++: protocols::splice::ResidueBBDofs::clear() –> void

cut_site(*args, **kwargs)

Overloaded function.

  1. cut_site(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs, c: int) -> None

C++: protocols::splice::ResidueBBDofs::cut_site(const unsigned long) –> void

  1. cut_site(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs) -> int

C++: protocols::splice::ResidueBBDofs::cut_site() const –> unsigned long

disulfide(*args, **kwargs)

Overloaded function.

  1. disulfide(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs) -> int

C++: protocols::splice::ResidueBBDofs::disulfide() const –> unsigned long

  1. disulfide(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs, s: int) -> None

C++: protocols::splice::ResidueBBDofs::disulfide(const unsigned long) –> void

dssp(*args, **kwargs)

Overloaded function.

  1. dssp(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs, s: str) -> None

C++: protocols::splice::ResidueBBDofs::dssp(const std::string &) –> void

  1. dssp(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs) -> str

C++: protocols::splice::ResidueBBDofs::dssp() const –> std::string

end(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs) __gnu_cxx::__normal_iterator<protocols::splice::BBDofs*, std::vector<protocols::splice::BBDofs, std::allocator<protocols::splice::BBDofs> > >

C++: protocols::splice::ResidueBBDofs::end() –> class __gnu_cxx::__normal_iterator<class protocols::splice::BBDofs *, class std::vector<class protocols::splice::BBDofs, class std::allocator<class protocols::splice::BBDofs> > >

push_back(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs, b: pyrosetta.rosetta.protocols.splice.BBDofs) None

C++: protocols::splice::ResidueBBDofs::push_back(const class protocols::splice::BBDofs &) –> void

size(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs) int

C++: protocols::splice::ResidueBBDofs::size() const –> unsigned long

source_pdb(*args, **kwargs)

Overloaded function.

  1. source_pdb(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs) -> str

C++: protocols::splice::ResidueBBDofs::source_pdb() const –> std::string

  1. source_pdb(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs, s: str) -> None

C++: protocols::splice::ResidueBBDofs::source_pdb(const std::string &) –> void

start_loop(*args, **kwargs)

Overloaded function.

  1. start_loop(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs) -> int

C++: protocols::splice::ResidueBBDofs::start_loop() const –> unsigned long

  1. start_loop(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs, s: int) -> None

C++: protocols::splice::ResidueBBDofs::start_loop(const unsigned long) –> void

stop_loop(*args, **kwargs)

Overloaded function.

  1. stop_loop(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs) -> int

C++: protocols::splice::ResidueBBDofs::stop_loop() const –> unsigned long

  1. stop_loop(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs, s: int) -> None

C++: protocols::splice::ResidueBBDofs::stop_loop(const unsigned long) –> void

tail_segment(*args, **kwargs)

Overloaded function.

  1. tail_segment(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs) -> str

C++: protocols::splice::ResidueBBDofs::tail_segment() const –> std::string

  1. tail_segment(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs, s: str) -> None

C++: protocols::splice::ResidueBBDofs::tail_segment(const std::string &) –> void

class pyrosetta.rosetta.protocols.splice.RotLibOut

Bases: pyrosetta.rosetta.protocols.moves.Mover

Rotamer_db_file(*args, **kwargs)

Overloaded function.

  1. Rotamer_db_file(self: pyrosetta.rosetta.protocols.splice.RotLibOut, s: str) -> None

C++: protocols::splice::RotLibOut::Rotamer_db_file(std::string) –> void

  1. Rotamer_db_file(self: pyrosetta.rosetta.protocols.splice.RotLibOut) -> str

C++: protocols::splice::RotLibOut::Rotamer_db_file() –> std::string

apply(self: pyrosetta.rosetta.protocols.splice.RotLibOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::RotLibOut::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.splice.RotLibOut, : pyrosetta.rosetta.protocols.splice.RotLibOut) pyrosetta.rosetta.protocols.splice.RotLibOut

C++: protocols::splice::RotLibOut::operator=(const class protocols::splice::RotLibOut &) –> class protocols::splice::RotLibOut &

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.splice.RotLibOut) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::splice::RotLibOut::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>

dump_pdb(*args, **kwargs)

Overloaded function.

  1. dump_pdb(self: pyrosetta.rosetta.protocols.splice.RotLibOut, b: bool) -> None

C++: protocols::splice::RotLibOut::dump_pdb(bool) –> void

  1. dump_pdb(self: pyrosetta.rosetta.protocols.splice.RotLibOut) -> bool

C++: protocols::splice::RotLibOut::dump_pdb() –> bool

find_matching_res(self: pyrosetta.rosetta.protocols.splice.RotLibOut, pose: pyrosetta.rosetta.core.pose.Pose, hit_pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::RotLibOut::find_matching_res(class core::pose::Pose &, class core::pose::Pose &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.splice.RotLibOut) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::splice::RotLibOut::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_min_dist(self: pyrosetta.rosetta.protocols.splice.RotLibOut) float

C++: protocols::splice::RotLibOut::get_min_dist() –> double

get_name(self: pyrosetta.rosetta.protocols.splice.RotLibOut) str

C++: protocols::splice::RotLibOut::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

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

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

non-const accessor

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

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

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

min_frag_length(*args, **kwargs)

Overloaded function.

  1. min_frag_length(self: pyrosetta.rosetta.protocols.splice.RotLibOut, i: int) -> None

C++: protocols::splice::RotLibOut::min_frag_length(unsigned long) –> void

  1. min_frag_length(self: pyrosetta.rosetta.protocols.splice.RotLibOut) -> int

C++: protocols::splice::RotLibOut::min_frag_length() –> unsigned long

static mover_name() str

C++: protocols::splice::RotLibOut::mover_name() –> std::string

static name() str

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

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

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

print(self: pyrosetta.rosetta.protocols.splice.RotLibOut) None

C++: protocols::splice::RotLibOut::print() –> void

print_lib_to_file(self: pyrosetta.rosetta.protocols.splice.RotLibOut) None

C++: protocols::splice::RotLibOut::print_lib_to_file() –> 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::splice::RotLibOut::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

seq_aln_file(*args, **kwargs)

Overloaded function.

  1. seq_aln_file(self: pyrosetta.rosetta.protocols.splice.RotLibOut, s: str) -> None

C++: protocols::splice::RotLibOut::seq_aln_file(std::string) –> void

  1. seq_aln_file(self: pyrosetta.rosetta.protocols.splice.RotLibOut) -> str

C++: protocols::splice::RotLibOut::seq_aln_file() –> std::string

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_min_dist(self: pyrosetta.rosetta.protocols.splice.RotLibOut, : float) None

C++: protocols::splice::RotLibOut::set_min_dist(double) –> 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.splice.RotLibOutCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.splice.RotLibOutCreator, : pyrosetta.rosetta.protocols.splice.RotLibOutCreator) pyrosetta.rosetta.protocols.splice.RotLibOutCreator

C++: protocols::splice::RotLibOutCreator::operator=(const class protocols::splice::RotLibOutCreator &) –> class protocols::splice::RotLibOutCreator &

create_mover(self: pyrosetta.rosetta.protocols.splice.RotLibOutCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.splice.RotLibOutCreator) str

C++: protocols::splice::RotLibOutCreator::keyname() const –> std::string

static mover_name() str

C++: protocols::splice::RotLibOutCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.splice.RotLibOutCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.splice.RotLibdb

Bases: pybind11_builtins.pybind11_object

add_segment_fname(self: pyrosetta.rosetta.protocols.splice.RotLibdb, file_name: str, segment_name: str) None

C++: protocols::splice::RotLibdb::add_segment_fname(const std::string &, const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.splice.RotLibdb, : pyrosetta.rosetta.protocols.splice.RotLibdb) pyrosetta.rosetta.protocols.splice.RotLibdb

C++: protocols::splice::RotLibdb::operator=(const class protocols::splice::RotLibdb &) –> class protocols::splice::RotLibdb &

fill_rotamer_matrix_from_db_file(self: pyrosetta.rosetta.protocols.splice.RotLibdb, fname: str) pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_splice_ROT_std_allocator_protocols_splice_ROT_t

C++: protocols::splice::RotLibdb::fill_rotamer_matrix_from_db_file(std::string) –> class utility::vector1<class utility::vector1<struct protocols::splice::ROT, class std::allocator<struct protocols::splice::ROT> >, class std::allocator<class utility::vector1<struct protocols::splice::ROT, class std::allocator<struct protocols::splice::ROT> > > >

get_segment_fname(self: pyrosetta.rosetta.protocols.splice.RotLibdb, segment_name: str) str

C++: protocols::splice::RotLibdb::get_segment_fname(const std::string &) –> std::string

pdb_profile(self: pyrosetta.rosetta.protocols.splice.RotLibdb, pdb_name: str) pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_splice_ROT_std_allocator_protocols_splice_ROT_t

C++: protocols::splice::RotLibdb::pdb_profile(const std::string &) –> class utility::vector1<class utility::vector1<struct protocols::splice::ROT, class std::allocator<struct protocols::splice::ROT> >, class std::allocator<class utility::vector1<struct protocols::splice::ROT, class std::allocator<struct protocols::splice::ROT> > > >

read_pdb_profile(self: pyrosetta.rosetta.protocols.splice.RotLibdb, file_name: str) None

C++: protocols::splice::RotLibdb::read_pdb_profile(const std::string &) –> void

read_profile(self: pyrosetta.rosetta.protocols.splice.RotLibdb, file_name: str, segment_name: str) None

C++: protocols::splice::RotLibdb::read_profile(const std::string &, const std::string &) –> void

class pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB

Bases: pyrosetta.rosetta.core.pack.task.operation.TaskOperation

SampleAtAlignedpositions(*args, **kwargs)

Overloaded function.

  1. SampleAtAlignedpositions(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::splice::SampleRotamersFromPDB::SampleAtAlignedpositions() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

  1. SampleAtAlignedpositions(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB, s: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::splice::SampleRotamersFromPDB::SampleAtAlignedpositions(const class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

apply(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) None

apply

C++: protocols::splice::SampleRotamersFromPDB::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB, : pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB) pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB

C++: protocols::splice::SampleRotamersFromPDB::operator=(const class protocols::splice::SampleRotamersFromPDB &) –> class protocols::splice::SampleRotamersFromPDB &

clone(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB) pyrosetta.rosetta.core.pack.task.operation.TaskOperation

make clone

C++: protocols::splice::SampleRotamersFromPDB::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

combine_rot_dbs(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_splice_ROT_std_allocator_protocols_splice_ROT_t

C++: protocols::splice::SampleRotamersFromPDB::combine_rot_dbs(const class core::pose::Pose &) const –> class utility::vector1<class utility::vector1<struct protocols::splice::ROT, class std::allocator<struct protocols::splice::ROT> >, class std::allocator<class utility::vector1<struct protocols::splice::ROT, class std::allocator<struct protocols::splice::ROT> > > >

concatenate_rot_matrix(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB, a: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_splice_ROT_std_allocator_protocols_splice_ROT_t, b: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_splice_ROT_std_allocator_protocols_splice_ROT_t) None

C++: protocols::splice::SampleRotamersFromPDB::concatenate_rot_matrix(class utility::vector1<class utility::vector1<struct protocols::splice::ROT, class std::allocator<struct protocols::splice::ROT> >, class std::allocator<class utility::vector1<struct protocols::splice::ROT, class std::allocator<struct protocols::splice::ROT> > > > &, const class utility::vector1<class utility::vector1<struct protocols::splice::ROT, class std::allocator<struct protocols::splice::ROT> >, class std::allocator<class utility::vector1<struct protocols::splice::ROT, class std::allocator<struct protocols::splice::ROT> > > > &) const –> void

static keyname() str

C++: protocols::splice::SampleRotamersFromPDB::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::SampleRotamersFromPDB::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::splice::SampleRotamersFromPDB::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDBCreator

Bases: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDBCreator, : pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDBCreator) pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDBCreator

C++: protocols::splice::SampleRotamersFromPDBCreator::operator=(const class protocols::splice::SampleRotamersFromPDBCreator &) –> class protocols::splice::SampleRotamersFromPDBCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDBCreator) pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: protocols::splice::SampleRotamersFromPDBCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDBCreator) str

C++: protocols::splice::SampleRotamersFromPDBCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDBCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation

Bases: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

ROT2res(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation, rot: pyrosetta.rosetta.protocols.splice.ROT, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.conformation.Residue

C++: protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::ROT2res(struct protocols::splice::ROT, const class core::pose::Pose &) –> class std::shared_ptr<class core::conformation::Residue>

add_pose(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

add_rotamer_constraints(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, seqnum: int, cur_rot: pyrosetta.rosetta.core.conformation.Residue) None

C++: protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_rotamer_constraints(class core::pose::Pose &, unsigned long, class std::shared_ptr<class core::conformation::Residue>) –> void

add_rotamer_to_rotamer_set(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, cur_rot: pyrosetta.rosetta.core.conformation.Residue) None

