splice¶

Bindings for protocols::splice namespace

class pyrosetta.rosetta.protocols.splice.AlignEndsMover¶

Bases: Mover

N_terminal_count(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

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

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.

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

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

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_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.

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

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

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.

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

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

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

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

odd(*args, **kwargs)¶

Overloaded function.

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

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

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

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

parallel(*args, **kwargs)¶

Overloaded function.

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

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

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: pyrosetta.rosetta.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.

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

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

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.

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

Outputs details about the Mover, including current settings.

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

stagger(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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>

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.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.splice.AlignEndsMoverCreator¶

Bases: 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: pyrosetta.rosetta.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_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.

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

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

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

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

phi(*args, **kwargs)¶

Overloaded function.

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

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

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

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

psi(*args, **kwargs)¶

Overloaded function.

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

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

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

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

resid(*args, **kwargs)¶

Overloaded function.

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

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

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

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

resn(*args, **kwargs)¶

Overloaded function.

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

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

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_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_t_std_allocator_std_pair_const_std_string_std_vector_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_t_std_allocator_std_pair_const_std_string_std_vector_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: 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.

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

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

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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::DesignInterfacesOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

repack_shell(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

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

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: 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::DesignInterfacesOperationCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool¶

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.protocols.splice.FindEndpointsOperation¶

Bases: RestrictOperationsBase

Find the endpoints on a beta barrel

Cterm_offset(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

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

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.

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

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

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.

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

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

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

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

odd(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::FindEndpointsOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

sequence_separation(*args, **kwargs)¶

Overloaded function.

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

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

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: 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::FindEndpointsOperationCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool¶

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.protocols.splice.RBInMover¶

Bases: Mover

RBDatabase_fname(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

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

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.

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

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

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.

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

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

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_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.

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> > >

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.

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

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

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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::RBInMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

Outputs details about the Mover, including current settings.

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

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

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

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

to_entry(*args, **kwargs)¶

Overloaded function.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.splice.RBInMoverCreator¶

Bases: 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::RBInMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.splice.RBOutMover¶

Bases: 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.

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

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

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_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.

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

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

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.

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

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

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: pyrosetta.rosetta.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.

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

Outputs details about the Mover, including current settings.

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

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.

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

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

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.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.splice.RBOutMoverCreator¶

Bases: 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: pyrosetta.rosetta.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_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_object

aa_sequence(*args, **kwargs)¶

Overloaded function.

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

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

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> >

clear(self: pyrosetta.rosetta.protocols.splice.ResidueBBDofs) → None¶: C++: protocols::splice::ResidueBBDofs::clear() –> void

cut_site(*args, **kwargs)¶

Overloaded function.

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

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

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

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

disulfide(*args, **kwargs)¶

Overloaded function.

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

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

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

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

dssp(*args, **kwargs)¶

Overloaded function.

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

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

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

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

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.

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

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

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.

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

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

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.

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

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

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.

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

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

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: Mover

Rotamer_db_file(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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_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.

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

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

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: pyrosetta.rosetta.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.

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

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

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.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.splice.RotLibOutCreator¶

Bases: 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: pyrosetta.rosetta.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_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: TaskOperation

SampleAtAlignedpositions(*args, **kwargs)¶

Overloaded function.

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> >

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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::SampleRotamersFromPDB::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDBCreator¶

Bases: 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::SampleRotamersFromPDBCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool¶

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation¶

Bases: 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: 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.

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
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
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.

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

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

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.

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

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

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.

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

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

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

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

chain_num(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

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

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

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

database_entry(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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

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

dbase_iterate(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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

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

delete_hairpin_c(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

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.

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

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

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

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

design_shell(*args, **kwargs)¶

Overloaded function.

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

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

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

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

design_task_factory(*args, **kwargs)¶

Overloaded function.

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>

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.

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

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

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.

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

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

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_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.

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

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

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.

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

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

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.

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

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

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.

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

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

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.

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

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

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.

