pose_creation

Bindings for protocols::pose_creation namespace

class pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Creates an extended, idealized pose from the sequence and residue

type set specified in the constructor.

C++: protocols::pose_creation::ExtendedPoseMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover, : pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover) → pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover

C++: protocols::pose_creation::ExtendedPoseMover::operator=(const class protocols::pose_creation::ExtendedPoseMover &) –> class protocols::pose_creation::ExtendedPoseMover &

chain(*args, **kwargs)

Overloaded function.

1. chain(self: pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover) -> str

C++: protocols::pose_creation::ExtendedPoseMover::chain() const –> std::string

2. chain(self: pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover, setting: str) -> None

C++: protocols::pose_creation::ExtendedPoseMover::chain(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.pose_creation.ExtendedPoseMover) → pyrosetta.rosetta.protocols.moves.Mover

Creates a replica of this protocols::moves::Mover

C++: protocols::pose_creation::ExtendedPoseMover::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.pose_creation.ExtendedPoseMover) → pyrosetta.rosetta.protocols.moves.Mover

Creates a new instance by calling the no-argument constructor

C++: protocols::pose_creation::ExtendedPoseMover::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.pose_creation.ExtendedPoseMover) → str

C++: protocols::pose_creation::ExtendedPoseMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static mover_name() → str

C++: protocols::pose_creation::ExtendedPoseMover::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

protocols::moves::Mover-specific parsing required by RosettaScripts

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

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

Provide citations to the passed CitationCollectionList

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

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

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

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

C++: protocols::pose_creation::ExtendedPoseMover::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

residue_type_set(*args, **kwargs)

Overloaded function.

1. residue_type_set(self: pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover) -> str

Returns the residue type set

C++: protocols::pose_creation::ExtendedPoseMover::residue_type_set() const –> const std::string &

2. residue_type_set(self: pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover, residue_type_set: str) -> None

Updates the residue type set to be used in calls to apply()

C++: protocols::pose_creation::ExtendedPoseMover::residue_type_set(const std::string &) –> void

sequence(*args, **kwargs)

Overloaded function.

1. sequence(self: pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover) -> str

Returns the sequence

C++: protocols::pose_creation::ExtendedPoseMover::sequence() const –> const std::string &

2. sequence(self: pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover, sequence: str) -> None

Updates the sequence to be used in calls to apply()

C++: protocols::pose_creation::ExtendedPoseMover::sequence(const std::string &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

valid(self: pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover) → bool

Returns true if this instance is valid (i.e. contains a sequence).

Since RosettaScripts mandates the existence of a no-argument constructor, we lose the ability to reason about the validity of a particular instance.

C++: protocols::pose_creation::ExtendedPoseMover::valid() const –> bool

class pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMoverCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMoverCreator, : pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMoverCreator) → pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMoverCreator

C++: protocols::pose_creation::ExtendedPoseMoverCreator::operator=(const class protocols::pose_creation::ExtendedPoseMoverCreator &) –> class protocols::pose_creation::ExtendedPoseMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMoverCreator) → str

C++: protocols::pose_creation::ExtendedPoseMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover

Bases: Mover

class Design

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover.Design, : pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover.Design) → pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover.Design

C++: protocols::pose_creation::MakeJunctionsMover::Design::operator=(const struct protocols::pose_creation::MakeJunctionsMover::Design &) –> struct protocols::pose_creation::MakeJunctionsMover::Design &

property c_term_pose

property c_term_stack

property n_term_pose

property n_term_stack

property name

print(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover.Design) → None

C++: protocols::pose_creation::MakeJunctionsMover::Design::print() –> void

property start_struct

apply(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pose_creation::MakeJunctionsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover, : pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover) → pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover

C++: protocols::pose_creation::MakeJunctionsMover::operator=(const class protocols::pose_creation::MakeJunctionsMover &) –> class protocols::pose_creation::MakeJunctionsMover &

assign_seq(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover, pose: pyrosetta.rosetta.core.pose.Pose, n_term_seq: str, c_term_seq: str) → None

