rosetta_scripts¶

Bindings for protocols::rosetta_scripts namespace

class pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper¶

Bases: Mover

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

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

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

get_additional_output(self: pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::rosetta_scripts::AdditionalOutputWrapper::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.rosetta_scripts.AdditionalOutputWrapper) → str¶: C++: protocols::rosetta_scripts::AdditionalOutputWrapper::get_name() const –> std::string

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

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

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

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

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

non-const accessor

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

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

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

parse_my_tag(self: pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::rosetta_scripts::AdditionalOutputWrapper::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

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

Provide citations to the passed CitationCollectionList

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

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

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

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapperCreator¶

Bases: MoverCreator

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

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

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

static mover_name() → str¶: C++: protocols::rosetta_scripts::AdditionalOutputWrapperCreator::mover_name() –> std::string

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

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

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

class pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper¶

Bases: Mover

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

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

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

get_additional_output(self: pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::rosetta_scripts::MultipleOutputWrapper::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.rosetta_scripts.MultipleOutputWrapper) → str¶: C++: protocols::rosetta_scripts::MultipleOutputWrapper::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::rosetta_scripts::MultipleOutputWrapper::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::rosetta_scripts::MultipleOutputWrapper::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::rosetta_scripts::MultipleOutputWrapper::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapperCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover¶

Bases: Mover

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

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

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

get_additional_output(self: pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::rosetta_scripts::MultiplePoseMover::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.rosetta_scripts.MultiplePoseMover) → str¶: C++: protocols::rosetta_scripts::MultiplePoseMover::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::rosetta_scripts::MultiplePoseMover::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::rosetta_scripts::MultiplePoseMover::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::rosetta_scripts::MultiplePoseMover::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_previous_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover, m: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Used by RosettaScripts to set the previous mover to pull poses from

C++: protocols::rosetta_scripts::MultiplePoseMover::set_previous_mover(const class std::shared_ptr<class protocols::moves::Mover>) –> void

set_rosetta_scripts_tag(self: pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover, tag: pyrosetta.rosetta.utility.tag.Tag) → None¶

sets rosettascripts tag

C++: protocols::rosetta_scripts::MultiplePoseMover::set_rosetta_scripts_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMoverCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol¶

Bases: Mover, ResId, JobOutputterObserver

class FilterReportTime¶

Bases: pybind11_object

Members:

AT_END

AFTER_APPLY

NONE

AFTER_APPLY = <FilterReportTime.AFTER_APPLY: 1>¶

AT_END = <FilterReportTime.AT_END: 0>¶

NONE = <FilterReportTime.NONE: 2>¶

property name¶

property value¶

class ParsedProtocolStep¶

Bases: pybind11_object

Represents a step in the ParsedProtocol Note that one or more of mover/filter/metrics may be null/empty.

assign(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.ParsedProtocolStep, : pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.ParsedProtocolStep) → pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.ParsedProtocolStep¶

Assignment operator.

C++: protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep::operator=(const struct protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep &) –> struct protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep &

property filter¶

property metric_labels¶

property metrics¶

property mover¶

property mover_user_name¶

report_after_apply(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.ParsedProtocolStep) → bool¶: C++: protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep::report_after_apply() const –> bool

report_at_end(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.ParsedProtocolStep) → bool¶: C++: protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep::report_at_end() const –> bool

add_step(*args, **kwargs)¶

Overloaded function.

add_step(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, mover: pyrosetta.rosetta.protocols.moves.Mover, mover_name: str, filter: pyrosetta.rosetta.protocols.filters.Filter) -> None
add_step(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, mover: pyrosetta.rosetta.protocols.moves.Mover, mover_name: str, filter: pyrosetta.rosetta.protocols.filters.Filter, report_filter_at_end: bool) -> None

Add a mover-filter pair.