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

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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::Splice::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize_cut(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

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

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

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

res_move(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

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

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.

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

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

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.

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

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

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.

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

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.

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

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

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.

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

Outputs details about the Mover, including current settings.

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

skip_alignment(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

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

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.

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

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

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.

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>

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.

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

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

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.

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>

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.

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

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

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.

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

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

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.

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

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

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.

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> >

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.

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

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

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.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.splice.SpliceCreator¶

Bases: 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::SpliceCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.splice.SpliceIn¶

Bases: 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.

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

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

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

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

database_entry(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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

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

dbase_file_name(*args, **kwargs)¶

Overloaded function.

dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> str

C++: protocols::splice::SpliceOut::dbase_file_name() const –> std::string

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.

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

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

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.

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

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

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

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

delete_hairpin_c(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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_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.

min_seg(self: pyrosetta.rosetta.protocols.splice.SpliceIn) -> bool

C++: protocols::splice::SpliceIn::min_seg() const –> bool

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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::SpliceIn::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize_cut(*args, **kwargs)¶

Overloaded function.

randomize_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

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

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

C++: protocols::splice::SpliceOut::randomize_cut() –> bool

rb_sensitive(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

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

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.

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

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.

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

Outputs details about the Mover, including current settings.

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

source_from_res(*args, **kwargs)¶

Overloaded function.

source_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_from_res(const unsigned long) –> void

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.

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

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

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.

source_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_to_res(const unsigned long) –> void

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.

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>

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.

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

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

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.

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

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

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.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

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: 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.

antibody_DB(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody, s: str) -> None

C++: protocols::splice::SpliceInAntibody::antibody_DB(const std::string &) –> void

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.

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

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

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

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

database_entry(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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

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

dbase_file_name(*args, **kwargs)¶

Overloaded function.

dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> str

C++: protocols::splice::SpliceOut::dbase_file_name() const –> std::string

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.

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

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

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.

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

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

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

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

delete_hairpin_c(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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_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.

min_seg(self: pyrosetta.rosetta.protocols.splice.SpliceInAntibody) -> bool

C++: protocols::splice::SpliceInAntibody::min_seg() const –> bool

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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::SpliceInAntibody::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize_cut(*args, **kwargs)¶

Overloaded function.

randomize_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

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

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

C++: protocols::splice::SpliceOut::randomize_cut() –> bool

rb_sensitive(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

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

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.

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

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.

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

Outputs details about the Mover, including current settings.

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

source_from_res(*args, **kwargs)¶

Overloaded function.

source_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_from_res(const unsigned long) –> void

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.

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

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

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.

source_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_to_res(const unsigned long) –> void

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.

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>

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.

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

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

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.

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

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

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.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

update_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: 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::SpliceInAntibodyCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.splice.SpliceInCreator¶

Bases: 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::SpliceInCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.splice.SpliceInTail¶

Bases: 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.

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

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

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

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

database_entry(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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

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

dbase_file_name(*args, **kwargs)¶

Overloaded function.

dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> str

C++: protocols::splice::SpliceOut::dbase_file_name() const –> std::string

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.

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

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

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.

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

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

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

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

delete_hairpin_c(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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_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.

min_seg(self: pyrosetta.rosetta.protocols.splice.SpliceIn) -> bool

C++: protocols::splice::SpliceIn::min_seg() const –> bool

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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::SpliceInTail::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize_cut(*args, **kwargs)¶

Overloaded function.

randomize_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

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

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

C++: protocols::splice::SpliceOut::randomize_cut() –> bool

rb_sensitive(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

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

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.

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

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.

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

Outputs details about the Mover, including current settings.

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

source_from_res(*args, **kwargs)¶

Overloaded function.

source_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_from_res(const unsigned long) –> void

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.

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

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

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.

source_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_to_res(const unsigned long) –> void

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.

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>

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.

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

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

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.

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

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

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.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

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: 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: pyrosetta.rosetta.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_object

add_coordinate_constraints(*args, **kwargs)¶

Overloaded function.