C++: protocols::pose_creation::MakeJunctionsMover::assign_seq(class core::pose::Pose &, std::string, std::string) –> void

attach_next_part(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover, pose: pyrosetta.rosetta.core.pose.Pose, attach_termini: str, attach_description: str) → bool

C++: protocols::pose_creation::MakeJunctionsMover::attach_next_part(class core::pose::Pose &, std::string, std::string) –> bool

check_all_junctions_good(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover, design: protocols::pose_creation::MakeJunctionsMover::Design) → bool

C++: protocols::pose_creation::MakeJunctionsMover::check_all_junctions_good(struct protocols::pose_creation::MakeJunctionsMover::Design) –> bool

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.pose_creation.MakeJunctionsMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::pose_creation::MakeJunctionsMover::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.pose_creation.MakeJunctionsMover) → pyrosetta.rosetta.protocols.moves.Mover

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

generate_start_pose(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover, pose: pyrosetta.rosetta.core.pose.Pose, background_pose: pyrosetta.rosetta.core.pose.Pose, attach_description: str) → None

C++: protocols::pose_creation::MakeJunctionsMover::generate_start_pose(class core::pose::Pose &, class core::pose::Pose &, std::string) –> void

get_additional_output(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover) → pyrosetta.rosetta.core.pose.Pose

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

get_and_cache_pdb(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover, pdb_location: str) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::pose_creation::MakeJunctionsMover::get_and_cache_pdb(std::string) –> 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.pose_creation.MakeJunctionsMover) → str

C++: protocols::pose_creation::MakeJunctionsMover::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

line_to_design(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover, line: str) → protocols::pose_creation::MakeJunctionsMover::Design

C++: protocols::pose_creation::MakeJunctionsMover::line_to_design(std::string) –> struct protocols::pose_creation::MakeJunctionsMover::Design

make_pose_from_design(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover, design: protocols::pose_creation::MakeJunctionsMover::Design, return_pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::pose_creation::MakeJunctionsMover::make_pose_from_design(struct protocols::pose_creation::MakeJunctionsMover::Design, class std::shared_ptr<class core::pose::Pose> &) –> bool

static mover_name() → str

C++: protocols::pose_creation::MakeJunctionsMover::mover_name() –> std::string

static name() → str

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

parse_attach_description(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover, attach_description: str, pdb_location: str, chain: str, n_term_trim: int, c_term_trim: int, n_repeats: int, n_term_attach_length: int, c_term_attach_length: int, n_term_seq: str, c_term_seq: str) → None

C++: protocols::pose_creation::MakeJunctionsMover::parse_attach_description(std::string, std::string &, char &, unsigned long &, unsigned long &, unsigned long &, unsigned long &, unsigned long &, std::string &, std::string &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

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

Provide citations to the passed CitationCollectionList

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

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

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

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

C++: protocols::pose_creation::MakeJunctionsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

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

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

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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

trim_pose(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover, pose: pyrosetta.rosetta.core.pose.Pose, n_term_trim: int, c_term_trim: int) → None

C++: protocols::pose_creation::MakeJunctionsMover::trim_pose(class core::pose::Pose &, unsigned long, unsigned long) –> void

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

2. 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.pose_creation.MakeJunctionsMoverCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMoverCreator, : pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMoverCreator) → pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMoverCreator

C++: protocols::pose_creation::MakeJunctionsMoverCreator::operator=(const class protocols::pose_creation::MakeJunctionsMoverCreator &) –> class protocols::pose_creation::MakeJunctionsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMoverCreator) → str

C++: protocols::pose_creation::MakeJunctionsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pose_creation::MakePolyXMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover, : pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover) → pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover

C++: protocols::pose_creation::MakePolyXMover::operator=(const class protocols::pose_creation::MakePolyXMover &) –> class protocols::pose_creation::MakePolyXMover &

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.pose_creation.MakePolyXMover) → pyrosetta.rosetta.protocols.moves.Mover

clone this object

C++: protocols::pose_creation::MakePolyXMover::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.pose_creation.MakePolyXMover) → pyrosetta.rosetta.protocols.moves.Mover

create this type of object

C++: protocols::pose_creation::MakePolyXMover::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.pose_creation.MakePolyXMover) → str