Indended for use OUTSIDE of a RosettaScripts context.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::rosetta_scripts::ParsedProtocol::add_step(class std::shared_ptr<class protocols::moves::Mover>, const std::string &, class std::shared_ptr<class protocols::filters::Filter>, const bool) –> void

add_step(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, step: protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep) -> None

Add a step to the protocol

Indended for use OUTSIDE of a RosettaScripts context.

C++: protocols::rosetta_scripts::ParsedProtocol::add_step(const struct protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep &) –> void

add_values_to_job(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.protocols.jd2.Job) → None¶: C++: protocols::rosetta_scripts::ParsedProtocol::add_values_to_job(const class core::pose::Pose &, class protocols::jd2::Job &) const –> void

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

apply_probability(*args, **kwargs)¶

Overloaded function.

apply_probability(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, a: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::rosetta_scripts::ParsedProtocol::apply_probability(const class utility::vector1<double, class std::allocator<double> > &) –> void

apply_probability(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::rosetta_scripts::ParsedProtocol::apply_probability() –> class utility::vector1<double, class std::allocator<double> >

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

call_order(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol) → str¶: C++: protocols::rosetta_scripts::ParsedProtocol::call_order() const –> std::string

clear(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol) → None¶: C++: protocols::rosetta_scripts::ParsedProtocol::clear() –> 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.rosetta_scripts.ParsedProtocol) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::rosetta_scripts::ParsedProtocol::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>

final_score(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rosetta_scripts::ParsedProtocol::final_score(class core::pose::Pose &) const –> void

final_scorefxn(*args, **kwargs)¶

Overloaded function.

final_scorefxn(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::rosetta_scripts::ParsedProtocol::final_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

final_scorefxn(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::rosetta_scripts::ParsedProtocol::final_scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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

get_additional_output(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::rosetta_scripts::ParsedProtocol::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_filter_status(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol) → bool¶

Get the status of any filters after running.

C++: protocols::rosetta_scripts::ParsedProtocol::get_filter_status() 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_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, mover_number: int) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::rosetta_scripts::ParsedProtocol::get_mover(const unsigned long) const –> class std::shared_ptr<const class protocols::moves::Mover>

get_name(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol) → str¶: C++: protocols::rosetta_scripts::ParsedProtocol::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_resid(self: pyrosetta.rosetta.protocols.moves.ResId, : pyrosetta.rosetta.core.pose.Pose) → int¶: C++: protocols::moves::ResId::get_resid(const class core::pose::Pose &) const –> unsigned long

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

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

get_step(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, step_number: int) → protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep¶: C++: protocols::rosetta_scripts::ParsedProtocol::get_step(const unsigned long) const –> struct protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep

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_attempted_mover_idx(*args, **kwargs)¶

Overloaded function.

last_attempted_mover_idx(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol) -> int

C++: protocols::rosetta_scripts::ParsedProtocol::last_attempted_mover_idx() –> unsigned long

last_attempted_mover_idx(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, s: int) -> None

C++: protocols::rosetta_scripts::ParsedProtocol::last_attempted_mover_idx(const unsigned long) –> void

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

mode(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol) → str¶: C++: protocols::rosetta_scripts::ParsedProtocol::mode() const –> std::string

modifiable(*args, **kwargs)¶

Overloaded function.

modifiable(self: pyrosetta.rosetta.protocols.moves.ResId) -> bool

should another method be able to modify resid_. This is used by modify_ResId_based_object as a test

C++: protocols::moves::ResId::modifiable() const –> bool

modifiable(self: pyrosetta.rosetta.protocols.moves.ResId, u: bool) -> None

C++: protocols::moves::ResId::modifiable(const bool) –> void

static mover_name() → str¶: C++: protocols::rosetta_scripts::ParsedProtocol::mover_name() –> std::string

n_steps_passed_in_previous_run(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol) → int¶: C++: protocols::rosetta_scripts::ParsedProtocol::n_steps_passed_in_previous_run() const –> unsigned long