C++: protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_rotamer_to_rotamer_set(const class core::pose::Pose &, class core::pack::rotamer_set::RotamerSet &, class std::shared_ptr<class core::conformation::Residue>) –> void

alter_rotamer_set(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.pack.task.PackerTask, : pyrosetta.rosetta.utility.graph.Graph, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) None

C++: protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class core::pack::rotamer_set::RotamerSet &) –> void

alter_rotamer_set_from_db(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) None

C++: protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db(const class core::pose::Pose &, const class core::pack::task::PackerTask &, class core::pack::rotamer_set::RotamerSet &) –> void

alter_rotamer_set_from_pdb(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) None

C++: protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(const class core::pose::Pose &, const class core::pack::task::PackerTask &, class core::pack::rotamer_set::RotamerSet &) –> void

assign(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation, : pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation) pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation

C++: protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::operator=(const class protocols::splice::SampleRotamersFromPDB_RotamerSetOperation &) –> class protocols::splice::SampleRotamersFromPDB_RotamerSetOperation &

clone(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation) pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

C++: protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetOperation>

copy_rotamer_matrix(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation, rm: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_splice_ROT_std_allocator_protocols_splice_ROT_t) None

C++: protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::copy_rotamer_matrix(const class utility::vector1<class utility::vector1<struct protocols::splice::ROT, class std::allocator<struct protocols::splice::ROT> >, class std::allocator<class utility::vector1<struct protocols::splice::ROT, class std::allocator<struct protocols::splice::ROT> > > > &) –> void

fill_rotamer_matrix_from_db_file(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation) None

C++: protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::fill_rotamer_matrix_from_db_file() –> void

increase_packer_residue_radius(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, the_task: pyrosetta.rosetta.core.pack.task.PackerTask, residue_in: int) float

C++: core::pack::rotamer_set::RotamerSetOperation::increase_packer_residue_radius(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, unsigned long) const –> double

initialize_from_command_line(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation) None

C++: protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::initialize_from_command_line() –> void

is_residue_allowed(self: pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation, restype: pyrosetta.rosetta.core.chemical.ResidueType, rtask: pyrosetta.rosetta.core.pack.task.ResidueLevelTask) bool

C++: protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::is_residue_allowed(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &) –> bool

class pyrosetta.rosetta.protocols.splice.Splice

Bases: pyrosetta.rosetta.protocols.moves.Mover

container for BBDofs, providing a convenient operator [], size, other methods and iterators that allow splice to treat ResidueBBDofs as a simple vector (even though it contains other elements as well)

add_coordinate_constraints(*args, **kwargs)

Overloaded function.

  1. add_coordinate_constraints(self: pyrosetta.rosetta.protocols.splice.Splice, pose: pyrosetta.rosetta.core.pose.Pose, source_pose: pyrosetta.rosetta.core.pose.Pose, nearest_to_from: int, nearest_to_to: int, anchor: int) -> None

  2. add_coordinate_constraints(self: pyrosetta.rosetta.protocols.splice.Splice, pose: pyrosetta.rosetta.core.pose.Pose, source_pose: pyrosetta.rosetta.core.pose.Pose, nearest_to_from: int, nearest_to_to: int, anchor: int, atom_type: str) -> None

  3. add_coordinate_constraints(self: pyrosetta.rosetta.protocols.splice.Splice, pose: pyrosetta.rosetta.core.pose.Pose, source_pose: pyrosetta.rosetta.core.pose.Pose, nearest_to_from: int, nearest_to_to: int, anchor: int, atom_type: str, task: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

C++: protocols::splice::Splice::add_coordinate_constraints(class core::pose::Pose &, const class core::pose::Pose &, unsigned long, unsigned long, unsigned long, std::string, class std::shared_ptr<class core::pack::task::PackerTask>) –> void

add_dihedral_constraints(self: pyrosetta.rosetta.protocols.splice.Splice, pose: pyrosetta.rosetta.core.pose.Pose, source_pose: pyrosetta.rosetta.core.pose.Pose, nearest_to_from: int, nearest_to_to: int) None

add dihedral constraint to grafted loop according to source pdb dihedral angles

C++: protocols::splice::Splice::add_dihedral_constraints(class core::pose::Pose &, const class core::pose::Pose &, unsigned long, unsigned long) –> void

add_sequence_constraints(self: pyrosetta.rosetta.protocols.splice.Splice, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::Splice::add_sequence_constraints(class core::pose::Pose &) –> void

add_sequence_constraints_only(*args, **kwargs)

Overloaded function.

  1. add_sequence_constraints_only(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::add_sequence_constraints_only() const –> bool

  1. add_sequence_constraints_only(self: pyrosetta.rosetta.protocols.splice.Splice, a: bool) -> None

C++: protocols::splice::Splice::add_sequence_constraints_only(const bool) –> void

allow_all_aa(*args, **kwargs)

Overloaded function.

  1. allow_all_aa(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::allow_all_aa() const –> bool

  1. allow_all_aa(self: pyrosetta.rosetta.protocols.splice.Splice, d: bool) -> None

C++: protocols::splice::Splice::allow_all_aa(const bool) –> void

apply(self: pyrosetta.rosetta.protocols.splice.Splice, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::Splice::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.splice.Splice, : pyrosetta.rosetta.protocols.splice.Splice) pyrosetta.rosetta.protocols.splice.Splice

C++: protocols::splice::Splice::operator=(const class protocols::splice::Splice &) –> class protocols::splice::Splice &

ccd(*args, **kwargs)

Overloaded function.

  1. ccd(self: pyrosetta.rosetta.protocols.splice.Splice, c: bool) -> None

C++: protocols::splice::Splice::ccd(const bool) –> void

  1. ccd(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::ccd() const –> bool

chain_num(*args, **kwargs)

Overloaded function.

  1. chain_num(self: pyrosetta.rosetta.protocols.splice.Splice) -> int

C++: protocols::splice::Splice::chain_num() const –> unsigned long

  1. chain_num(self: pyrosetta.rosetta.protocols.splice.Splice, c: int) -> None

C++: protocols::splice::Splice::chain_num(const unsigned long) –> void

checkpointing_file(*args, **kwargs)

Overloaded function.

  1. checkpointing_file(self: pyrosetta.rosetta.protocols.splice.Splice) -> str

C++: protocols::splice::Splice::checkpointing_file() const –> std::string

  1. checkpointing_file(self: pyrosetta.rosetta.protocols.splice.Splice, cf: str) -> None

C++: protocols::splice::Splice::checkpointing_file(const std::string &) –> 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.splice.Splice) pyrosetta.rosetta.protocols.moves.Mover

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

coor_const(self: pyrosetta.rosetta.protocols.splice.Splice) float

C++: protocols::splice::Splice::coor_const() const –> double

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>

cut_secondarystruc(*args, **kwargs)

Overloaded function.

  1. cut_secondarystruc(self: pyrosetta.rosetta.protocols.splice.Splice, r: bool) -> None

C++: protocols::splice::Splice::cut_secondarystruc(const bool) –> void

  1. cut_secondarystruc(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::cut_secondarystruc() const –> bool

database_entry(*args, **kwargs)

Overloaded function.

  1. database_entry(self: pyrosetta.rosetta.protocols.splice.Splice) -> int

C++: protocols::splice::Splice::database_entry() const –> unsigned long

  1. database_entry(self: pyrosetta.rosetta.protocols.splice.Splice, d: int) -> None

C++: protocols::splice::Splice::database_entry(const unsigned long) –> void

database_pdb_entry(*args, **kwargs)

Overloaded function.

  1. database_pdb_entry(self: pyrosetta.rosetta.protocols.splice.Splice, s: str) -> None

C++: protocols::splice::Splice::database_pdb_entry(const std::string &) –> void

  1. database_pdb_entry(self: pyrosetta.rosetta.protocols.splice.Splice) -> str

C++: protocols::splice::Splice::database_pdb_entry() const –> std::string

dbase_begin(self: pyrosetta.rosetta.protocols.splice.Splice) __gnu_cxx::__normal_iterator<unsigned long const*, std::vector<unsigned long, std::allocator<unsigned long> > >

C++: protocols::splice::Splice::dbase_begin() const –> class __gnu_cxx::__normal_iterator<const unsigned long *, class std::vector<unsigned long, class std::allocator<unsigned long> > >

dbase_end(self: pyrosetta.rosetta.protocols.splice.Splice) __gnu_cxx::__normal_iterator<unsigned long const*, std::vector<unsigned long, std::allocator<unsigned long> > >

C++: protocols::splice::Splice::dbase_end() const –> class __gnu_cxx::__normal_iterator<const unsigned long *, class std::vector<unsigned long, class std::allocator<unsigned long> > >

dbase_iterate(*args, **kwargs)

Overloaded function.

  1. dbase_iterate(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::dbase_iterate() const –> bool

  1. dbase_iterate(self: pyrosetta.rosetta.protocols.splice.Splice, d: bool) -> None

C++: protocols::splice::Splice::dbase_iterate(const bool) –> void

delete_hairpin(*args, **kwargs)

Overloaded function.

  1. delete_hairpin(self: pyrosetta.rosetta.protocols.splice.Splice, b: bool) -> None

C++: protocols::splice::Splice::delete_hairpin(const bool) –> void

  1. delete_hairpin(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::delete_hairpin() const –> bool

delete_hairpin_c(*args, **kwargs)

Overloaded function.

  1. delete_hairpin_c(self: pyrosetta.rosetta.protocols.splice.Splice) -> int

C++: protocols::splice::Splice::delete_hairpin_c() const –> unsigned long

  1. delete_hairpin_c(self: pyrosetta.rosetta.protocols.splice.Splice, c: int) -> None

C++: protocols::splice::Splice::delete_hairpin_c(const unsigned long) –> void

delete_hairpin_n(*args, **kwargs)

Overloaded function.

  1. delete_hairpin_n(self: pyrosetta.rosetta.protocols.splice.Splice) -> int

C++: protocols::splice::Splice::delete_hairpin_n() const –> unsigned long

  1. delete_hairpin_n(self: pyrosetta.rosetta.protocols.splice.Splice, c: int) -> None

C++: protocols::splice::Splice::delete_hairpin_n(const unsigned long) –> void

delta_lengths(*args, **kwargs)

Overloaded function.

  1. delta_lengths(self: pyrosetta.rosetta.protocols.splice.Splice, dl: pyrosetta.rosetta.utility.vector1_int) -> None

C++: protocols::splice::Splice::delta_lengths(const class utility::vector1<int, class std::allocator<int> > &) –> void

  1. delta_lengths(self: pyrosetta.rosetta.protocols.splice.Splice) -> pyrosetta.rosetta.utility.vector1_int

C++: protocols::splice::Splice::delta_lengths() –> class utility::vector1<int, class std::allocator<int> >

design(*args, **kwargs)

Overloaded function.

  1. design(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::design() const –> bool

  1. design(self: pyrosetta.rosetta.protocols.splice.Splice, d: bool) -> None

C++: protocols::splice::Splice::design(const bool) –> void

design_shell(*args, **kwargs)

Overloaded function.

  1. design_shell(self: pyrosetta.rosetta.protocols.splice.Splice, c: float) -> None

C++: protocols::splice::Splice::design_shell(const double) –> void

  1. design_shell(self: pyrosetta.rosetta.protocols.splice.Splice) -> float

C++: protocols::splice::Splice::design_shell() const –> double

design_task_factory(*args, **kwargs)

Overloaded function.

  1. design_task_factory(self: pyrosetta.rosetta.protocols.splice.Splice) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::splice::Splice::design_task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

  1. design_task_factory(self: pyrosetta.rosetta.protocols.splice.Splice, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::splice::Splice::design_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

dihedral_const(self: pyrosetta.rosetta.protocols.splice.Splice) float

C++: protocols::splice::Splice::dihedral_const() const –> double

equal_length(*args, **kwargs)

Overloaded function.

  1. equal_length(self: pyrosetta.rosetta.protocols.splice.Splice, e: bool) -> None

C++: protocols::splice::Splice::equal_length(const bool) –> void

  1. equal_length(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::equal_length() const –> bool

find_dbase_entry(self: pyrosetta.rosetta.protocols.splice.Splice, pose: pyrosetta.rosetta.core.pose.Pose) int

C++: protocols::splice::Splice::find_dbase_entry(const class core::pose::Pose &) –> unsigned long

fold_tree(self: pyrosetta.rosetta.protocols.splice.Splice, pose: pyrosetta.rosetta.core.pose.Pose, start: int, stop: int, cut: int) None

C++: protocols::splice::Splice::fold_tree(class core::pose::Pose &, const unsigned long, const unsigned long, const unsigned long) const –> void

fresh_instance(self: pyrosetta.rosetta.protocols.splice.Splice) pyrosetta.rosetta.protocols.moves.Mover

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

from_res(*args, **kwargs)

Overloaded function.