C++: protocols::pose_creation::MakePolyXMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static mover_name() → str

C++: protocols::pose_creation::MakePolyXMover::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

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

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

Provide citations to the passed CitationCollectionList

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

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

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

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

C++: protocols::pose_creation::MakePolyXMover::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_chis(self: pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover, chis: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::pose_creation::MakePolyXMover::set_chis(class utility::vector1<double, class std::allocator<double> >) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

2. 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.pose_creation.MakePolyXMoverCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_creation.MakePolyXMoverCreator, : pyrosetta.rosetta.protocols.pose_creation.MakePolyXMoverCreator) → pyrosetta.rosetta.protocols.pose_creation.MakePolyXMoverCreator

C++: protocols::pose_creation::MakePolyXMoverCreator::operator=(const class protocols::pose_creation::MakePolyXMoverCreator &) –> class protocols::pose_creation::MakePolyXMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_creation.MakePolyXMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.pose_creation.MakePolyXMoverCreator) → str

C++: protocols::pose_creation::MakePolyXMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_creation.MakePolyXMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.pose_creation.MergePDBMover

Bases: Mover

class Overlap

Bases: pybind11_object

property end_overlap_pose

property end_overlap_xmlPose

name(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMover.Overlap) → str

C++: protocols::pose_creation::MergePDBMover::Overlap::name() –> std::string

property output_poseOP

property output_yet

print(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMover.Overlap) → None

C++: protocols::pose_creation::MergePDBMover::Overlap::print() –> void

property start_overlap_pose

property start_overlap_xmlPose

apply(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pose_creation::MergePDBMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMover, : pyrosetta.rosetta.protocols.pose_creation.MergePDBMover) → pyrosetta.rosetta.protocols.pose_creation.MergePDBMover

C++: protocols::pose_creation::MergePDBMover::operator=(const class protocols::pose_creation::MergePDBMover &) –> class protocols::pose_creation::MergePDBMover &

check_duplicate(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool

fast check to maake sure the pose isn’t a structural duplicate

C++: protocols::pose_creation::MergePDBMover::check_duplicate(class core::pose::Pose &) –> bool

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.pose_creation.MergePDBMover) → pyrosetta.rosetta.protocols.moves.Mover

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

closest_non_overlap_residue(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMover, pose: pyrosetta.rosetta.core.pose.Pose, resid: int, start_overlap_resid: int, end_overlap_resid: int) → int

Figures out the closest residue that’s not part of the overlap.

C++: protocols::pose_creation::MergePDBMover::closest_non_overlap_residue(const class core::pose::Pose &, unsigned long, unsigned long, unsigned long) –> unsigned long

copy_sequence(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMover, start_overlap_resid: int, end_overlap_resid: int, start_overlap_input_pose_resid: int, start_overlap_xml_pose_resid: int, input_pose: pyrosetta.rosetta.core.pose.Pose, xml_pose: pyrosetta.rosetta.core.pose.Pose, output_pose: pyrosetta.rosetta.core.pose.Pose) → None

Copies the sequence in the overlap region as appropriate. This sets the initial residues before the pack and minimize is called

C++: protocols::pose_creation::MergePDBMover::copy_sequence(unsigned long, unsigned long, unsigned long, unsigned long, const class core::pose::Pose &, const class core::pose::Pose &, class core::pose::Pose &) –> 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>

determine_overlap(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMover, pose: pyrosetta.rosetta.core.pose.Pose, chain_id: int) → None

Determines the overlaps. stores the start and end position in the struct Overlap

C++: protocols::pose_creation::MergePDBMover::determine_overlap(const class core::pose::Pose, unsigned long) –> void

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

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

generate_overlaps(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMover, pose: pyrosetta.rosetta.core.pose.Pose, chain_id: int) → None

Uses the overlap to generate poses

C++: protocols::pose_creation::MergePDBMover::generate_overlaps(class core::pose::Pose &, unsigned long) –> void

get_additional_output(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMover) → pyrosetta.rosetta.core.pose.Pose

any poses that score lower than the input files is output

C++: protocols::pose_creation::MergePDBMover::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.pose_creation.MergePDBMover) → str