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
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
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.

add_sequence_constraints_only(self: pyrosetta.rosetta.protocols.splice.SpliceManager, b: bool) -> None

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

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.

allowed_cuts(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::allowed_cuts() const –> unsigned long

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.

anchor_res(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::anchor_res() –> unsigned long

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.

chain_num(self: pyrosetta.rosetta.protocols.splice.SpliceManager, i: int) -> None

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

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.

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

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

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

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

dbase_file_name(*args, **kwargs)¶

Overloaded function.

dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceManager, s: str) -> None

C++: protocols::splice::SpliceManager::dbase_file_name(const std::string &) –> void

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.

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

C++: protocols::splice::SpliceManager::debug() const –> bool

debug(self: pyrosetta.rosetta.protocols.splice.SpliceManager, s: bool) -> None

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

design_shell(*args, **kwargs)¶

Overloaded function.

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

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

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

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

dofs(*args, **kwargs)¶

Overloaded function.

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

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.

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>

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.

mover_name(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> str

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

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.

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

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.

pose_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::pose_from_res() –> unsigned long

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.

pose_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::pose_to_res() –> unsigned long

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.

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

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

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.

rb_sensitive(self: pyrosetta.rosetta.protocols.splice.SpliceManager, b: bool) -> None

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

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

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

repack_shell(*args, **kwargs)¶

Overloaded function.

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

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

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

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

residue_diff(*args, **kwargs)¶

Overloaded function.

residue_diff(self: pyrosetta.rosetta.protocols.splice.SpliceManager, c: int) -> None

C++: protocols::splice::SpliceManager::residue_diff(const unsigned long) –> void

residue_diff(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::residue_diff() –> int

scorefxn(*args, **kwargs)¶

Overloaded function.

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

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.

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

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.

segment_type(self: pyrosetta.rosetta.protocols.splice.SpliceManager, s: str) -> None

C++: protocols::splice::SpliceManager::segment_type(const std::string &) –> void

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.

source_pdb_name(self: pyrosetta.rosetta.protocols.splice.SpliceManager, s: str) -> None

C++: protocols::splice::SpliceManager::source_pdb_name(const std::string &) –> void

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.

splice_segments(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_splice_SpliceSegment_t_std_allocator_std_pair_const_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> > > > &

splice_segments(self: pyrosetta.rosetta.protocols.splice.SpliceManager, m: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_splice_SpliceSegment_t_std_allocator_std_pair_const_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.

tail_seg(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> str

C++: protocols::splice::SpliceManager::tail_seg() –> std::string

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.

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>

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.

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

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

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.

template_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::template_from_res() –> unsigned long

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.

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>

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.

template_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceManager) -> int

C++: protocols::splice::SpliceManager::template_to_res() –> unsigned long

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.

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

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

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.

use_sequence_profiles(self: pyrosetta.rosetta.protocols.splice.SpliceManager, b: bool) -> None

C++: protocols::splice::SpliceManager::use_sequence_profiles(const bool) –> void

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: 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.

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

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

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

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

dbase_file_name(*args, **kwargs)¶

Overloaded function.

dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> str

C++: protocols::splice::SpliceOut::dbase_file_name() const –> std::string

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.

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

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

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

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

delete_hairpin_c(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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_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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::SpliceOut::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize_cut(*args, **kwargs)¶

Overloaded function.

randomize_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

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

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

C++: protocols::splice::SpliceOut::randomize_cut() –> bool

rb_sensitive(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

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

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.

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

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.

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

Outputs details about the Mover, including current settings.

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

source_from_res(*args, **kwargs)¶

Overloaded function.

source_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_from_res(const unsigned long) –> void

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.

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

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

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.

source_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_to_res(const unsigned long) –> void

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.

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>

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.

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

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

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.