  1. from_res(self: pyrosetta.rosetta.protocols.splice.Splice, f: int) -> None

C++: protocols::splice::Splice::from_res(const unsigned long) –> void

  1. from_res(self: pyrosetta.rosetta.protocols.splice.Splice, pose: pyrosetta.rosetta.core.pose.Pose) -> int

C++: protocols::splice::Splice::from_res(const class core::pose::Pose &) const –> unsigned long

generate_sequence_profile(self: pyrosetta.rosetta.protocols.splice.Splice, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.sequence.SequenceProfile

C++: protocols::splice::Splice::generate_sequence_profile(class core::pose::Pose &) –> class std::shared_ptr<class core::sequence::SequenceProfile>

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_seg(self: pyrosetta.rosetta.protocols.splice.Splice) int

C++: protocols::splice::Splice::get_current_seg() –> unsigned long

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_dofs_pdb_name(self: pyrosetta.rosetta.protocols.splice.Splice) str

C++: protocols::splice::Splice::get_dofs_pdb_name() 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.splice.Splice) str

C++: protocols::splice::Splice::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_segment_names_ordered(self: pyrosetta.rosetta.protocols.splice.Splice) pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::splice::Splice::get_segment_names_ordered() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

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

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

non-const accessor

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

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

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

load_from_checkpoint(self: pyrosetta.rosetta.protocols.splice.Splice) None

C++: protocols::splice::Splice::load_from_checkpoint() –> void

load_pdb_segments_from_pose_comments(self: pyrosetta.rosetta.protocols.splice.Splice, p: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::Splice::load_pdb_segments_from_pose_comments(const class core::pose::Pose &) –> void

locked_res(*args, **kwargs)

Overloaded function.

  1. locked_res(self: pyrosetta.rosetta.protocols.splice.Splice) -> int

C++: protocols::splice::Splice::locked_res() const –> unsigned long

  1. locked_res(self: pyrosetta.rosetta.protocols.splice.Splice, r: int) -> None

C++: protocols::splice::Splice::locked_res(const unsigned long) –> void

locked_res_id(*args, **kwargs)

Overloaded function.

  1. locked_res_id(self: pyrosetta.rosetta.protocols.splice.Splice, c: str) -> None

C++: protocols::splice::Splice::locked_res_id(const char) –> void

  1. locked_res_id(self: pyrosetta.rosetta.protocols.splice.Splice) -> str

C++: protocols::splice::Splice::locked_res_id() const –> char

loop_dbase_file_name(*args, **kwargs)

Overloaded function.

  1. loop_dbase_file_name(self: pyrosetta.rosetta.protocols.splice.Splice) -> str

C++: protocols::splice::Splice::loop_dbase_file_name() const –> std::string

  1. loop_dbase_file_name(self: pyrosetta.rosetta.protocols.splice.Splice, f: str) -> None

C++: protocols::splice::Splice::loop_dbase_file_name(const std::string &) –> void

loop_pdb_source(*args, **kwargs)

Overloaded function.

  1. loop_pdb_source(self: pyrosetta.rosetta.protocols.splice.Splice, l: str) -> None

C++: protocols::splice::Splice::loop_pdb_source(const std::string &) –> void

  1. loop_pdb_source(self: pyrosetta.rosetta.protocols.splice.Splice) -> str

C++: protocols::splice::Splice::loop_pdb_source() const –> std::string

modify_pdb_segments_with_current_segment(self: pyrosetta.rosetta.protocols.splice.Splice, pdb_name: str) None

C++: protocols::splice::Splice::modify_pdb_segments_with_current_segment(const std::string &) –> void

static mover_name() str

C++: protocols::splice::Splice::mover_name() –> std::string

static name() str

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

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

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

poly_ala(*args, **kwargs)

Overloaded function.

  1. poly_ala(self: pyrosetta.rosetta.protocols.splice.Splice, p: bool) -> None

C++: protocols::splice::Splice::poly_ala(const bool) –> void

  1. poly_ala(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::poly_ala() const –> bool

profile_weight_away_from_interface(*args, **kwargs)

Overloaded function.

  1. profile_weight_away_from_interface(self: pyrosetta.rosetta.protocols.splice.Splice, p: float) -> None

C++: protocols::splice::Splice::profile_weight_away_from_interface(const double) –> void

  1. profile_weight_away_from_interface(self: pyrosetta.rosetta.protocols.splice.Splice) -> float

C++: protocols::splice::Splice::profile_weight_away_from_interface() const –> double

protein_family(self: pyrosetta.rosetta.protocols.splice.Splice, s: str) None

C++: protocols::splice::Splice::protein_family(const std::string &) –> 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::splice::Splice::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize_cut(*args, **kwargs)

Overloaded function.

  1. randomize_cut(self: pyrosetta.rosetta.protocols.splice.Splice, r: bool) -> None

C++: protocols::splice::Splice::randomize_cut(const bool) –> void

  1. randomize_cut(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::randomize_cut() const –> bool

rb_adjust_template(self: pyrosetta.rosetta.protocols.splice.Splice, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::Splice::rb_adjust_template(const class core::pose::Pose &) –> void

rb_sensitive(*args, **kwargs)

Overloaded function.

  1. rb_sensitive(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::rb_sensitive() const –> bool

  1. rb_sensitive(self: pyrosetta.rosetta.protocols.splice.Splice, r: bool) -> None

C++: protocols::splice::Splice::rb_sensitive(const bool) –> void

read_splice_segments(self: pyrosetta.rosetta.protocols.splice.Splice, segment_type: str, segment_name: str, file_name: str) None
sequence profiles

Splice changes the backbone of the current pose and the following methods deal with dynamically constructing a sequence profile for the current backbone choices.

C++: protocols::splice::Splice::read_splice_segments(const std::string &, const std::string &, const std::string &) –> void

read_torsion_database(self: pyrosetta.rosetta.protocols.splice.Splice) None

C++: protocols::splice::Splice::read_torsion_database() –> 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

remove_hairpin(self: pyrosetta.rosetta.protocols.splice.Splice, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::Splice::remove_hairpin(class core::pose::Pose &) const –> void

repack_shell(*args, **kwargs)

Overloaded function.

  1. repack_shell(self: pyrosetta.rosetta.protocols.splice.Splice, c: float) -> None

C++: protocols::splice::Splice::repack_shell(const double) –> void

  1. repack_shell(self: pyrosetta.rosetta.protocols.splice.Splice) -> float

C++: protocols::splice::Splice::repack_shell() const –> double

res_move(*args, **kwargs)

Overloaded function.

  1. res_move(self: pyrosetta.rosetta.protocols.splice.Splice, r: int) -> None

C++: protocols::splice::Splice::res_move(const unsigned long) –> void

  1. res_move(self: pyrosetta.rosetta.protocols.splice.Splice) -> int

C++: protocols::splice::Splice::res_move() const –> unsigned long

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

restrict_to_repacking_chain2(*args, **kwargs)

Overloaded function.

  1. restrict_to_repacking_chain2(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::restrict_to_repacking_chain2() const –> bool

  1. restrict_to_repacking_chain2(self: pyrosetta.rosetta.protocols.splice.Splice, r: bool) -> None

C++: protocols::splice::Splice::restrict_to_repacking_chain2(const bool) –> void

rms_cutoff(*args, **kwargs)

Overloaded function.

  1. rms_cutoff(self: pyrosetta.rosetta.protocols.splice.Splice) -> float

C++: protocols::splice::Splice::rms_cutoff() const –> double

  1. rms_cutoff(self: pyrosetta.rosetta.protocols.splice.Splice, r: float) -> None

C++: protocols::splice::Splice::rms_cutoff(const double) –> void

rms_cutoff_loop(*args, **kwargs)

Overloaded function.

  1. rms_cutoff_loop(self: pyrosetta.rosetta.protocols.splice.Splice) -> float

C++: protocols::splice::Splice::rms_cutoff_loop() const –> double

  1. rms_cutoff_loop(self: pyrosetta.rosetta.protocols.splice.Splice, r: float) -> None

C++: protocols::splice::Splice::rms_cutoff_loop(const double) –> void

rtmin(*args, **kwargs)

Overloaded function.

  1. rtmin(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::rtmin() const –> bool

  1. rtmin(self: pyrosetta.rosetta.protocols.splice.Splice, d: bool) -> None

C++: protocols::splice::Splice::rtmin(const bool) –> void

save_to_checkpoint(self: pyrosetta.rosetta.protocols.splice.Splice) None

C++: protocols::splice::Splice::save_to_checkpoint() const –> void

scorefxn(*args, **kwargs)

Overloaded function.

  1. scorefxn(self: pyrosetta.rosetta.protocols.splice.Splice, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::splice::Splice::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

  1. scorefxn(self: pyrosetta.rosetta.protocols.splice.Splice) -> pyrosetta.rosetta.core.scoring.ScoreFunction

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

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_cut_res(*args, **kwargs)

Overloaded function.

  1. set_cut_res(self: pyrosetta.rosetta.protocols.splice.Splice, r: int) -> None

C++: protocols::splice::Splice::set_cut_res(const unsigned long) –> void

  1. set_cut_res(self: pyrosetta.rosetta.protocols.splice.Splice) -> int

C++: protocols::splice::Splice::set_cut_res() const –> unsigned long

set_dofs_pdb_name(self: pyrosetta.rosetta.protocols.splice.Splice, dofsPDBname: str) None

C++: protocols::splice::Splice::set_dofs_pdb_name(std::string) –> void

set_fold_tree(self: pyrosetta.rosetta.protocols.splice.Splice, pose: pyrosetta.rosetta.core.pose.Pose, vl_vh_cut: int) None

C++: protocols::splice::Splice::set_fold_tree(class core::pose::Pose &, const unsigned long) –> void

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

setter for poses contained for rms

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

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

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

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

set_segment_names_ordered(self: pyrosetta.rosetta.protocols.splice.Splice, SegNameOrder: pyrosetta.rosetta.utility.vector1_std_string) None

C++: protocols::splice::Splice::set_segment_names_ordered(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.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

skip_alignment(*args, **kwargs)

Overloaded function.

  1. skip_alignment(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::skip_alignment() const –> bool

  1. skip_alignment(self: pyrosetta.rosetta.protocols.splice.Splice, b: bool) -> None

C++: protocols::splice::Splice::skip_alignment(const bool) –> void

source_pdb(*args, **kwargs)

Overloaded function.

  1. source_pdb(self: pyrosetta.rosetta.protocols.splice.Splice) -> str

C++: protocols::splice::Splice::source_pdb() const –> std::string

  1. source_pdb(self: pyrosetta.rosetta.protocols.splice.Splice, s: str) -> None

C++: protocols::splice::Splice::source_pdb(const std::string &) –> void

source_pdb_from_res(*args, **kwargs)

Overloaded function.

  1. source_pdb_from_res(self: pyrosetta.rosetta.protocols.splice.Splice) -> int

C++: protocols::splice::Splice::source_pdb_from_res() const –> unsigned long

  1. source_pdb_from_res(self: pyrosetta.rosetta.protocols.splice.Splice, s: int) -> None

C++: protocols::splice::Splice::source_pdb_from_res(const unsigned long) –> void

source_pdb_to_res(*args, **kwargs)

Overloaded function.

  1. source_pdb_to_res(self: pyrosetta.rosetta.protocols.splice.Splice) -> int

C++: protocols::splice::Splice::source_pdb_to_res() const –> unsigned long

  1. source_pdb_to_res(self: pyrosetta.rosetta.protocols.splice.Splice, s: int) -> None

C++: protocols::splice::Splice::source_pdb_to_res(const unsigned long) –> void

splice_filter(*args, **kwargs)

Overloaded function.

  1. splice_filter(self: pyrosetta.rosetta.protocols.splice.Splice) -> pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::splice::Splice::splice_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

  1. splice_filter(self: pyrosetta.rosetta.protocols.splice.Splice, f: pyrosetta.rosetta.protocols.filters.Filter) -> None

C++: protocols::splice::Splice::splice_filter(class std::shared_ptr<class protocols::filters::Filter>) –> void

superimposed(*args, **kwargs)

Overloaded function.

  1. superimposed(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::superimposed() const –> bool

  1. superimposed(self: pyrosetta.rosetta.protocols.splice.Splice, b: bool) -> None

C++: protocols::splice::Splice::superimposed(const bool) –> void

tail_fold_tree(self: pyrosetta.rosetta.protocols.splice.Splice, pose: pyrosetta.rosetta.core.pose.Pose, vl_vh_cut: int, chain_break: int, segment_name: str) None

C++: protocols::splice::Splice::tail_fold_tree(class core::pose::Pose &, const unsigned long, unsigned long, std::string) const –> void

task_factory(*args, **kwargs)

Overloaded function.

  1. task_factory(self: pyrosetta.rosetta.protocols.splice.Splice) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::splice::Splice::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

  1. task_factory(self: pyrosetta.rosetta.protocols.splice.Splice, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::splice::Splice::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

template_file(*args, **kwargs)

Overloaded function.

  1. template_file(self: pyrosetta.rosetta.protocols.splice.Splice) -> str

C++: protocols::splice::Splice::template_file() const –> std::string

  1. template_file(self: pyrosetta.rosetta.protocols.splice.Splice, s: str) -> None

C++: protocols::splice::Splice::template_file(const 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

thread_original_sequence(*args, **kwargs)

Overloaded function.