C++: protocols::pose_creation::MergePDBMover::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

increase_range_to_ignore_ss_element(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMover, pose: pyrosetta.rosetta.core.pose.Pose, init_start: int, init_end: int, ss_start: int, ss_end: int) → None

Gets the entire SS element the match is on

C++: protocols::pose_creation::MergePDBMover::increase_range_to_ignore_ss_element(const class core::pose::Pose &, unsigned long, unsigned long, unsigned long &, unsigned long &) –> 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

static mover_name() → str

C++: protocols::pose_creation::MergePDBMover::mover_name() –> std::string

static name() → str

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

pack_and_minimize(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMover, pose: pyrosetta.rosetta.core.pose.Pose, baseline_score: float) → None

packs and minimizes if no clashes as determined by score0

C++: protocols::pose_creation::MergePDBMover::pack_and_minimize(const class core::pose::Pose, double) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

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

Provide citations to the passed CitationCollectionList

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

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

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

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

C++: protocols::pose_creation::MergePDBMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

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

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

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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

2. 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.pose_creation.MergePDBMoverCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMoverCreator, : pyrosetta.rosetta.protocols.pose_creation.MergePDBMoverCreator) → pyrosetta.rosetta.protocols.pose_creation.MergePDBMoverCreator

C++: protocols::pose_creation::MergePDBMoverCreator::operator=(const class protocols::pose_creation::MergePDBMoverCreator &) –> class protocols::pose_creation::MergePDBMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMoverCreator) → str

C++: protocols::pose_creation::MergePDBMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pose_creation::MergePDBatOverlapMover::apply(class core::pose::Pose &) –> void

apply_helper(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::pose_creation::MergePDBatOverlapMover::apply_helper(class core::pose::Pose &) –> bool

assign(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover, : pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover) → pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover

C++: protocols::pose_creation::MergePDBatOverlapMover::operator=(const class protocols::pose_creation::MergePDBatOverlapMover &) –> class protocols::pose_creation::MergePDBatOverlapMover &

assign_seq(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover, pose: pyrosetta.rosetta.core.pose.Pose, residue_type: str, position: int) → None

C++: protocols::pose_creation::MergePDBatOverlapMover::assign_seq(class core::pose::Pose &, char, unsigned long) –> 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.pose_creation.MergePDBatOverlapMover) → pyrosetta.rosetta.protocols.moves.Mover

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

closest_non_overlap_residue(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover, pose: pyrosetta.rosetta.core.pose.Pose, resid: int, start_overlap_resid: int, end_overlap_resid: int) → int

C++: protocols::pose_creation::MergePDBatOverlapMover::closest_non_overlap_residue(const class core::pose::Pose &, unsigned long, unsigned long, unsigned long) –> unsigned long

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.pose_creation.MergePDBatOverlapMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::pose_creation::MergePDBatOverlapMover::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.pose_creation.MergePDBatOverlapMover) → str

C++: protocols::pose_creation::MergePDBatOverlapMover::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

increase_range_to_ignore_ss_element(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover, pose: pyrosetta.rosetta.core.pose.Pose, init_start: int, init_end: int, ss_start: int, ss_end: int) → None

C++: protocols::pose_creation::MergePDBatOverlapMover::increase_range_to_ignore_ss_element(const class core::pose::Pose &, unsigned long, unsigned long, unsigned long &, unsigned long &) –> 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

makeJunctions_apply(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover, pose: pyrosetta.rosetta.core.pose.Pose, attach_pose: pyrosetta.rosetta.core.pose.Pose, overlap_length: int, max_overlap_rmsd: float, attachment_termini: str, chain: str) → bool

C++: protocols::pose_creation::MergePDBatOverlapMover::makeJunctions_apply(class core::pose::Pose &, const class core::pose::Pose &, unsigned long, double, std::string, char) –> bool

merge_junction_sequence(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover, pose: pyrosetta.rosetta.core.pose.Pose, pose_junction_seq: str, attach_pose_junction_seq: str, first_overlap_position: int) → None