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

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

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.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

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.SpliceOutAntibody¶

Bases: SpliceOutTail

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.SpliceOutTail, tag: pyrosetta.rosetta.utility.tag.Tag) → None¶: C++: protocols::splice::SpliceOutTail::abstract_parse_tag(const class std::shared_ptr<const class utility::tag::Tag>) –> void

adjust_n_ter_tail_length(self: pyrosetta.rosetta.protocols.splice.SpliceOutAntibody, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::SpliceOutAntibody::adjust_n_ter_tail_length(class core::pose::Pose &) –> void

antibody_DB(*args, **kwargs)¶

Overloaded function.

antibody_DB(self: pyrosetta.rosetta.protocols.splice.SpliceOutAntibody, s: str) -> None

C++: protocols::splice::SpliceOutAntibody::antibody_DB(const std::string &) –> void

antibody_DB(self: pyrosetta.rosetta.protocols.splice.SpliceOutAntibody) -> str

C++: protocols::splice::SpliceOutAntibody::antibody_DB() –> std::string

apply(self: pyrosetta.rosetta.protocols.splice.SpliceOutAntibody, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::SpliceOutAntibody::apply(class core::pose::Pose &) –> void

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

assign_from_res_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOutAntibody, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::SpliceOutAntibody::assign_from_res_to_res(const class core::pose::Pose &) –> void

build_ideal_segment(self: pyrosetta.rosetta.protocols.splice.SpliceOutAntibody, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::SpliceOutAntibody::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.SpliceOutAntibody) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::splice::SpliceOutAntibody::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.

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

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

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

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

dbase_file_name(*args, **kwargs)¶

Overloaded function.

dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> str

C++: protocols::splice::SpliceOut::dbase_file_name() const –> std::string

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.

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

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

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

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

delete_hairpin_c(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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

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

find_disulfide_postions(self: pyrosetta.rosetta.protocols.splice.SpliceOutAntibody, pose: pyrosetta.rosetta.core.pose.Pose, cys_pos: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::splice::SpliceOutAntibody::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.SpliceOutAntibody, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::SpliceOutAntibody::find_vl_vh_cut(class core::pose::Pose) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.splice.SpliceOutAntibody) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::splice::SpliceOutAntibody::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.SpliceOutAntibody) → str¶: C++: protocols::splice::SpliceOutAntibody::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

handle_tail_mover_tag(self: pyrosetta.rosetta.protocols.splice.SpliceOutAntibody, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::splice::SpliceOutAntibody::handle_tail_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_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::SpliceOutAntibody::mover_name() –> std::string

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

name_for_filter(self: pyrosetta.rosetta.protocols.splice.SpliceOutAntibody) → str¶: C++: protocols::splice::SpliceOutAntibody::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.SpliceOutAntibody, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::splice::SpliceOutAntibody::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.SpliceOutAntibody, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::SpliceOutAntibody::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::SpliceOutAntibody::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize_cut(*args, **kwargs)¶

Overloaded function.

randomize_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

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

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

C++: protocols::splice::SpliceOut::randomize_cut() –> bool

rb_sensitive(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

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

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.

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

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.SpliceOutAntibody) → int¶: C++: protocols::splice::SpliceOutAntibody::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.SpliceOutAntibody, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::SpliceOutAntibody::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.SpliceOutAntibody, llc: pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange) → None¶: C++: protocols::splice::SpliceOutAntibody::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.SpliceOutAntibody) → None¶: C++: protocols::splice::SpliceOutAntibody::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.

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

Outputs details about the Mover, including current settings.

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

source_from_res(*args, **kwargs)¶

Overloaded function.

source_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_from_res(const unsigned long) –> void

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.

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

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

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.

source_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_to_res(const unsigned long) –> void

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.