  1. thread_original_sequence(self: pyrosetta.rosetta.protocols.splice.Splice) -> bool

C++: protocols::splice::Splice::thread_original_sequence() const –> bool

  1. thread_original_sequence(self: pyrosetta.rosetta.protocols.splice.Splice, s: bool) -> None

C++: protocols::splice::Splice::thread_original_sequence(const bool) –> void

to_res(*args, **kwargs)

Overloaded function.

  1. to_res(self: pyrosetta.rosetta.protocols.splice.Splice, t: int) -> None

C++: protocols::splice::Splice::to_res(const unsigned long) –> void

  1. to_res(self: pyrosetta.rosetta.protocols.splice.Splice, pose: pyrosetta.rosetta.core.pose.Pose) -> int

C++: protocols::splice::Splice::to_res(const class core::pose::Pose &) const –> unsigned long

torsion_database(*args, **kwargs)

Overloaded function.

  1. torsion_database(self: pyrosetta.rosetta.protocols.splice.Splice) -> pyrosetta.rosetta.utility.vector1_protocols_splice_ResidueBBDofs

C++: protocols::splice::Splice::torsion_database() const –> class utility::vector1<class protocols::splice::ResidueBBDofs, class std::allocator<class protocols::splice::ResidueBBDofs> >

  1. torsion_database(self: pyrosetta.rosetta.protocols.splice.Splice, d: pyrosetta.rosetta.utility.vector1_protocols_splice_ResidueBBDofs) -> None

C++: protocols::splice::Splice::torsion_database(const class utility::vector1<class protocols::splice::ResidueBBDofs, class std::allocator<class protocols::splice::ResidueBBDofs> > &) –> void

torsion_database_fname(*args, **kwargs)

Overloaded function.

  1. torsion_database_fname(self: pyrosetta.rosetta.protocols.splice.Splice) -> str

C++: protocols::splice::Splice::torsion_database_fname() const –> std::string

  1. torsion_database_fname(self: pyrosetta.rosetta.protocols.splice.Splice, d: str) -> None

C++: protocols::splice::Splice::torsion_database_fname(const std::string &) –> 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.splice.SpliceCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.splice.SpliceCreator, : pyrosetta.rosetta.protocols.splice.SpliceCreator) pyrosetta.rosetta.protocols.splice.SpliceCreator

C++: protocols::splice::SpliceCreator::operator=(const class protocols::splice::SpliceCreator &) –> class protocols::splice::SpliceCreator &

create_mover(self: pyrosetta.rosetta.protocols.splice.SpliceCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.splice.SpliceCreator) str

C++: protocols::splice::SpliceCreator::keyname() const –> std::string

static mover_name() str

C++: protocols::splice::SpliceCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.splice.SpliceCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.splice.SpliceIn

Bases: pyrosetta.rosetta.protocols.splice.SpliceOut

SpliceOutFilter(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) int

C++: protocols::splice::SpliceOut::SpliceOutFilter(class core::pose::Pose *) –> int

SpliceOutRMSDFilter(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) int

C++: protocols::splice::SpliceOut::SpliceOutRMSDFilter(class core::pose::Pose *) –> int

abstract_parse_tag(self: pyrosetta.rosetta.protocols.splice.SpliceOut, tag: pyrosetta.rosetta.utility.tag.Tag) None

C++: protocols::splice::SpliceOut::abstract_parse_tag(const class std::shared_ptr<const class utility::tag::Tag>) –> void

apply(self: pyrosetta.rosetta.protocols.splice.SpliceIn, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceIn::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.splice.SpliceIn, : pyrosetta.rosetta.protocols.splice.SpliceIn) pyrosetta.rosetta.protocols.splice.SpliceIn

C++: protocols::splice::SpliceIn::operator=(const class protocols::splice::SpliceIn &) –> class protocols::splice::SpliceIn &

assign_from_res_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceIn, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceIn::assign_from_res_to_res(const class core::pose::Pose &) –> void

build_ideal_segment(self: pyrosetta.rosetta.protocols.splice.SpliceIn, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceIn::build_ideal_segment(class core::pose::Pose &) –> void

ccd_mover(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::splice::SpliceOut::ccd_mover(class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> void

check_source_segment(self: pyrosetta.rosetta.protocols.splice.SpliceOut) None

C++: protocols::splice::SpliceOut::check_source_segment() –> 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.splice.SpliceIn) pyrosetta.rosetta.protocols.moves.Mover

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

copy_dofs_from_source(self: pyrosetta.rosetta.protocols.splice.SpliceOut) None

C++: protocols::splice::SpliceOut::copy_dofs_from_source() –> void

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>

cut_secondarystruc(*args, **kwargs)

Overloaded function.

  1. cut_secondarystruc(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: bool) -> None

C++: protocols::splice::SpliceOut::cut_secondarystruc(const bool) –> void

  1. cut_secondarystruc(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::cut_secondarystruc() const –> bool

database_entry(*args, **kwargs)

Overloaded function.

  1. database_entry(self: pyrosetta.rosetta.protocols.splice.SpliceIn) -> int

C++: protocols::splice::SpliceIn::database_entry() const –> unsigned long

  1. database_entry(self: pyrosetta.rosetta.protocols.splice.SpliceIn, d: int) -> None

C++: protocols::splice::SpliceIn::database_entry(const unsigned long) –> void

database_pdb_entry(*args, **kwargs)

Overloaded function.

  1. database_pdb_entry(self: pyrosetta.rosetta.protocols.splice.SpliceIn, s: str) -> None

C++: protocols::splice::SpliceIn::database_pdb_entry(const std::string &) –> void

  1. database_pdb_entry(self: pyrosetta.rosetta.protocols.splice.SpliceIn) -> str

C++: protocols::splice::SpliceIn::database_pdb_entry() const –> std::string

dbase_begin(self: pyrosetta.rosetta.protocols.splice.SpliceIn) __gnu_cxx::__normal_iterator<unsigned long const*, std::vector<unsigned long, std::allocator<unsigned long> > >

C++: protocols::splice::SpliceIn::dbase_begin() const –> class __gnu_cxx::__normal_iterator<const unsigned long *, class std::vector<unsigned long, class std::allocator<unsigned long> > >

dbase_end(self: pyrosetta.rosetta.protocols.splice.SpliceIn) __gnu_cxx::__normal_iterator<unsigned long const*, std::vector<unsigned long, std::allocator<unsigned long> > >

C++: protocols::splice::SpliceIn::dbase_end() const –> class __gnu_cxx::__normal_iterator<const unsigned long *, class std::vector<unsigned long, class std::allocator<unsigned long> > >

dbase_file_name(*args, **kwargs)

Overloaded function.

  1. dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> str

C++: protocols::splice::SpliceOut::dbase_file_name() const –> std::string

  1. dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceOut, f: str) -> None

C++: protocols::splice::SpliceOut::dbase_file_name(const std::string &) –> void

dbase_iterate(*args, **kwargs)

Overloaded function.

  1. dbase_iterate(self: pyrosetta.rosetta.protocols.splice.SpliceIn) -> bool

C++: protocols::splice::SpliceIn::dbase_iterate() const –> bool

  1. dbase_iterate(self: pyrosetta.rosetta.protocols.splice.SpliceIn, d: bool) -> None

C++: protocols::splice::SpliceIn::dbase_iterate(const bool) –> void

delete_hairpin(*args, **kwargs)

Overloaded function.

  1. delete_hairpin(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

C++: protocols::splice::SpliceOut::delete_hairpin(const bool) –> void

  1. delete_hairpin(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::delete_hairpin() const –> bool

delete_hairpin_c(*args, **kwargs)

Overloaded function.

  1. delete_hairpin_c(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> int

C++: protocols::splice::SpliceOut::delete_hairpin_c() const –> unsigned long

  1. delete_hairpin_c(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::delete_hairpin_c(const unsigned long) –> void

delete_hairpin_n(*args, **kwargs)

Overloaded function.

  1. delete_hairpin_n(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> int

C++: protocols::splice::SpliceOut::delete_hairpin_n() const –> unsigned long

  1. delete_hairpin_n(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::delete_hairpin_n(const unsigned long) –> void

find_dbase_entry(self: pyrosetta.rosetta.protocols.splice.SpliceIn, pose: pyrosetta.rosetta.core.pose.Pose) int

C++: protocols::splice::SpliceIn::find_dbase_entry(const class core::pose::Pose &) –> unsigned long

fresh_instance(self: pyrosetta.rosetta.protocols.splice.SpliceIn) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::splice::SpliceIn::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.splice.SpliceIn) str

C++: protocols::splice::SpliceIn::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

handle_mover_tag(self: pyrosetta.rosetta.protocols.splice.SpliceOut, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::SpliceOut::handle_mover_tag(const class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

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

non-const accessor

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

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

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

load_from_checkpoint(self: pyrosetta.rosetta.protocols.splice.SpliceIn) None

C++: protocols::splice::SpliceIn::load_from_checkpoint() –> void

load_pdb_segments_from_pose_comments(self: pyrosetta.rosetta.protocols.splice.SpliceOut, p: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::load_pdb_segments_from_pose_comments(const class core::pose::Pose &) –> void

min_mover(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::splice::SpliceOut::min_mover(class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> void

min_seg(*args, **kwargs)

Overloaded function.

  1. min_seg(self: pyrosetta.rosetta.protocols.splice.SpliceIn) -> bool

C++: protocols::splice::SpliceIn::min_seg() const –> bool

  1. min_seg(self: pyrosetta.rosetta.protocols.splice.SpliceIn, d: bool) -> None

C++: protocols::splice::SpliceIn::min_seg(const bool) –> void

minimize_segment(self: pyrosetta.rosetta.protocols.splice.SpliceIn, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceIn::minimize_segment(class core::pose::Pose &) –> void

static mover_name() str

C++: protocols::splice::SpliceIn::mover_name() –> std::string

static name() str

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

name_for_filter(self: pyrosetta.rosetta.protocols.splice.SpliceOut) str

C++: protocols::splice::SpliceOut::name_for_filter() –> std::string

pack(self: pyrosetta.rosetta.protocols.splice.SpliceIn, pose: pyrosetta.rosetta.core.pose.Pose, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::splice::SpliceIn::pack(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

parse_SpliceOut_tags(self: pyrosetta.rosetta.protocols.splice.SpliceOut, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::SpliceOut::parse_SpliceOut_tags(const class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

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

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

place_cut_site_in_segment(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::place_cut_site_in_segment(const class core::pose::Pose &) –> 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::splice::SpliceIn::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize_cut(*args, **kwargs)

Overloaded function.

  1. randomize_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

C++: protocols::splice::SpliceOut::randomize_cut(const bool) –> void

  1. randomize_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::randomize_cut() –> bool

rb_sensitive(*args, **kwargs)

Overloaded function.

  1. rb_sensitive(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::rb_sensitive() const –> bool

  1. rb_sensitive(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: bool) -> None

C++: protocols::splice::SpliceOut::rb_sensitive(const bool) –> void

read_torsion_database(self: pyrosetta.rosetta.protocols.splice.SpliceIn) None

C++: protocols::splice::SpliceIn::read_torsion_database() –> 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

remove_hairpin(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::remove_hairpin(class core::pose::Pose &) const –> void

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

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

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

rms_cutoff(*args, **kwargs)

Overloaded function.

  1. rms_cutoff(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> float

C++: protocols::splice::SpliceOut::rms_cutoff() const –> double

  1. rms_cutoff(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: float) -> None

C++: protocols::splice::SpliceOut::rms_cutoff(const double) –> void

rms_cutoff_loop(*args, **kwargs)

Overloaded function.

  1. rms_cutoff_loop(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> float

C++: protocols::splice::SpliceOut::rms_cutoff_loop() const –> double

  1. rms_cutoff_loop(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: float) -> None

C++: protocols::splice::SpliceOut::rms_cutoff_loop(const double) –> void

rtmin(self: pyrosetta.rosetta.protocols.splice.SpliceIn, pose: pyrosetta.rosetta.core.pose.Pose, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::splice::SpliceIn::rtmin(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

scorefxn(*args, **kwargs)

Overloaded function.

  1. scorefxn(self: pyrosetta.rosetta.protocols.splice.SpliceIn, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::splice::SpliceIn::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

  1. scorefxn(self: pyrosetta.rosetta.protocols.splice.SpliceIn) -> pyrosetta.rosetta.core.scoring.ScoreFunction

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

set_anchor_res(self: pyrosetta.rosetta.protocols.splice.SpliceIn) int

C++: protocols::splice::SpliceIn::set_anchor_res() –> unsigned long

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_fold_tree_nodes(self: pyrosetta.rosetta.protocols.splice.SpliceIn, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceIn::set_fold_tree_nodes(const class core::pose::Pose &) –> 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_loop_length_change(self: pyrosetta.rosetta.protocols.splice.SpliceIn, llc: pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange) None

C++: protocols::splice::SpliceIn::set_loop_length_change(class protocols::protein_interface_design::movers::LoopLengthChange &) –> 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_source_from_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut) None

C++: protocols::splice::SpliceOut::set_source_from_to_res() –> 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

source_from_res(*args, **kwargs)

Overloaded function.