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

parse_my_tag(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::rosetta_scripts::ParsedProtocol::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

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

Provide the citation.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::rosetta_scripts::ParsedProtocol::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

report_all(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rosetta_scripts::ParsedProtocol::report_all(const class core::pose::Pose &) const –> void

report_call_order(*args, **kwargs)¶

Overloaded function.

report_call_order(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol) -> bool

C++: protocols::rosetta_scripts::ParsedProtocol::report_call_order() const –> bool

report_call_order(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, c: bool) -> None

C++: protocols::rosetta_scripts::ParsedProtocol::report_call_order(const bool) –> void

report_filters_to_pose(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(class core::pose::Pose &) const –> void

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

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

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

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_resid(*args, **kwargs)¶

Overloaded function.

set_resid(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, resid: int) -> None

C++: protocols::rosetta_scripts::ParsedProtocol::set_resid(const unsigned long) –> void

set_resid(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol, r: pyrosetta.rosetta.core.pose.ResidueIndexDescription) -> None

C++: protocols::rosetta_scripts::ParsedProtocol::set_resid(class std::shared_ptr<const class core::pose::ResidueIndexDescription>) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

size(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol) → int¶: C++: protocols::rosetta_scripts::ParsedProtocol::size() –> unsigned long

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocolCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporter¶

Bases: pybind11_object

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

get_name(self: pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporter) → str¶

Each derived selector must specify its name

C++: protocols::rosetta_scripts::PosePropertyReporter::get_name() const –> std::string

static name() → str¶: C++: protocols::rosetta_scripts::PosePropertyReporter::name() –> std::string

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

Called by PosePropertyReporterFactory when constructing new PosePropertyReporters. Takes care of the specific selector’s parsing.

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

report_property(*args, **kwargs)¶

Overloaded function.

report_property(self: pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporter, p: pyrosetta.rosetta.core.pose.Pose) -> float

Reports a specific property for the provided pose

C++: protocols::rosetta_scripts::PosePropertyReporter::report_property(class core::pose::Pose &) const –> double

report_property(self: pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporter, p1: pyrosetta.rosetta.core.pose.Pose, p2: pyrosetta.rosetta.core.pose.Pose) -> float

Reports a specific property for the combination of two provided poses

C++: protocols::rosetta_scripts::PosePropertyReporter::report_property(class core::pose::Pose &, class core::pose::Pose &) const –> double

class pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator¶

Bases: pybind11_object

Abstract base class for a PosePropertyReporter factory; the Creator class is responsible for creating a particular PosePropertyReporter class.

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

create_reporter(self: pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator) → protocols::rosetta_scripts::PosePropertyReporter¶: C++: protocols::rosetta_scripts::PosePropertyReporterCreator::create_reporter() const –> class std::shared_ptr<class protocols::rosetta_scripts::PosePropertyReporter>

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

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

class pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterFactory¶

Bases: SingletonBase_protocols_rosetta_scripts_PosePropertyReporterFactory_t

static complex_type_name_for_pose_reporter(reporter_name: str) → str¶: C++: protocols::rosetta_scripts::PosePropertyReporterFactory::complex_type_name_for_pose_reporter(const std::string &) –> std::string

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

factory_register(self: pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterFactory, creator: pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator) → None¶: C++: protocols::rosetta_scripts::PosePropertyReporterFactory::factory_register(class std::shared_ptr<class protocols::rosetta_scripts::PosePropertyReporterCreator>) –> void

static get_instance() → protocols::rosetta_scripts::PosePropertyReporterFactory¶: C++: utility::SingletonBase<protocols::rosetta_scripts::PosePropertyReporterFactory>::get_instance() –> class protocols::rosetta_scripts::PosePropertyReporterFactory *

newPosePropertyReporter(*args, **kwargs)¶

Overloaded function.

newPosePropertyReporter(self: pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterFactory, : str) -> pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporter