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>

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.SpliceOutAntibody, pose: pyrosetta.rosetta.core.pose.Pose, source_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::SpliceOutAntibody::superimpose_source_on_pose(const class core::pose::Pose &, class core::pose::Pose &) –> void

superimposed(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

update_vl_vh_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOutAntibody) → None¶: C++: protocols::splice::SpliceOutAntibody::update_vl_vh_cut() –> void

vl_vh_cut(*args, **kwargs)¶

Overloaded function.

vl_vh_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOutAntibody, i: int) -> None

C++: protocols::splice::SpliceOutAntibody::vl_vh_cut(unsigned long) –> void

vl_vh_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOutAntibody) -> int

C++: protocols::splice::SpliceOutAntibody::vl_vh_cut() –> unsigned long

write_database_to_file(self: pyrosetta.rosetta.protocols.splice.SpliceOutAntibody, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::SpliceOutAntibody::write_database_to_file(const class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.splice.SpliceOutAntibodyCreator¶

Bases: MoverCreator

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

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

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

static mover_name() → str¶: C++: protocols::splice::SpliceOutAntibodyCreator::mover_name() –> std::string

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

class pyrosetta.rosetta.protocols.splice.SpliceOutCreator¶

Bases: MoverCreator

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

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

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

static mover_name() → str¶: C++: protocols::splice::SpliceOutCreator::mover_name() –> std::string

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

class pyrosetta.rosetta.protocols.splice.SpliceOutTail¶

Bases: 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.SpliceOutTail, tag: pyrosetta.rosetta.utility.tag.Tag) → None¶: C++: protocols::splice::SpliceOutTail::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.SpliceOutTail, : pyrosetta.rosetta.protocols.splice.SpliceOutTail) → pyrosetta.rosetta.protocols.splice.SpliceOutTail¶: C++: protocols::splice::SpliceOutTail::operator=(const class protocols::splice::SpliceOutTail &) –> class protocols::splice::SpliceOutTail &

build_ideal_segment(self: pyrosetta.rosetta.protocols.splice.SpliceOutTail, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::SpliceOutTail::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.SpliceOutTail) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::splice::SpliceOutTail::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.

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

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

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

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

dbase_file_name(*args, **kwargs)¶

Overloaded function.

dbase_file_name(self: pyrosetta.rosetta.protocols.splice.SpliceOut) -> str

C++: protocols::splice::SpliceOut::dbase_file_name() const –> std::string

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.

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

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

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

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

delete_hairpin_c(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.SpliceOutTail) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::splice::SpliceOutTail::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.SpliceOutTail) → str¶: C++: protocols::splice::SpliceOutTail::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_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::SpliceOutTail::mover_name() –> std::string

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

name_for_filter(self: pyrosetta.rosetta.protocols.splice.SpliceOutTail) → str¶: C++: protocols::splice::SpliceOutTail::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.SpliceOutTail, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::SpliceOutTail::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::SpliceOutTail::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize_cut(*args, **kwargs)¶

Overloaded function.

randomize_cut(self: pyrosetta.rosetta.protocols.splice.SpliceOut, b: bool) -> None

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

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

C++: protocols::splice::SpliceOut::randomize_cut() –> bool

rb_sensitive(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

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

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.

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

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.SpliceOutTail) → int¶: C++: protocols::splice::SpliceOutTail::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.SpliceOutTail, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::SpliceOutTail::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.SpliceOutTail, llc: pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange) → None¶: C++: protocols::splice::SpliceOutTail::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.SpliceOutTail) → None¶: C++: protocols::splice::SpliceOutTail::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.

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

Outputs details about the Mover, including current settings.

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

source_from_res(*args, **kwargs)¶

Overloaded function.

source_from_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_from_res(const unsigned long) –> void

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.

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

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

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.

source_to_res(self: pyrosetta.rosetta.protocols.splice.SpliceOut, c: int) -> None

C++: protocols::splice::SpliceOut::source_to_res(const unsigned long) –> void

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.