  1. source_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_from_res(const unsigned long) –> void

  1. source_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> int

C++: protocols::splice::SpliceOut::source_from_res() –> unsigned long

source_pdb(*args, **kwargs)

Overloaded function.

  1. source_pdb(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> str

C++: protocols::splice::SpliceOut::source_pdb() const –> std::string

  1. source_pdb(self: pyrosetta.rosetta.protocols.splice.SpliceOut, s: str) -> None

C++: protocols::splice::SpliceOut::source_pdb(const std::string &) –> void

source_to_res(*args, **kwargs)

Overloaded function.

  1. source_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_to_res(const unsigned long) –> void

  1. source_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> int

C++: protocols::splice::SpliceOut::source_to_res() –> unsigned long

splice_filter(*args, **kwargs)

Overloaded function.

  1. splice_filter(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::splice::SpliceOut::splice_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

  1. splice_filter(self: pyrosetta.rosetta.protocols.splice.SpliceOut, f: pyrosetta.rosetta.protocols.filters.Filter) -> None

C++: protocols::splice::SpliceOut::splice_filter(class std::shared_ptr<class protocols::filters::Filter>) –> void

superimpose_source_on_pose(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose, source_pose: pyrosetta.rosetta.core.pose.Pose) None

add dihedral constraint to grafted loop according to source pdb dihedral angles

C++: protocols::splice::SpliceOut::superimpose_source_on_pose(const class core::pose::Pose &, class core::pose::Pose &) –> void

superimposed(*args, **kwargs)

Overloaded function.

  1. superimposed(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

C++: protocols::splice::SpliceOut::superimposed(const bool) –> void

  1. superimposed(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::superimposed() –> bool

tail_mover(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::splice::SpliceOut::tail_mover(class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> 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

thread_original_sequence(*args, **kwargs)

Overloaded function.

  1. thread_original_sequence(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::thread_original_sequence() const –> bool

  1. thread_original_sequence(self: pyrosetta.rosetta.protocols.splice.SpliceOut, s: bool) -> None

C++: protocols::splice::SpliceOut::thread_original_sequence(const bool) –> 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 &

write_database_to_file(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::write_database_to_file(const class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.splice.SpliceInAntibody

Bases: pyrosetta.rosetta.protocols.splice.SpliceInTail

SpliceOutFilter(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) int

C++: protocols::splice::SpliceOut::SpliceOutFilter(class core::pose::Pose *) –> int

SpliceOutRMSDFilter(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) int

C++: protocols::splice::SpliceOut::SpliceOutRMSDFilter(class core::pose::Pose *) –> int

abstract_parse_tag(self: pyrosetta.rosetta.protocols.splice.SpliceOut, tag: pyrosetta.rosetta.utility.tag.Tag) None

C++: protocols::splice::SpliceOut::abstract_parse_tag(const class std::shared_ptr<const class utility::tag::Tag>) –> void

adjust_n_ter_tail_length(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceInAntibody::adjust_n_ter_tail_length(class core::pose::Pose &) –> void

adjust_template_jump(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceInAntibody::adjust_template_jump(class core::pose::Pose &) –> void

antibody_DB(*args, **kwargs)

Overloaded function.

  1. antibody_DB(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, s: str) -> None

C++: protocols::splice::SpliceInAntibody::antibody_DB(const std::string &) –> void

  1. antibody_DB(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody) -> str

C++: protocols::splice::SpliceInAntibody::antibody_DB() –> std::string

apply(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceInAntibody::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, : pyrosetta.rosetta.protocols.splice.SpliceInAntibody) pyrosetta.rosetta.protocols.splice.SpliceInAntibody

C++: protocols::splice::SpliceInAntibody::operator=(const class protocols::splice::SpliceInAntibody &) –> class protocols::splice::SpliceInAntibody &

assign_from_res_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceInAntibody::assign_from_res_to_res(const class core::pose::Pose &) –> void

build_ideal_segment(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceInAntibody::build_ideal_segment(class core::pose::Pose &) –> void

ccd_mover(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::splice::SpliceOut::ccd_mover(class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> void

check_source_segment(self: pyrosetta.rosetta.protocols.splice.SpliceOut) None

C++: protocols::splice::SpliceOut::check_source_segment() –> 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.splice.SpliceInAntibody) pyrosetta.rosetta.protocols.moves.Mover

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

copy_dofs_from_source(self: pyrosetta.rosetta.protocols.splice.SpliceOut) None

C++: protocols::splice::SpliceOut::copy_dofs_from_source() –> void

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>

cut_secondarystruc(*args, **kwargs)

Overloaded function.

  1. cut_secondarystruc(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: bool) -> None

C++: protocols::splice::SpliceOut::cut_secondarystruc(const bool) –> void

  1. cut_secondarystruc(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::cut_secondarystruc() const –> bool

database_entry(*args, **kwargs)

Overloaded function.

  1. database_entry(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody) -> int

C++: protocols::splice::SpliceInAntibody::database_entry() const –> unsigned long

  1. database_entry(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, d: int) -> None

C++: protocols::splice::SpliceInAntibody::database_entry(const unsigned long) –> void

database_pdb_entry(*args, **kwargs)

Overloaded function.

  1. database_pdb_entry(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, s: str) -> None

C++: protocols::splice::SpliceInAntibody::database_pdb_entry(const std::string &) –> void

  1. database_pdb_entry(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody) -> str

C++: protocols::splice::SpliceInAntibody::database_pdb_entry() const –> std::string

dbase_begin(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody) __gnu_cxx::__normal_iterator<unsigned long const*, std::vector<unsigned long, std::allocator<unsigned long> > >

C++: protocols::splice::SpliceInAntibody::dbase_begin() const –> class __gnu_cxx::__normal_iterator<const unsigned long *, class std::vector<unsigned long, class std::allocator<unsigned long> > >

dbase_end(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody) __gnu_cxx::__normal_iterator<unsigned long const*, std::vector<unsigned long, std::allocator<unsigned long> > >

C++: protocols::splice::SpliceInAntibody::dbase_end() const –> class __gnu_cxx::__normal_iterator<const unsigned long *, class std::vector<unsigned long, class std::allocator<unsigned long> > >

dbase_file_name(*args, **kwargs)

Overloaded function.

  1. dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> str

C++: protocols::splice::SpliceOut::dbase_file_name() const –> std::string

  1. dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceOut, f: str) -> None

C++: protocols::splice::SpliceOut::dbase_file_name(const std::string &) –> void

dbase_iterate(*args, **kwargs)

Overloaded function.

  1. dbase_iterate(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody) -> bool

C++: protocols::splice::SpliceInAntibody::dbase_iterate() const –> bool

  1. dbase_iterate(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, d: bool) -> None

C++: protocols::splice::SpliceInAntibody::dbase_iterate(const bool) –> void

delete_hairpin(*args, **kwargs)

Overloaded function.

  1. delete_hairpin(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

C++: protocols::splice::SpliceOut::delete_hairpin(const bool) –> void

  1. delete_hairpin(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::delete_hairpin() const –> bool

delete_hairpin_c(*args, **kwargs)

Overloaded function.

  1. delete_hairpin_c(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> int

C++: protocols::splice::SpliceOut::delete_hairpin_c() const –> unsigned long

  1. delete_hairpin_c(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::delete_hairpin_c(const unsigned long) –> void

delete_hairpin_n(*args, **kwargs)

Overloaded function.

  1. delete_hairpin_n(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> int

C++: protocols::splice::SpliceOut::delete_hairpin_n() const –> unsigned long

  1. delete_hairpin_n(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::delete_hairpin_n(const unsigned long) –> void

find_dbase_entry(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, pose: pyrosetta.rosetta.core.pose.Pose) int

C++: protocols::splice::SpliceInAntibody::find_dbase_entry(const class core::pose::Pose &) –> unsigned long

find_disulfide_postions(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, pose: pyrosetta.rosetta.core.pose.Pose, cys_pos: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: protocols::splice::SpliceInAntibody::find_disulfide_postions(const class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

find_vl_vh_cut(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceInAntibody::find_vl_vh_cut(class core::pose::Pose) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::splice::SpliceInAntibody::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.splice.SpliceInAntibody) str

C++: protocols::splice::SpliceInAntibody::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

handle_mover_tag(self: pyrosetta.rosetta.protocols.splice.SpliceOut, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::SpliceOut::handle_mover_tag(const class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

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

non-const accessor

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

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

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

load_from_checkpoint(self: pyrosetta.rosetta.protocols.splice.SpliceIn) None

C++: protocols::splice::SpliceIn::load_from_checkpoint() –> void

load_pdb_segments_from_pose_comments(self: pyrosetta.rosetta.protocols.splice.SpliceOut, p: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::load_pdb_segments_from_pose_comments(const class core::pose::Pose &) –> void

min_mover(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::splice::SpliceOut::min_mover(class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> void

min_seg(*args, **kwargs)

Overloaded function.

  1. min_seg(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody) -> bool

C++: protocols::splice::SpliceInAntibody::min_seg() const –> bool

  1. min_seg(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, d: bool) -> None

C++: protocols::splice::SpliceInAntibody::min_seg(const bool) –> void

minimize_segment(self: pyrosetta.rosetta.protocols.splice.SpliceIn, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceIn::minimize_segment(class core::pose::Pose &) –> void

static mover_name() str

C++: protocols::splice::SpliceInAntibody::mover_name() –> std::string

static name() str

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

name_for_filter(self: pyrosetta.rosetta.protocols.splice.SpliceOut) str

C++: protocols::splice::SpliceOut::name_for_filter() –> std::string

pack(self: pyrosetta.rosetta.protocols.splice.SpliceIn, pose: pyrosetta.rosetta.core.pose.Pose, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::splice::SpliceIn::pack(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

parse_SpliceOut_tags(self: pyrosetta.rosetta.protocols.splice.SpliceOut, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::SpliceOut::parse_SpliceOut_tags(const class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

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

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

place_cut_site_in_segment(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::place_cut_site_in_segment(const class core::pose::Pose &) –> 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::splice::SpliceInAntibody::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize_cut(*args, **kwargs)

Overloaded function.

  1. randomize_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

C++: protocols::splice::SpliceOut::randomize_cut(const bool) –> void

  1. randomize_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::randomize_cut() –> bool

rb_sensitive(*args, **kwargs)

Overloaded function.

  1. rb_sensitive(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::rb_sensitive() const –> bool

  1. rb_sensitive(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: bool) -> None

C++: protocols::splice::SpliceOut::rb_sensitive(const bool) –> void

read_torsion_database(self: pyrosetta.rosetta.protocols.splice.SpliceIn) None

C++: protocols::splice::SpliceIn::read_torsion_database() –> 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

remove_hairpin(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::remove_hairpin(class core::pose::Pose &) const –> void

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

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

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

rms_cutoff(*args, **kwargs)

Overloaded function.

  1. rms_cutoff(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> float

C++: protocols::splice::SpliceOut::rms_cutoff() const –> double

  1. rms_cutoff(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: float) -> None

C++: protocols::splice::SpliceOut::rms_cutoff(const double) –> void

rms_cutoff_loop(*args, **kwargs)

Overloaded function.

  1. rms_cutoff_loop(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> float

C++: protocols::splice::SpliceOut::rms_cutoff_loop() const –> double

  1. rms_cutoff_loop(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: float) -> None

C++: protocols::splice::SpliceOut::rms_cutoff_loop(const double) –> void

rtmin(self: pyrosetta.rosetta.protocols.splice.SpliceIn, pose: pyrosetta.rosetta.core.pose.Pose, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::splice::SpliceIn::rtmin(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

scorefxn(*args, **kwargs)

Overloaded function.

  1. scorefxn(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::splice::SpliceInAntibody::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

  1. scorefxn(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody) -> pyrosetta.rosetta.core.scoring.ScoreFunction

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

set_anchor_res(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody) int

C++: protocols::splice::SpliceInAntibody::set_anchor_res() –> unsigned long

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_fold_tree_nodes(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceInAntibody::set_fold_tree_nodes(const class core::pose::Pose &) –> 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_loop_length_change(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, llc: pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange) None

C++: protocols::splice::SpliceInAntibody::set_loop_length_change(class protocols::protein_interface_design::movers::LoopLengthChange &) –> 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_source_from_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut) None

C++: protocols::splice::SpliceOut::set_source_from_to_res() –> 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

source_from_res(*args, **kwargs)

Overloaded function.

  1. source_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_from_res(const unsigned long) –> void

  1. source_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> int

C++: protocols::splice::SpliceOut::source_from_res() –> unsigned long

source_pdb(*args, **kwargs)

Overloaded function.

  1. source_pdb(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> str

C++: protocols::splice::SpliceOut::source_pdb() const –> std::string

  1. source_pdb(self: pyrosetta.rosetta.protocols.splice.SpliceOut, s: str) -> None

C++: protocols::splice::SpliceOut::source_pdb(const std::string &) –> void

source_to_res(*args, **kwargs)

Overloaded function.