C++: protocols::pose_creation::MergePDBatOverlapMover::merge_junction_sequence(class core::pose::Pose &, std::string, std::string, unsigned long) –> void

merge_poses(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover, pose: pyrosetta.rosetta.core.pose.Pose, attach_pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::pose_creation::MergePDBatOverlapMover::merge_poses(class core::pose::Pose &, class core::pose::Pose &) –> bool

minimize_overlap(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover, pose: pyrosetta.rosetta.core.pose.Pose, overlap_start: int, overlap_end: int) → None

C++: protocols::pose_creation::MergePDBatOverlapMover::minimize_overlap(class core::pose::Pose &, unsigned long, unsigned long) –> void

static mover_name() → str

C++: protocols::pose_creation::MergePDBatOverlapMover::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

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

Provide citations to the passed CitationCollectionList

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

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

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

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

C++: protocols::pose_creation::MergePDBatOverlapMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

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

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

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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

2. 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.pose_creation.MergePDBatOverlapMoverCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMoverCreator, : pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMoverCreator) → pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMoverCreator

C++: protocols::pose_creation::MergePDBatOverlapMoverCreator::operator=(const class protocols::pose_creation::MergePDBatOverlapMoverCreator &) –> class protocols::pose_creation::MergePDBatOverlapMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMoverCreator) → str

C++: protocols::pose_creation::MergePDBatOverlapMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover

Bases: Mover

A class for generating a pose from a sequence/fasta

apply(self: pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Apply the mover

C++: protocols::pose_creation::PoseFromSequenceMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover, src: pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover) → pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover

C++: protocols::pose_creation::PoseFromSequenceMover::operator=(const class protocols::pose_creation::PoseFromSequenceMover &) –> class protocols::pose_creation::PoseFromSequenceMover &

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.pose_creation.PoseFromSequenceMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::pose_creation::PoseFromSequenceMover::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.pose_creation.PoseFromSequenceMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::pose_creation::PoseFromSequenceMover::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_extended(self: pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover) → bool

C++: protocols::pose_creation::PoseFromSequenceMover::get_extended() const –> bool

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.pose_creation.PoseFromSequenceMover) → str

C++: protocols::pose_creation::PoseFromSequenceMover::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_residue_type_set(self: pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover) → str

C++: protocols::pose_creation::PoseFromSequenceMover::get_residue_type_set() const –> const std::string &

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

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

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

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

get_sequence(self: pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover) → str

C++: protocols::pose_creation::PoseFromSequenceMover::get_sequence() const –> const std::string &

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

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

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

non-const accessor

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

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

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

static mover_name() → str

C++: protocols::pose_creation::PoseFromSequenceMover::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

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

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

Provide citations to the passed CitationCollectionList

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

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

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

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

C++: protocols::pose_creation::PoseFromSequenceMover::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_extended(self: pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover, : bool) → None

C++: protocols::pose_creation::PoseFromSequenceMover::set_extended(const bool) –> void

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

setter for poses contained for rms

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

set_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_residue_type_set(self: pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover, : str) → None

C++: protocols::pose_creation::PoseFromSequenceMover::set_residue_type_set(const std::string &) –> void

set_sequence(self: pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover, : str) → None

C++: protocols::pose_creation::PoseFromSequenceMover::set_sequence(const std::string &) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover) -> None

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

C++: protocols::pose_creation::PoseFromSequenceMover::show(std::ostream &) const –> void

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

2. 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.pose_creation.PoseFromSequenceMoverCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMoverCreator, : pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMoverCreator) → pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMoverCreator

C++: protocols::pose_creation::PoseFromSequenceMoverCreator::operator=(const class protocols::pose_creation::PoseFromSequenceMoverCreator &) –> class protocols::pose_creation::PoseFromSequenceMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMoverCreator) → str

C++: protocols::pose_creation::PoseFromSequenceMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover

Bases: Mover

class Chunk

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.Chunk, : pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.Chunk) → pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.Chunk