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>

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.SpliceOutTail, pose: pyrosetta.rosetta.core.pose.Pose, source_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::SpliceOutTail::superimpose_source_on_pose(const class core::pose::Pose &, class core::pose::Pose &) –> void

superimposed(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

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.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

write_database_to_file(self: pyrosetta.rosetta.protocols.splice.SpliceOutTail, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::SpliceOutTail::write_database_to_file(const class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.splice.SpliceOutTailCreator¶

Bases: MoverCreator

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

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

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

static mover_name() → str¶: C++: protocols::splice::SpliceOutTailCreator::mover_name() –> std::string

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

class pyrosetta.rosetta.protocols.splice.SpliceSegment¶

Bases: pybind11_object

utility class and functions for dealing with sequence profiles for varying segments in Splice

add_pdb_profile_pair(self: pyrosetta.rosetta.protocols.splice.SpliceSegment, pdb: str, profile_name: str) → None¶: C++: protocols::splice::SpliceSegment::add_pdb_profile_pair(const std::string &, const std::string &) –> void

add_profile(self: pyrosetta.rosetta.protocols.splice.SpliceSegment, pdb_name: str, prof: pyrosetta.rosetta.core.sequence.SequenceProfile) → None¶: C++: protocols::splice::SpliceSegment::add_profile(const std::string &, const class std::shared_ptr<class core::sequence::SequenceProfile>) –> void

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

get_cluster_name_by_PDB(self: pyrosetta.rosetta.protocols.splice.SpliceSegment, pdbNAme: str) → str¶: C++: protocols::splice::SpliceSegment::get_cluster_name_by_PDB(std::string) –> std::string

get_profile(self: pyrosetta.rosetta.protocols.splice.SpliceSegment, segment_name: str) → pyrosetta.rosetta.core.sequence.SequenceProfile¶

read the pdb-profile match from a disk file

C++: protocols::splice::SpliceSegment::get_profile(const std::string &) –> class std::shared_ptr<class core::sequence::SequenceProfile>

pdb_profile(self: pyrosetta.rosetta.protocols.splice.SpliceSegment, pdb_name: str) → pyrosetta.rosetta.core.sequence.SequenceProfile¶

add a sequence profile

C++: protocols::splice::SpliceSegment::pdb_profile(const std::string &) –> class std::shared_ptr<class core::sequence::SequenceProfile>

pdb_to_profile_map(self: pyrosetta.rosetta.protocols.splice.SpliceSegment) → pyrosetta.rosetta.std.map_std_string_std_string¶: C++: protocols::splice::SpliceSegment::pdb_to_profile_map() –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >

read_many(self: pyrosetta.rosetta.protocols.splice.SpliceSegment, protein_family: str, segmetn: str) → None¶

read pssm

C++: protocols::splice::SpliceSegment::read_many(const std::string &, const std::string &) –> void

read_pdb_profile(self: pyrosetta.rosetta.protocols.splice.SpliceSegment, file_name: str) → None¶: C++: protocols::splice::SpliceSegment::read_pdb_profile(const std::string &) –> void

read_pdb_profile_file(self: pyrosetta.rosetta.protocols.splice.SpliceSegment, s: str, : str) → None¶

read pssm

C++: protocols::splice::SpliceSegment::read_pdb_profile_file(const std::string &, const std::string &) –> void

read_profile(self: pyrosetta.rosetta.protocols.splice.SpliceSegment, file_name: str, segment_name: str) → None¶: C++: protocols::splice::SpliceSegment::read_profile(const std::string &, const std::string &) –> void

sequence_profile(self: pyrosetta.rosetta.protocols.splice.SpliceSegment, profile_name: str) → pyrosetta.rosetta.core.sequence.SequenceProfile¶: C++: protocols::splice::SpliceSegment::sequence_profile(const std::string &) –> class std::shared_ptr<class core::sequence::SequenceProfile>

class pyrosetta.rosetta.protocols.splice.TailSegmentMover¶

Bases: Mover

FloppyTail mover

apply(self: pyrosetta.rosetta.protocols.splice.TailSegmentMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::TailSegmentMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.splice.TailSegmentMover, rhs: pyrosetta.rosetta.protocols.splice.TailSegmentMover) → pyrosetta.rosetta.protocols.splice.TailSegmentMover¶

assignment operator

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

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

fullatom_scorefunction(self: pyrosetta.rosetta.protocols.splice.TailSegmentMover, SF_in: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::splice::TailSegmentMover::fullatom_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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.TailSegmentMover) → str¶: C++: protocols::splice::TailSegmentMover::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_scorefunction(self: pyrosetta.rosetta.protocols.splice.TailSegmentMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::splice::TailSegmentMover::get_scorefunction() –> class std::shared_ptr<class core::scoring::ScoreFunction>