  1. source_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_to_res(const unsigned long) –> void

  1. source_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> int

C++: protocols::splice::SpliceOut::source_to_res() –> unsigned long

splice_filter(*args, **kwargs)

Overloaded function.

  1. splice_filter(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::splice::SpliceOut::splice_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

  1. splice_filter(self: pyrosetta.rosetta.protocols.splice.SpliceOut, f: pyrosetta.rosetta.protocols.filters.Filter) -> None

C++: protocols::splice::SpliceOut::splice_filter(class std::shared_ptr<class protocols::filters::Filter>) –> void

superimpose_source_on_pose(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose, source_pose: pyrosetta.rosetta.core.pose.Pose) None

add dihedral constraint to grafted loop according to source pdb dihedral angles

C++: protocols::splice::SpliceOut::superimpose_source_on_pose(const class core::pose::Pose &, class core::pose::Pose &) –> void

superimposed(*args, **kwargs)

Overloaded function.

  1. superimposed(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

C++: protocols::splice::SpliceOut::superimposed(const bool) –> void

  1. superimposed(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::superimposed() –> bool

tail_mover(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::splice::SpliceOut::tail_mover(class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> 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

thread_original_sequence(*args, **kwargs)

Overloaded function.

  1. thread_original_sequence(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::thread_original_sequence() const –> bool

  1. thread_original_sequence(self: pyrosetta.rosetta.protocols.splice.SpliceOut, s: bool) -> None

C++: protocols::splice::SpliceOut::thread_original_sequence(const bool) –> 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_vl_vh_cut(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody) None

C++: protocols::splice::SpliceInAntibody::update_vl_vh_cut() –> void

write_database_to_file(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::write_database_to_file(const class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.splice.SpliceInAntibodyCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibodyCreator, : pyrosetta.rosetta.protocols.splice.SpliceInAntibodyCreator) pyrosetta.rosetta.protocols.splice.SpliceInAntibodyCreator

C++: protocols::splice::SpliceInAntibodyCreator::operator=(const class protocols::splice::SpliceInAntibodyCreator &) –> class protocols::splice::SpliceInAntibodyCreator &

create_mover(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibodyCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibodyCreator) str

C++: protocols::splice::SpliceInAntibodyCreator::keyname() const –> std::string

static mover_name() str

C++: protocols::splice::SpliceInAntibodyCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibodyCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.splice.SpliceInCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.splice.SpliceInCreator, : pyrosetta.rosetta.protocols.splice.SpliceInCreator) pyrosetta.rosetta.protocols.splice.SpliceInCreator

C++: protocols::splice::SpliceInCreator::operator=(const class protocols::splice::SpliceInCreator &) –> class protocols::splice::SpliceInCreator &

create_mover(self: pyrosetta.rosetta.protocols.splice.SpliceInCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.splice.SpliceInCreator) str

C++: protocols::splice::SpliceInCreator::keyname() const –> std::string

static mover_name() str

C++: protocols::splice::SpliceInCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.splice.SpliceInCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.splice.SpliceInTail

Bases: pyrosetta.rosetta.protocols.splice.SpliceIn

SpliceOutFilter(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) int

C++: protocols::splice::SpliceOut::SpliceOutFilter(class core::pose::Pose *) –> int

SpliceOutRMSDFilter(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) int

C++: protocols::splice::SpliceOut::SpliceOutRMSDFilter(class core::pose::Pose *) –> int

abstract_parse_tag(self: pyrosetta.rosetta.protocols.splice.SpliceOut, tag: pyrosetta.rosetta.utility.tag.Tag) None

C++: protocols::splice::SpliceOut::abstract_parse_tag(const class std::shared_ptr<const class utility::tag::Tag>) –> void

apply(self: pyrosetta.rosetta.protocols.splice.SpliceInTail, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceInTail::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.splice.SpliceInTail, : pyrosetta.rosetta.protocols.splice.SpliceInTail) pyrosetta.rosetta.protocols.splice.SpliceInTail

C++: protocols::splice::SpliceInTail::operator=(const class protocols::splice::SpliceInTail &) –> class protocols::splice::SpliceInTail &

assign_from_res_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceInTail, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceInTail::assign_from_res_to_res(const class core::pose::Pose &) –> void

build_ideal_segment(self: pyrosetta.rosetta.protocols.splice.SpliceInTail, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceInTail::build_ideal_segment(class core::pose::Pose &) –> void

ccd_mover(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::splice::SpliceOut::ccd_mover(class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> void

check_source_segment(self: pyrosetta.rosetta.protocols.splice.SpliceOut) None

C++: protocols::splice::SpliceOut::check_source_segment() –> 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.splice.SpliceInTail) pyrosetta.rosetta.protocols.moves.Mover

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

copy_dofs_from_source(self: pyrosetta.rosetta.protocols.splice.SpliceOut) None

C++: protocols::splice::SpliceOut::copy_dofs_from_source() –> void

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>

cut_secondarystruc(*args, **kwargs)

Overloaded function.

  1. cut_secondarystruc(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: bool) -> None

C++: protocols::splice::SpliceOut::cut_secondarystruc(const bool) –> void

  1. cut_secondarystruc(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::cut_secondarystruc() const –> bool

database_entry(*args, **kwargs)

Overloaded function.

  1. database_entry(self: pyrosetta.rosetta.protocols.splice.SpliceIn) -> int

C++: protocols::splice::SpliceIn::database_entry() const –> unsigned long

  1. database_entry(self: pyrosetta.rosetta.protocols.splice.SpliceIn, d: int) -> None

C++: protocols::splice::SpliceIn::database_entry(const unsigned long) –> void

database_pdb_entry(*args, **kwargs)

Overloaded function.

  1. database_pdb_entry(self: pyrosetta.rosetta.protocols.splice.SpliceIn, s: str) -> None

C++: protocols::splice::SpliceIn::database_pdb_entry(const std::string &) –> void

  1. database_pdb_entry(self: pyrosetta.rosetta.protocols.splice.SpliceIn) -> str

C++: protocols::splice::SpliceIn::database_pdb_entry() const –> std::string

dbase_begin(self: pyrosetta.rosetta.protocols.splice.SpliceInTail) __gnu_cxx::__normal_iterator<unsigned long const*, std::vector<unsigned long, std::allocator<unsigned long> > >

C++: protocols::splice::SpliceInTail::dbase_begin() const –> class __gnu_cxx::__normal_iterator<const unsigned long *, class std::vector<unsigned long, class std::allocator<unsigned long> > >

dbase_end(self: pyrosetta.rosetta.protocols.splice.SpliceInTail) __gnu_cxx::__normal_iterator<unsigned long const*, std::vector<unsigned long, std::allocator<unsigned long> > >

C++: protocols::splice::SpliceInTail::dbase_end() const –> class __gnu_cxx::__normal_iterator<const unsigned long *, class std::vector<unsigned long, class std::allocator<unsigned long> > >

dbase_file_name(*args, **kwargs)

Overloaded function.

  1. dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> str

C++: protocols::splice::SpliceOut::dbase_file_name() const –> std::string

  1. dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceOut, f: str) -> None

C++: protocols::splice::SpliceOut::dbase_file_name(const std::string &) –> void

dbase_iterate(*args, **kwargs)

Overloaded function.

  1. dbase_iterate(self: pyrosetta.rosetta.protocols.splice.SpliceIn) -> bool

C++: protocols::splice::SpliceIn::dbase_iterate() const –> bool

  1. dbase_iterate(self: pyrosetta.rosetta.protocols.splice.SpliceIn, d: bool) -> None

C++: protocols::splice::SpliceIn::dbase_iterate(const bool) –> void

delete_hairpin(*args, **kwargs)

Overloaded function.

  1. delete_hairpin(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

C++: protocols::splice::SpliceOut::delete_hairpin(const bool) –> void

  1. delete_hairpin(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::delete_hairpin() const –> bool

delete_hairpin_c(*args, **kwargs)

Overloaded function.

  1. delete_hairpin_c(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> int

C++: protocols::splice::SpliceOut::delete_hairpin_c() const –> unsigned long

  1. delete_hairpin_c(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::delete_hairpin_c(const unsigned long) –> void

delete_hairpin_n(*args, **kwargs)

Overloaded function.

  1. delete_hairpin_n(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> int

C++: protocols::splice::SpliceOut::delete_hairpin_n() const –> unsigned long

  1. delete_hairpin_n(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::delete_hairpin_n(const unsigned long) –> void

find_dbase_entry(self: pyrosetta.rosetta.protocols.splice.SpliceInTail, pose: pyrosetta.rosetta.core.pose.Pose) int

C++: protocols::splice::SpliceInTail::find_dbase_entry(const class core::pose::Pose &) –> unsigned long

fresh_instance(self: pyrosetta.rosetta.protocols.splice.SpliceInTail) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::splice::SpliceInTail::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.splice.SpliceInTail) str

C++: protocols::splice::SpliceInTail::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

handle_mover_tag(self: pyrosetta.rosetta.protocols.splice.SpliceOut, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::SpliceOut::handle_mover_tag(const class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

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

non-const accessor

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

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

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

load_from_checkpoint(self: pyrosetta.rosetta.protocols.splice.SpliceIn) None

C++: protocols::splice::SpliceIn::load_from_checkpoint() –> void

load_pdb_segments_from_pose_comments(self: pyrosetta.rosetta.protocols.splice.SpliceOut, p: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::load_pdb_segments_from_pose_comments(const class core::pose::Pose &) –> void

min_mover(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::splice::SpliceOut::min_mover(class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> void

min_seg(*args, **kwargs)

Overloaded function.

  1. min_seg(self: pyrosetta.rosetta.protocols.splice.SpliceIn) -> bool

C++: protocols::splice::SpliceIn::min_seg() const –> bool

  1. min_seg(self: pyrosetta.rosetta.protocols.splice.SpliceIn, d: bool) -> None

C++: protocols::splice::SpliceIn::min_seg(const bool) –> void

minimize_segment(self: pyrosetta.rosetta.protocols.splice.SpliceIn, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceIn::minimize_segment(class core::pose::Pose &) –> void

static mover_name() str

C++: protocols::splice::SpliceInTail::mover_name() –> std::string

static name() str

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

name_for_filter(self: pyrosetta.rosetta.protocols.splice.SpliceOut) str

C++: protocols::splice::SpliceOut::name_for_filter() –> std::string

pack(self: pyrosetta.rosetta.protocols.splice.SpliceIn, pose: pyrosetta.rosetta.core.pose.Pose, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::splice::SpliceIn::pack(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

parse_SpliceOut_tags(self: pyrosetta.rosetta.protocols.splice.SpliceOut, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::SpliceOut::parse_SpliceOut_tags(const class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

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

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

place_cut_site_in_segment(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::place_cut_site_in_segment(const class core::pose::Pose &) –> 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::splice::SpliceInTail::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize_cut(*args, **kwargs)

Overloaded function.

  1. randomize_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

C++: protocols::splice::SpliceOut::randomize_cut(const bool) –> void

  1. randomize_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::randomize_cut() –> bool

rb_sensitive(*args, **kwargs)

Overloaded function.

  1. rb_sensitive(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::rb_sensitive() const –> bool

  1. rb_sensitive(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: bool) -> None

C++: protocols::splice::SpliceOut::rb_sensitive(const bool) –> void

read_torsion_database(self: pyrosetta.rosetta.protocols.splice.SpliceIn) None

C++: protocols::splice::SpliceIn::read_torsion_database() –> 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

remove_hairpin(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::remove_hairpin(class core::pose::Pose &) const –> void

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

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

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

rms_cutoff(*args, **kwargs)

Overloaded function.

  1. rms_cutoff(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> float

C++: protocols::splice::SpliceOut::rms_cutoff() const –> double

  1. rms_cutoff(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: float) -> None

C++: protocols::splice::SpliceOut::rms_cutoff(const double) –> void

rms_cutoff_loop(*args, **kwargs)

Overloaded function.

  1. rms_cutoff_loop(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> float

C++: protocols::splice::SpliceOut::rms_cutoff_loop() const –> double

  1. rms_cutoff_loop(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: float) -> None

C++: protocols::splice::SpliceOut::rms_cutoff_loop(const double) –> void

rtmin(self: pyrosetta.rosetta.protocols.splice.SpliceIn, pose: pyrosetta.rosetta.core.pose.Pose, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::splice::SpliceIn::rtmin(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

scorefxn(*args, **kwargs)

Overloaded function.

  1. scorefxn(self: pyrosetta.rosetta.protocols.splice.SpliceIn, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::splice::SpliceIn::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

  1. scorefxn(self: pyrosetta.rosetta.protocols.splice.SpliceIn) -> pyrosetta.rosetta.core.scoring.ScoreFunction

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

set_anchor_res(self: pyrosetta.rosetta.protocols.splice.SpliceInTail) int

C++: protocols::splice::SpliceInTail::set_anchor_res() –> unsigned long

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_fold_tree_nodes(self: pyrosetta.rosetta.protocols.splice.SpliceInTail, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceInTail::set_fold_tree_nodes(const class core::pose::Pose &) –> 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_loop_length_change(self: pyrosetta.rosetta.protocols.splice.SpliceInTail, llc: pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange) None

C++: protocols::splice::SpliceInTail::set_loop_length_change(class protocols::protein_interface_design::movers::LoopLengthChange &) –> 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_source_from_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut) None

C++: protocols::splice::SpliceOut::set_source_from_to_res() –> 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

source_from_res(*args, **kwargs)

Overloaded function.