Create a PosePropertyReporter given its identifying string

C++: protocols::rosetta_scripts::PosePropertyReporterFactory::newPosePropertyReporter(const std::string &) –> class std::shared_ptr<class protocols::rosetta_scripts::PosePropertyReporter>

newPosePropertyReporter(self: pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterFactory, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporter

return new PosePropertyReporter by Tag parsing; the identifying string for the PosePropertyReporter is in the Tag

C++: protocols::rosetta_scripts::PosePropertyReporterFactory::newPosePropertyReporter(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::rosetta_scripts::PosePropertyReporter>

static pose_reporter_group_name() → str¶: C++: protocols::rosetta_scripts::PosePropertyReporterFactory::pose_reporter_group_name() –> std::string

class pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelector¶

Bases: pybind11_object

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

get_flags(self: pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelector) → pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFlags¶

Report selector flags

C++: protocols::rosetta_scripts::PoseSelector::get_flags() const –> enum protocols::rosetta_scripts::PoseSelectorFlags

get_name(self: pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelector) → str¶

Each derived selector must specify its name

C++: protocols::rosetta_scripts::PoseSelector::get_name() const –> std::string

static name() → str¶: C++: protocols::rosetta_scripts::PoseSelector::name() –> std::string

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

Called by PoseSelectorFactory when constructing new PoseSelectors. Takes care of the specific selector’s parsing.

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

select_poses(self: pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelector, poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) → pyrosetta.rosetta.utility.vector1_bool¶

Select poses from provided vector by applying the selection criteria parsed from Tag

C++: protocols::rosetta_scripts::PoseSelector::select_poses(class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >) –> class utility::vector1<bool, class std::allocator<bool> >

class pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator¶

Bases: pybind11_object

Abstract base class for a PoseSelector factory; the Creator class is responsible for creating a particular PoseSelector class.

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

create_selector(self: pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator) → protocols::rosetta_scripts::PoseSelector¶: C++: protocols::rosetta_scripts::PoseSelectorCreator::create_selector() const –> class std::shared_ptr<class protocols::rosetta_scripts::PoseSelector>

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

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

class pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFactory¶

Bases: SingletonBase_protocols_rosetta_scripts_PoseSelectorFactory_t

static complex_type_name_for_pose_selector(selector_name: str) → str¶: C++: protocols::rosetta_scripts::PoseSelectorFactory::complex_type_name_for_pose_selector(const std::string &) –> std::string

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

factory_register(self: pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFactory, creator: pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator) → None¶: C++: protocols::rosetta_scripts::PoseSelectorFactory::factory_register(class std::shared_ptr<class protocols::rosetta_scripts::PoseSelectorCreator>) –> void

static get_instance() → protocols::rosetta_scripts::PoseSelectorFactory¶: C++: utility::SingletonBase<protocols::rosetta_scripts::PoseSelectorFactory>::get_instance() –> class protocols::rosetta_scripts::PoseSelectorFactory *

newPoseSelector(*args, **kwargs)¶

Overloaded function.

newPoseSelector(self: pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFactory, : str) -> pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelector

Create a PoseSelector given its identifying string

C++: protocols::rosetta_scripts::PoseSelectorFactory::newPoseSelector(const std::string &) –> class std::shared_ptr<class protocols::rosetta_scripts::PoseSelector>

newPoseSelector(self: pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFactory, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelector

return new PoseSelector by Tag parsing; the identifying string for the PoseSelector is in the Tag

C++: protocols::rosetta_scripts::PoseSelectorFactory::newPoseSelector(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::rosetta_scripts::PoseSelector>

static pose_selector_group_name() → str¶: C++: protocols::rosetta_scripts::PoseSelectorFactory::pose_selector_group_name() –> std::string

class pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFlags¶

Bases: pybind11_object

Members:

PSF_NONE

PSF_NEED_FULL_POSE_SET

PSF_NEED_FULL_POSE_SET = <PoseSelectorFlags.PSF_NEED_FULL_POSE_SET: 1>¶

PSF_NONE = <PoseSelectorFlags.PSF_NONE: 0>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen¶

Bases: StandardJobQueen

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

completed_job_summary(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, job: pyrosetta.rosetta.protocols.jd3.LarvalJob, result_index: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_ResultIndex_t, summary: pyrosetta.rosetta.protocols.jd3.JobSummary) → None¶

As each job completes, this function is called for each result coming from a LarvalJob.