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

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

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

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

non-const accessor

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

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

static mover_name() → str¶: C++: protocols::splice::TailSegmentMover::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.splice.TailSegmentMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::splice::TailSegmentMover::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::splice::TailSegmentMover::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.splice.TailSegmentMover) → bool¶: C++: protocols::splice::TailSegmentMover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.splice.TailSegmentMover) → bool¶: C++: protocols::splice::TailSegmentMover::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_fa_scorefxn(self: pyrosetta.rosetta.protocols.splice.TailSegmentMover, fa_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::splice::TailSegmentMover::set_fa_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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_movemap(self: pyrosetta.rosetta.protocols.splice.TailSegmentMover, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None¶

set the movemap instead of initializing it from cmd-line

C++: protocols::splice::TailSegmentMover::set_movemap(const class std::shared_ptr<class core::kinematics::MoveMap>) –> void

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

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

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

set_task_factory(self: pyrosetta.rosetta.protocols.splice.TailSegmentMover, task_factory_in: pyrosetta.rosetta.core.pack.task.TaskFactory) → None¶: C++: protocols::splice::TailSegmentMover::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

temp_final(self: pyrosetta.rosetta.protocols.splice.TailSegmentMover, value: float) → None¶: C++: protocols::splice::TailSegmentMover::temp_final(double) –> void

temp_initial(self: pyrosetta.rosetta.protocols.splice.TailSegmentMover, value: float) → None¶: C++: protocols::splice::TailSegmentMover::temp_initial(double) –> void

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.splice.TailSegmentMoverCreator¶

Bases: MoverCreator

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

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

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

static mover_name() → str¶: C++: protocols::splice::TailSegmentMoverCreator::mover_name() –> std::string

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

pyrosetta.rosetta.protocols.splice.calculate_rmsd(*args, **kwargs)¶

Overloaded function.

calculate_rmsd(pose: pyrosetta.rosetta.core.pose.Pose, source_pose: pyrosetta.rosetta.core.pose.Pose, total_residue_new: int, nearest_to_from: int, from_res: int, rms_A: float) -> bool
calculate_rmsd(pose: pyrosetta.rosetta.core.pose.Pose, source_pose: pyrosetta.rosetta.core.pose.Pose, total_residue_new: int, nearest_to_from: int, from_res: int, rms_A: float, rms_B: float) -> bool

C++: protocols::splice::calculate_rmsd(class core::pose::Pose &, const class core::pose::Pose &, unsigned long, unsigned long, unsigned long, double, double) –> bool

pyrosetta.rosetta.protocols.splice.coords(pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t¶: C++: protocols::splice::coords(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

pyrosetta.rosetta.protocols.splice.find_disulfs_in_range(pose: pyrosetta.rosetta.core.pose.Pose, start: int, end: int) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t¶

utility function for finding disulfide bonded pairs

C++: protocols::splice::find_disulfs_in_range(const class core::pose::Pose &, const unsigned long, const unsigned long) –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

pyrosetta.rosetta.protocols.splice.find_residues_on_chain1_inside_interface(pose: pyrosetta.rosetta.core.pose.Pose, chainNum: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::splice::find_residues_on_chain1_inside_interface(const class core::pose::Pose &, unsigned long) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.splice.fix_chain_break_residue(pose: pyrosetta.rosetta.core.pose.Pose, splicemanager: pyrosetta.rosetta.protocols.splice.SpliceManager) → None¶: C++: protocols::splice::fix_chain_break_residue(class core::pose::Pose &, class protocols::splice::SpliceManager) –> void