  1. source_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_from_res(const unsigned long) –> void

  1. source_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> int

C++: protocols::splice::SpliceOut::source_from_res() –> unsigned long

source_pdb(*args, **kwargs)

Overloaded function.

  1. source_pdb(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> str

C++: protocols::splice::SpliceOut::source_pdb() const –> std::string

  1. source_pdb(self: pyrosetta.rosetta.protocols.splice.SpliceOut, s: str) -> None

C++: protocols::splice::SpliceOut::source_pdb(const std::string &) –> void

source_to_res(*args, **kwargs)

Overloaded function.

  1. source_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_to_res(const unsigned long) –> void

  1. source_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> int

C++: protocols::splice::SpliceOut::source_to_res() –> unsigned long

splice_filter(*args, **kwargs)

Overloaded function.

  1. splice_filter(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::splice::SpliceOut::splice_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

  1. splice_filter(self: pyrosetta.rosetta.protocols.splice.SpliceOut, f: pyrosetta.rosetta.protocols.filters.Filter) -> None

C++: protocols::splice::SpliceOut::splice_filter(class std::shared_ptr<class protocols::filters::Filter>) –> void

superimpose_source_on_pose(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose, source_pose: pyrosetta.rosetta.core.pose.Pose) None

add dihedral constraint to grafted loop according to source pdb dihedral angles

C++: protocols::splice::SpliceOut::superimpose_source_on_pose(const class core::pose::Pose &, class core::pose::Pose &) –> void

superimposed(*args, **kwargs)

Overloaded function.

  1. superimposed(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

C++: protocols::splice::SpliceOut::superimposed(const bool) –> void

  1. superimposed(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::superimposed() –> bool

tail_mover(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::splice::SpliceOut::tail_mover(class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> 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

thread_original_sequence(*args, **kwargs)

Overloaded function.

  1. thread_original_sequence(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::thread_original_sequence() const –> bool

  1. thread_original_sequence(self: pyrosetta.rosetta.protocols.splice.SpliceOut, s: bool) -> None

C++: protocols::splice::SpliceOut::thread_original_sequence(const bool) –> 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 &

write_database_to_file(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::write_database_to_file(const class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.splice.SpliceInTailCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.splice.SpliceInTailCreator, : pyrosetta.rosetta.protocols.splice.SpliceInTailCreator) pyrosetta.rosetta.protocols.splice.SpliceInTailCreator

C++: protocols::splice::SpliceInTailCreator::operator=(const class protocols::splice::SpliceInTailCreator &) –> class protocols::splice::SpliceInTailCreator &

create_mover(self: pyrosetta.rosetta.protocols.splice.SpliceInTailCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.splice.SpliceInTailCreator) str

C++: protocols::splice::SpliceInTailCreator::keyname() const –> std::string

static mover_name() str

C++: protocols::splice::SpliceInTailCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.splice.SpliceInTailCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.splice.SpliceManager

Bases: pybind11_builtins.pybind11_object

add_coordinate_constraints(*args, **kwargs)

Overloaded function.

  1. add_coordinate_constraints(self: pyrosetta.rosetta.protocols.splice.SpliceManager, pose: pyrosetta.rosetta.core.pose.Pose, source_pose: pyrosetta.rosetta.core.pose.Pose, nearest_to_from: int, nearest_to_to: int, anchor: int) -> None

  2. add_coordinate_constraints(self: pyrosetta.rosetta.protocols.splice.SpliceManager, pose: pyrosetta.rosetta.core.pose.Pose, source_pose: pyrosetta.rosetta.core.pose.Pose, nearest_to_from: int, nearest_to_to: int, anchor: int, atom_type: str) -> None

  3. add_coordinate_constraints(self: pyrosetta.rosetta.protocols.splice.SpliceManager, pose: pyrosetta.rosetta.core.pose.Pose, source_pose: pyrosetta.rosetta.core.pose.Pose, nearest_to_from: int, nearest_to_to: int, anchor: int, atom_type: str, task: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

C++: protocols::splice::SpliceManager::add_coordinate_constraints(class core::pose::Pose &, const class core::pose::Pose &, unsigned long, unsigned long, unsigned long, std::string, class std::shared_ptr<class core::pack::task::PackerTask>) –> void

add_dihedral_constraints(self: pyrosetta.rosetta.protocols.splice.SpliceManager, pose: pyrosetta.rosetta.core.pose.Pose, source_pose: pyrosetta.rosetta.core.pose.Pose, nearest_to_from: int, nearest_to_to: int) None

C++: protocols::splice::SpliceManager::add_dihedral_constraints(class core::pose::Pose &, const class core::pose::Pose &, unsigned long, unsigned long) –> void

add_sequence_constraints(self: pyrosetta.rosetta.protocols.splice.SpliceManager, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceManager::add_sequence_constraints(class core::pose::Pose &) –> void

add_sequence_constraints_only(*args, **kwargs)

Overloaded function.

  1. add_sequence_constraints_only(self: pyrosetta.rosetta.protocols.splice.SpliceManager, b: bool) -> None

C++: protocols::splice::SpliceManager::add_sequence_constraints_only(const bool) –> void

  1. add_sequence_constraints_only(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> bool

C++: protocols::splice::SpliceManager::add_sequence_constraints_only() –> bool

adjust_stem_positions_by_template(self: pyrosetta.rosetta.protocols.splice.SpliceManager, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceManager::adjust_stem_positions_by_template(const class core::pose::Pose &) –> void

property adjust_stem_positions_by_template_
allowed_cuts(*args, **kwargs)

Overloaded function.

  1. allowed_cuts(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::allowed_cuts() const –> unsigned long

  1. allowed_cuts(self: pyrosetta.rosetta.protocols.splice.SpliceManager, s: int) -> None

C++: protocols::splice::SpliceManager::allowed_cuts(const unsigned long) –> void

anchor_res(*args, **kwargs)

Overloaded function.

  1. anchor_res(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::anchor_res() –> unsigned long

  1. anchor_res(self: pyrosetta.rosetta.protocols.splice.SpliceManager, c: int) -> None

C++: protocols::splice::SpliceManager::anchor_res(const unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.splice.SpliceManager, : pyrosetta.rosetta.protocols.splice.SpliceManager) pyrosetta.rosetta.protocols.splice.SpliceManager

C++: protocols::splice::SpliceManager::operator=(const class protocols::splice::SpliceManager &) –> class protocols::splice::SpliceManager &

chain_num(*args, **kwargs)

Overloaded function.

  1. chain_num(self: pyrosetta.rosetta.protocols.splice.SpliceManager, i: int) -> None

C++: protocols::splice::SpliceManager::chain_num(const unsigned long) –> void

  1. chain_num(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::chain_num() const –> unsigned long

chainbreak_check(self: pyrosetta.rosetta.protocols.splice.SpliceManager, pose: pyrosetta.rosetta.core.pose.Pose, tolerance: float, fail_retry_if_found: bool, crash_if_found: bool) None

C++: protocols::splice::SpliceManager::chainbreak_check(const class core::pose::Pose &, const double, bool, bool) –> void

check_sequence_profile(self: pyrosetta.rosetta.protocols.splice.SpliceManager, pose: pyrosetta.rosetta.core.pose.Pose, smap: pyrosetta.rosetta.core.id.SequenceMapping, seqprof: pyrosetta.rosetta.core.sequence.SequenceProfile) None

C++: protocols::splice::SpliceManager::check_sequence_profile(class core::pose::Pose &, class std::shared_ptr<class core::id::SequenceMapping>, class std::shared_ptr<class core::sequence::SequenceProfile>) –> void

cut_site(*args, **kwargs)

Overloaded function.

  1. cut_site(self: pyrosetta.rosetta.protocols.splice.SpliceManager, c: int) -> None

C++: protocols::splice::SpliceManager::cut_site(const unsigned long) –> void

  1. cut_site(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::cut_site() –> unsigned long

dbase_file_name(*args, **kwargs)

Overloaded function.

  1. dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceManager, s: str) -> None

C++: protocols::splice::SpliceManager::dbase_file_name(const std::string &) –> void

  1. dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> str

C++: protocols::splice::SpliceManager::dbase_file_name() const –> std::string

debug(*args, **kwargs)

Overloaded function.

  1. debug(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> bool

C++: protocols::splice::SpliceManager::debug() const –> bool

  1. debug(self: pyrosetta.rosetta.protocols.splice.SpliceManager, s: bool) -> None

C++: protocols::splice::SpliceManager::debug(const bool) –> void

design_shell(*args, **kwargs)

Overloaded function.

  1. design_shell(self: pyrosetta.rosetta.protocols.splice.SpliceManager, c: float) -> None

C++: protocols::splice::SpliceManager::design_shell(const double) –> void

  1. design_shell(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> float

C++: protocols::splice::SpliceManager::design_shell() const –> double

dofs(*args, **kwargs)

Overloaded function.

  1. dofs(self: pyrosetta.rosetta.protocols.splice.SpliceManager, d: pyrosetta.rosetta.protocols.splice.ResidueBBDofs) -> None

C++: protocols::splice::SpliceManager::dofs(const class protocols::splice::ResidueBBDofs &) –> void

  1. dofs(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> pyrosetta.rosetta.protocols.splice.ResidueBBDofs

C++: protocols::splice::SpliceManager::dofs() –> class protocols::splice::ResidueBBDofs &

fold_tree(self: pyrosetta.rosetta.protocols.splice.SpliceManager, pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_std_array_int_3_t) None

C++: protocols::splice::SpliceManager::fold_tree(class core::pose::Pose &, class utility::vector1<struct std::array<int, 3>, class std::allocator<struct std::array<int, 3> > >) const –> void

generate_profile_from_seq(self: pyrosetta.rosetta.protocols.splice.SpliceManager, segment_seq_map: pyrosetta.rosetta.std.map_std_string_std_string, segmentName: str, sourcename: str, SpliceSegment: protocols::splice::SpliceSegment) None

C++: protocols::splice::SpliceManager::generate_profile_from_seq(class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >, std::string, std::string, class std::shared_ptr<class protocols::splice::SpliceSegment>) –> void

generate_sequence_profile(self: pyrosetta.rosetta.protocols.splice.SpliceManager, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.sequence.SequenceProfile

C++: protocols::splice::SpliceManager::generate_sequence_profile(class core::pose::Pose &) –> class std::shared_ptr<class core::sequence::SequenceProfile>

mm(*args, **kwargs)

Overloaded function.

  1. mm(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::splice::SpliceManager::mm() –> class std::shared_ptr<class core::kinematics::MoveMap>

  1. mm(self: pyrosetta.rosetta.protocols.splice.SpliceManager, m: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::splice::SpliceManager::mm(const class std::shared_ptr<class core::kinematics::MoveMap>) –> void

modify_pdb_segments_with_current_segment(self: pyrosetta.rosetta.protocols.splice.SpliceManager, pdb_name: str) None

C++: protocols::splice::SpliceManager::modify_pdb_segments_with_current_segment(const std::string &) –> void

mover_name(*args, **kwargs)

Overloaded function.

  1. mover_name(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> str

C++: protocols::splice::SpliceManager::mover_name() const –> std::string

  1. mover_name(self: pyrosetta.rosetta.protocols.splice.SpliceManager, s: str) -> None

C++: protocols::splice::SpliceManager::mover_name(const std::string &) –> void

parse_segments(self: pyrosetta.rosetta.protocols.splice.SpliceManager, sub_tags: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_utility_tag_Tag_t, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::SpliceManager::parse_segments(const class utility::vector1<class std::shared_ptr<const class utility::tag::Tag>, class std::allocator<class std::shared_ptr<const class utility::tag::Tag> > > &, const class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_tags(self: pyrosetta.rosetta.protocols.splice.SpliceManager, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::SpliceManager::parse_tags(const class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pdb_segments(*args, **kwargs)

Overloaded function.

  1. pdb_segments(self: pyrosetta.rosetta.protocols.splice.SpliceManager, m: pyrosetta.rosetta.std.map_std_string_std_string) -> None

C++: protocols::splice::SpliceManager::pdb_segments(const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &) –> void

  1. pdb_segments(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> pyrosetta.rosetta.std.map_std_string_std_string

C++: protocols::splice::SpliceManager::pdb_segments() –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

pose_from_res(*args, **kwargs)

Overloaded function.

  1. pose_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::pose_from_res() –> unsigned long

  1. pose_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceManager, i: int) -> None

C++: protocols::splice::SpliceManager::pose_from_res(const unsigned long) –> void

pose_to_res(*args, **kwargs)

Overloaded function.

  1. pose_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::pose_to_res() –> unsigned long

  1. pose_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceManager, i: int) -> None

C++: protocols::splice::SpliceManager::pose_to_res(const unsigned long) –> void

profile_weight_away_from_interface(*args, **kwargs)

Overloaded function.