Override this method to store any results you need.

C++: protocols::jd3::standard::StandardJobQueen::completed_job_summary(class std::shared_ptr<const class protocols::jd3::LarvalJob>, struct utility::StrongT<unsigned long, struct protocols::jd3::ResultIndex_>, class std::shared_ptr<class protocols::jd3::JobSummary>) –> void

create_and_set_initial_job_dag(self: pyrosetta.rosetta.protocols.jd3.JobQueen) → pyrosetta.rosetta.protocols.jd3.JobDigraph¶

Creates the initial job dag using create_initial_job_dag function and sets it to the JQ.

Decorator to create_initial_job_dag

C++: protocols::jd3::JobQueen::create_and_set_initial_job_dag() –> class std::shared_ptr<class protocols::jd3::JobDigraph>

deallocation_messages(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t¶

the RosettaScriptsJobQueen needs to tell remote nodes to deallocate Resources held by the ResourceManager that are no longer needed

C++: protocols::rosetta_scripts::RosettaScriptsJobQueen::deallocation_messages() –> class std::list<class std::shared_ptr<class protocols::jd3::deallocation::DeallocationMessage>, class std::allocator<class std::shared_ptr<class protocols::jd3::deallocation::DeallocationMessage> > >

derived_process_deallocation_message(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen, message: pyrosetta.rosetta.protocols.jd3.deallocation.DeallocationMessage) → None¶

A deallocation message first sent to the JobDistributor on this host originating from: a remote JobQueen

C++: protocols::rosetta_scripts::RosettaScriptsJobQueen::derived_process_deallocation_message(class std::shared_ptr<class protocols::jd3::deallocation::DeallocationMessage>) –> void

determine_job_list(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, job_dag_node_index: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_JobDAGNodeID_t, max_njobs: int) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_LarvalJob_t¶

Create a list of LarvalJobs for each Node Index. Only can create max_njobs to save memory.

The %StandardJobQueen manages the process of creating the list of LarvalJobs that
will later be matured into actual jobs and run by the JobDistributor. It is not recommended that derived job queens override this method; doing so will mean that some of the data the SJQ relies on will not be initialized – see comments on the SJQs data members below to understand the consequences of overriding this method.

It is recommended to override next_batch_of_larval_jobs_for_job_node instead of this method
However, if you do override this - especially for more complicated protocols - be sure to call similar functions here

C++: protocols::jd3::standard::StandardJobQueen::determine_job_list(struct utility::StrongT<unsigned long, struct protocols::jd3::JobDAGNodeID_>, unsigned long) –> class std::list<class std::shared_ptr<class protocols::jd3::LarvalJob>, class std::allocator<class std::shared_ptr<class protocols::jd3::LarvalJob> > >

determine_job_list_and_track(self: pyrosetta.rosetta.protocols.jd3.JobQueen, job_dag_node_index: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_JobDAGNodeID_t, max_njobs: int) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_LarvalJob_t¶

Call determine_job_list in derived classes and track the jobs using the JobTracker.

Decorator to determine_job_list

C++: protocols::jd3::JobQueen::determine_job_list_and_track(struct utility::StrongT<unsigned long, struct protocols::jd3::JobDAGNodeID_>, unsigned long) –> class std::list<class std::shared_ptr<class protocols::jd3::LarvalJob>, class std::allocator<class std::shared_ptr<class protocols::jd3::LarvalJob> > >

determine_preliminary_job_list_from_xml_file(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, job_def_string: str) → None¶

Read from an input string representing the contents of the job-definiton XML file: and construct a set of PreliminaryLarvalJobs; this function is primarily useful for testing, but could be used to organize jobs by an enterprising job distributor or by another JobQueen.