pyrosetta.rosetta.protocols.splice.load_pdb_segments_from_pose_comments(pose: pyrosetta.rosetta.core.pose.Pose, pdb_segments: pyrosetta.rosetta.std.map_std_string_std_string) → None¶: C++: protocols::splice::load_pdb_segments_from_pose_comments(const class core::pose::Pose &, class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &) –> void

pyrosetta.rosetta.protocols.splice.min_seg(pose: pyrosetta.rosetta.core.pose.Pose, dofs: pyrosetta.rosetta.protocols.splice.ResidueBBDofs, debug: bool, from_res: int, tail_segment: str, cut_site: int, cut_vl_vh_after_llc: int, tail_dofs: pyrosetta.rosetta.protocols.splice.ResidueBBDofs, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, segment_type: str) → None¶: C++: protocols::splice::min_seg(class core::pose::Pose &, class protocols::splice::ResidueBBDofs, bool, unsigned long, std::string, unsigned long, unsigned long, class protocols::splice::ResidueBBDofs, class std::shared_ptr<class core::scoring::ScoreFunction>, std::string) –> void

pyrosetta.rosetta.protocols.splice.modify_dbase_with_compatible_backbones(torsion_database: pyrosetta.rosetta.utility.vector1_protocols_splice_ResidueBBDofs, dbase: pyrosetta.rosetta.utility.vector1_unsigned_long, intersect_pdbs: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: protocols::splice::modify_dbase_with_compatible_backbones(class utility::vector1<class protocols::splice::ResidueBBDofs, class std::allocator<class protocols::splice::ResidueBBDofs> >, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<std::string, class std::allocator<std::string > >) –> void

pyrosetta.rosetta.protocols.splice.nearest_to_entry_stop_on_pose(pose: pyrosetta.rosetta.core.pose.Pose, template_pose: pyrosetta.rosetta.core.pose.Pose, residue: int, tail_segment: str, protein_family: str, chain: int, segment: str) → int¶: C++: protocols::splice::nearest_to_entry_stop_on_pose(const class core::pose::Pose &, const class core::pose::Pose &, unsigned long, std::string, std::string, unsigned long, std::string) –> unsigned long

pyrosetta.rosetta.protocols.splice.neighbors_in_vector(pose: pyrosetta.rosetta.core.pose.Pose, target_res: int, neighbors: pyrosetta.rosetta.utility.vector1_unsigned_long, dist_threshold: float, dssp: pyrosetta.rosetta.core.scoring.dssp.Dssp, sequence_separation: int) → int¶: C++: protocols::splice::neighbors_in_vector(const class core::pose::Pose &, const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double, class core::scoring::dssp::Dssp &, const unsigned long) –> unsigned long

pyrosetta.rosetta.protocols.splice.parse_pdb_code(pdb_file_name: str) → str¶: C++: protocols::splice::parse_pdb_code(std::string) –> std::string

pyrosetta.rosetta.protocols.splice.read_H3_seq(Protein_family_path: str) → pyrosetta.rosetta.std.map_std_string_std_string¶: C++: protocols::splice::read_H3_seq(const std::string &) –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >

pyrosetta.rosetta.protocols.splice.read_pdb_seq(Protein_family_path: str) → pyrosetta.rosetta.std.map_std_string_std_string¶: C++: protocols::splice::read_pdb_seq(const std::string &) –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >

pyrosetta.rosetta.protocols.splice.report_coordinate_constraints(pose: pyrosetta.rosetta.core.pose.Pose) → int¶: C++: protocols::splice::report_coordinate_constraints(const class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.splice.report_des_pack_res(pose: pyrosetta.rosetta.core.pose.Pose, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) → None¶: C++: protocols::splice::report_des_pack_res(const class core::pose::Pose &, class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

pyrosetta.rosetta.protocols.splice.report_designable_packable_residues(tf: pyrosetta.rosetta.core.pack.task.TaskFactory, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::splice::report_designable_packable_residues(const class std::shared_ptr<class core::pack::task::TaskFactory>, class core::pose::Pose) –> void