  1. profile_weight_away_from_interface(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> float

C++: protocols::splice::SpliceManager::profile_weight_away_from_interface() const –> double

  1. profile_weight_away_from_interface(self: pyrosetta.rosetta.protocols.splice.SpliceManager, p: float) -> None

C++: protocols::splice::SpliceManager::profile_weight_away_from_interface(const double) –> void

rb_adjust_template(self: pyrosetta.rosetta.protocols.splice.SpliceManager, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceManager::rb_adjust_template(const class core::pose::Pose &) const –> void

rb_sensitive(*args, **kwargs)

Overloaded function.

  1. rb_sensitive(self: pyrosetta.rosetta.protocols.splice.SpliceManager, b: bool) -> None

C++: protocols::splice::SpliceManager::rb_sensitive(const bool) –> void

  1. rb_sensitive(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> bool

C++: protocols::splice::SpliceManager::rb_sensitive() const –> bool

repack_shell(*args, **kwargs)

Overloaded function.

  1. repack_shell(self: pyrosetta.rosetta.protocols.splice.SpliceManager, c: float) -> None

C++: protocols::splice::SpliceManager::repack_shell(const double) –> void

  1. repack_shell(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> float

C++: protocols::splice::SpliceManager::repack_shell() const –> double

residue_diff(*args, **kwargs)

Overloaded function.

  1. residue_diff(self: pyrosetta.rosetta.protocols.splice.SpliceManager, c: int) -> None

C++: protocols::splice::SpliceManager::residue_diff(const unsigned long) –> void

  1. residue_diff(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::residue_diff() –> int

scorefxn(*args, **kwargs)

Overloaded function.

  1. scorefxn(self: pyrosetta.rosetta.protocols.splice.SpliceManager, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::splice::SpliceManager::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

  1. scorefxn(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> pyrosetta.rosetta.core.scoring.ScoreFunction

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

segment_names_ordered(*args, **kwargs)

Overloaded function.

  1. segment_names_ordered(self: pyrosetta.rosetta.protocols.splice.SpliceManager, SegNameOrder: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: protocols::splice::SpliceManager::segment_names_ordered(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

  1. segment_names_ordered(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::splice::SpliceManager::segment_names_ordered() –> class utility::vector1<std::string, class std::allocator<std::string > > &

segment_type(*args, **kwargs)

Overloaded function.

  1. segment_type(self: pyrosetta.rosetta.protocols.splice.SpliceManager, s: str) -> None

C++: protocols::splice::SpliceManager::segment_type(const std::string &) –> void

  1. segment_type(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> str

C++: protocols::splice::SpliceManager::segment_type() –> std::string

set_BB_dofs(self: pyrosetta.rosetta.protocols.splice.SpliceManager, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceManager::set_BB_dofs(class core::pose::Pose &) –> void

source_pdb_name(*args, **kwargs)

Overloaded function.

  1. source_pdb_name(self: pyrosetta.rosetta.protocols.splice.SpliceManager, s: str) -> None

C++: protocols::splice::SpliceManager::source_pdb_name(const std::string &) –> void

  1. source_pdb_name(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> str

C++: protocols::splice::SpliceManager::source_pdb_name() –> std::string

splice_segments(*args, **kwargs)

Overloaded function.

  1. splice_segments(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_splice_SpliceSegment_t

C++: protocols::splice::SpliceManager::splice_segments() –> class std::map<std::string, class std::shared_ptr<class protocols::splice::SpliceSegment>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<class protocols::splice::SpliceSegment> > > > &

  1. splice_segments(self: pyrosetta.rosetta.protocols.splice.SpliceManager, m: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_splice_SpliceSegment_t) -> None

C++: protocols::splice::SpliceManager::splice_segments(const class std::map<std::string, class std::shared_ptr<class protocols::splice::SpliceSegment>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<class protocols::splice::SpliceSegment> > > > &) –> void

tail_seg(*args, **kwargs)

Overloaded function.

  1. tail_seg(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> str

C++: protocols::splice::SpliceManager::tail_seg() –> std::string

  1. tail_seg(self: pyrosetta.rosetta.protocols.splice.SpliceManager, s: str) -> None

C++: protocols::splice::SpliceManager::tail_seg(const std::string &) –> void

task_factory(*args, **kwargs)

Overloaded function.

  1. task_factory(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::splice::SpliceManager::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

  1. task_factory(self: pyrosetta.rosetta.protocols.splice.SpliceManager, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::splice::SpliceManager::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

template_file(*args, **kwargs)

Overloaded function.

  1. template_file(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> str

C++: protocols::splice::SpliceManager::template_file() const –> std::string

  1. template_file(self: pyrosetta.rosetta.protocols.splice.SpliceManager, s: str) -> None

C++: protocols::splice::SpliceManager::template_file(const std::string &) –> void

template_from_res(*args, **kwargs)

Overloaded function.

  1. template_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::template_from_res() –> unsigned long

  1. template_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceManager, i: int) -> None

C++: protocols::splice::SpliceManager::template_from_res(const unsigned long) –> void

template_pose(*args, **kwargs)

Overloaded function.

  1. template_pose(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::splice::SpliceManager::template_pose() –> class std::shared_ptr<class core::pose::Pose>

  1. template_pose(self: pyrosetta.rosetta.protocols.splice.SpliceManager, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::splice::SpliceManager::template_pose(const class std::shared_ptr<class core::pose::Pose>) –> void

template_to_res(*args, **kwargs)

Overloaded function.

  1. template_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::template_to_res() –> unsigned long

  1. template_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceManager, i: int) -> None

C++: protocols::splice::SpliceManager::template_to_res(const unsigned long) –> void

thread_original_sequence(*args, **kwargs)

Overloaded function.

  1. thread_original_sequence(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> bool

C++: protocols::splice::SpliceManager::thread_original_sequence() const –> bool

  1. thread_original_sequence(self: pyrosetta.rosetta.protocols.splice.SpliceManager, s: bool) -> None

C++: protocols::splice::SpliceManager::thread_original_sequence(const bool) –> void

update_pose_stem_positions(self: pyrosetta.rosetta.protocols.splice.SpliceManager) None

C++: protocols::splice::SpliceManager::update_pose_stem_positions() –> void

use_sequence_profiles(*args, **kwargs)

Overloaded function.

  1. use_sequence_profiles(self: pyrosetta.rosetta.protocols.splice.SpliceManager, b: bool) -> None

C++: protocols::splice::SpliceManager::use_sequence_profiles(const bool) –> void

  1. use_sequence_profiles(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::use_sequence_profiles() –> unsigned long

class pyrosetta.rosetta.protocols.splice.SpliceOut

Bases: pyrosetta.rosetta.protocols.moves.Mover

SpliceOutFilter(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) int

C++: protocols::splice::SpliceOut::SpliceOutFilter(class core::pose::Pose *) –> int

SpliceOutRMSDFilter(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) int

C++: protocols::splice::SpliceOut::SpliceOutRMSDFilter(class core::pose::Pose *) –> int

abstract_parse_tag(self: pyrosetta.rosetta.protocols.splice.SpliceOut, tag: pyrosetta.rosetta.utility.tag.Tag) None

C++: protocols::splice::SpliceOut::abstract_parse_tag(const class std::shared_ptr<const class utility::tag::Tag>) –> void

apply(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.splice.SpliceOut, : pyrosetta.rosetta.protocols.splice.SpliceOut) pyrosetta.rosetta.protocols.splice.SpliceOut

C++: protocols::splice::SpliceOut::operator=(const class protocols::splice::SpliceOut &) –> class protocols::splice::SpliceOut &

build_ideal_segment(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::build_ideal_segment(class core::pose::Pose &) –> void

ccd_mover(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::splice::SpliceOut::ccd_mover(class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> void

check_source_segment(self: pyrosetta.rosetta.protocols.splice.SpliceOut) None

C++: protocols::splice::SpliceOut::check_source_segment() –> 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.splice.SpliceOut) pyrosetta.rosetta.protocols.moves.Mover

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

copy_dofs_from_source(self: pyrosetta.rosetta.protocols.splice.SpliceOut) None

C++: protocols::splice::SpliceOut::copy_dofs_from_source() –> void

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>

cut_secondarystruc(*args, **kwargs)

Overloaded function.

  1. cut_secondarystruc(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: bool) -> None

C++: protocols::splice::SpliceOut::cut_secondarystruc(const bool) –> void

  1. cut_secondarystruc(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::cut_secondarystruc() const –> bool

dbase_file_name(*args, **kwargs)

Overloaded function.

  1. dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> str

C++: protocols::splice::SpliceOut::dbase_file_name() const –> std::string

  1. dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceOut, f: str) -> None

C++: protocols::splice::SpliceOut::dbase_file_name(const std::string &) –> void

delete_hairpin(*args, **kwargs)

Overloaded function.

  1. delete_hairpin(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

C++: protocols::splice::SpliceOut::delete_hairpin(const bool) –> void

  1. delete_hairpin(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::delete_hairpin() const –> bool

delete_hairpin_c(*args, **kwargs)

Overloaded function.

  1. delete_hairpin_c(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> int

C++: protocols::splice::SpliceOut::delete_hairpin_c() const –> unsigned long

  1. delete_hairpin_c(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::delete_hairpin_c(const unsigned long) –> void

delete_hairpin_n(*args, **kwargs)

Overloaded function.

  1. delete_hairpin_n(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> int

C++: protocols::splice::SpliceOut::delete_hairpin_n() const –> unsigned long

  1. delete_hairpin_n(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::delete_hairpin_n(const unsigned long) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.splice.SpliceOut) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::splice::SpliceOut::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.splice.SpliceOut) str

C++: protocols::splice::SpliceOut::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

handle_mover_tag(self: pyrosetta.rosetta.protocols.splice.SpliceOut, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::SpliceOut::handle_mover_tag(const class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

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

non-const accessor

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

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

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

load_pdb_segments_from_pose_comments(self: pyrosetta.rosetta.protocols.splice.SpliceOut, p: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::load_pdb_segments_from_pose_comments(const class core::pose::Pose &) –> void

min_mover(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::splice::SpliceOut::min_mover(class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> void

minimize_segment(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::minimize_segment(class core::pose::Pose &) –> void

static mover_name() str

C++: protocols::splice::SpliceOut::mover_name() –> std::string

static name() str

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

name_for_filter(self: pyrosetta.rosetta.protocols.splice.SpliceOut) str

C++: protocols::splice::SpliceOut::name_for_filter() –> std::string

parse_SpliceOut_tags(self: pyrosetta.rosetta.protocols.splice.SpliceOut, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::splice::SpliceOut::parse_SpliceOut_tags(const class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

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

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

place_cut_site_in_segment(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::place_cut_site_in_segment(const class core::pose::Pose &) –> 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::splice::SpliceOut::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize_cut(*args, **kwargs)

Overloaded function.

  1. randomize_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

C++: protocols::splice::SpliceOut::randomize_cut(const bool) –> void

  1. randomize_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::randomize_cut() –> bool

rb_sensitive(*args, **kwargs)

Overloaded function.

  1. rb_sensitive(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> bool

C++: protocols::splice::SpliceOut::rb_sensitive() const –> bool

  1. rb_sensitive(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: bool) -> None

C++: protocols::splice::SpliceOut::rb_sensitive(const 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

remove_hairpin(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::remove_hairpin(class core::pose::Pose &) const –> void

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

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

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

rms_cutoff(*args, **kwargs)

Overloaded function.

  1. rms_cutoff(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> float

C++: protocols::splice::SpliceOut::rms_cutoff() const –> double

  1. rms_cutoff(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: float) -> None

C++: protocols::splice::SpliceOut::rms_cutoff(const double) –> void

rms_cutoff_loop(*args, **kwargs)

Overloaded function.

  1. rms_cutoff_loop(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> float

C++: protocols::splice::SpliceOut::rms_cutoff_loop() const –> double

  1. rms_cutoff_loop(self: pyrosetta.rosetta.protocols.splice.SpliceOut, r: float) -> None

C++: protocols::splice::SpliceOut::rms_cutoff_loop(const double) –> void

scorefxn(*args, **kwargs)

Overloaded function.

  1. scorefxn(self: pyrosetta.rosetta.protocols.splice.SpliceOut, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::splice::SpliceOut::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

  1. scorefxn(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> pyrosetta.rosetta.core.scoring.ScoreFunction

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

set_anchor_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut) int

C++: protocols::splice::SpliceOut::set_anchor_res() –> unsigned long

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_fold_tree_nodes(self: pyrosetta.rosetta.protocols.splice.SpliceOut, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::splice::SpliceOut::set_fold_tree_nodes(const class core::pose::Pose &) –> 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_loop_length_change(self: pyrosetta.rosetta.protocols.splice.SpliceOut, llc: pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange) None

C++: protocols::splice::SpliceOut::set_loop_length_change(class protocols::protein_interface_design::movers::LoopLengthChange &) –> 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_source_from_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut) None

C++: protocols::splice::SpliceOut::set_source_from_to_res() –> 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