C++: protocols::pose_creation::SliceToMiniProteinMover::Chunk::operator=(const struct protocols::pose_creation::SliceToMiniProteinMover::Chunk &) –> struct protocols::pose_creation::SliceToMiniProteinMover::Chunk &

property ddg

property end_res

property outputed

property pose

property start_res

class SSElement

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.SSElement, : pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.SSElement) → pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.SSElement

C++: protocols::pose_creation::SliceToMiniProteinMover::SSElement::operator=(const struct protocols::pose_creation::SliceToMiniProteinMover::SSElement &) –> struct protocols::pose_creation::SliceToMiniProteinMover::SSElement &

property end_res

property start_res

property type

apply(self: pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pose_creation::SliceToMiniProteinMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover, : pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover) → pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover

C++: protocols::pose_creation::SliceToMiniProteinMover::operator=(const class protocols::pose_creation::SliceToMiniProteinMover &) –> class protocols::pose_creation::SliceToMiniProteinMover &

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.pose_creation.SliceToMiniProteinMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::pose_creation::SliceToMiniProteinMover::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>

filter_chunks(self: pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover, chunks: pyrosetta.rosetta.utility.vector1_protocols_pose_creation_SliceToMiniProteinMover_Chunk) → pyrosetta.rosetta.utility.vector1_protocols_pose_creation_SliceToMiniProteinMover_Chunk

filter chunks based on ddg

C++: protocols::pose_creation::SliceToMiniProteinMover::filter_chunks(class utility::vector1<struct protocols::pose_creation::SliceToMiniProteinMover::Chunk, class std::allocator<struct protocols::pose_creation::SliceToMiniProteinMover::Chunk> >) –> class utility::vector1<struct protocols::pose_creation::SliceToMiniProteinMover::Chunk, class std::allocator<struct protocols::pose_creation::SliceToMiniProteinMover::Chunk> >

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

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

get_additional_output(self: pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::pose_creation::SliceToMiniProteinMover::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.pose_creation.SliceToMiniProteinMover) → str

C++: protocols::pose_creation::SliceToMiniProteinMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static mover_name() → str

C++: protocols::pose_creation::SliceToMiniProteinMover::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

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

Provide citations to the passed CitationCollectionList

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

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

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

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

C++: protocols::pose_creation::SliceToMiniProteinMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

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

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

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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

setup_chunks_for_output(self: pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover, chunks: pyrosetta.rosetta.utility.vector1_protocols_pose_creation_SliceToMiniProteinMover_Chunk) → None

setups chunks for output. all, longest or best_ddg

C++: protocols::pose_creation::SliceToMiniProteinMover::setup_chunks_for_output(class utility::vector1<struct protocols::pose_creation::SliceToMiniProteinMover::Chunk, class std::allocator<struct protocols::pose_creation::SliceToMiniProteinMover::Chunk> > &) –> void

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

trim_chunks(self: pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover, chunks: pyrosetta.rosetta.utility.vector1_protocols_pose_creation_SliceToMiniProteinMover_Chunk) → pyrosetta.rosetta.utility.vector1_protocols_pose_creation_SliceToMiniProteinMover_Chunk

trim any overhanging helices and helices that are slightly too long

C++: protocols::pose_creation::SliceToMiniProteinMover::trim_chunks(class utility::vector1<struct protocols::pose_creation::SliceToMiniProteinMover::Chunk, class std::allocator<struct protocols::pose_creation::SliceToMiniProteinMover::Chunk> >) –> class utility::vector1<struct protocols::pose_creation::SliceToMiniProteinMover::Chunk, class std::allocator<struct protocols::pose_creation::SliceToMiniProteinMover::Chunk> >

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

2. 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.pose_creation.SliceToMiniProteinMoverCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMoverCreator, : pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMoverCreator) → pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMoverCreator

C++: protocols::pose_creation::SliceToMiniProteinMoverCreator::operator=(const class protocols::pose_creation::SliceToMiniProteinMoverCreator &) –> class protocols::pose_creation::SliceToMiniProteinMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMoverCreator) → str

C++: protocols::pose_creation::SliceToMiniProteinMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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