C++: protocols::jd3::standard::StandardJobQueen::determine_preliminary_job_list_from_xml_file(const std::string &) –> void

flush(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen) → None¶: C++: protocols::jd3::standard::StandardJobQueen::flush() –> void

has_job_previously_been_output(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, job: pyrosetta.rosetta.protocols.jd3.LarvalJob) → bool¶

Checks the outputter to see if the job already has been output. Used for JD override behavior.

Gets the outputter from the Job, which is cached in the SJQ.

You should not need to override this method

C++: protocols::jd3::standard::StandardJobQueen::has_job_previously_been_output(class std::shared_ptr<const class protocols::jd3::LarvalJob>) –> bool

initialize_resources_for_preliminary_job_nodes(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen) → None¶: C++: protocols::rosetta_scripts::RosettaScriptsJobQueen::initialize_resources_for_preliminary_job_nodes() –> void

static job_def_complex_type_name(type: str) → str¶

Naming function for the complexTypes in the job-definition XSD

C++: protocols::jd3::standard::StandardJobQueen::job_def_complex_type_name(const std::string &) –> std::string

job_definition_xsd(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen) → str¶

The %StandardJobQueen assembles the XSD from virtual functions she invokes on: the derived %JobQueen: append_job_tag_subelements, append_common_tag_subelements, and add_option/add_options.

C++: protocols::jd3::standard::StandardJobQueen::job_definition_xsd() const –> std::string

job_results_that_should_be_discarded(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen) → pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_t¶

The IDs of jobs that should be discarded, IE not kept in memory for the next set of job nodes.

Override this method to note which jobs we don’t need for the next set of Job Nodes.

C++: protocols::jd3::standard::StandardJobQueen::job_results_that_should_be_discarded() –> class std::list<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

jobs_that_should_be_output(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_t¶

By default outputs all recently finished jobs for JD output (stored in recent_successes_).: Override this method if you want to cull these lists

C++: protocols::jd3::standard::StandardJobQueen::jobs_that_should_be_output() –> class std::list<class std::shared_ptr<class protocols::jd3::output::OutputSpecification>, class std::allocator<class std::shared_ptr<class protocols::jd3::output::OutputSpecification> > >

note_job_completed(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, job: pyrosetta.rosetta.protocols.jd3.LarvalJob, status: pyrosetta.rosetta.protocols.jd3.JobStatus, nresults: int) → None¶

The JD calls this function on completion of a LarvalJob, after updating the JobTracker

If you override this method, call the SJQs version first for PJN tracking and output.

C++: protocols::jd3::standard::StandardJobQueen::note_job_completed(class std::shared_ptr<const class protocols::jd3::LarvalJob>, enum protocols::jd3::JobStatus, unsigned long) –> void

note_job_completed_and_track(self: pyrosetta.rosetta.protocols.jd3.JobQueen, job: protocols::jd3::LarvalJob, status: pyrosetta.rosetta.protocols.jd3.JobStatus, nresults: int) → None¶

Call note_job_completed in derived classes and track the job using the JobTracker.

Decorator to note_job_completed

C++: protocols::jd3::JobQueen::note_job_completed_and_track(class std::shared_ptr<const class protocols::jd3::LarvalJob>, enum protocols::jd3::JobStatus, unsigned long) –> void

note_preliminary_job_node_is_complete(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen, pjn_index: pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_PrelimJobNodeID_t) → None¶: C++: protocols::rosetta_scripts::RosettaScriptsJobQueen::note_preliminary_job_node_is_complete(struct utility::StrongT<unsigned long, struct protocols::jd3::PrelimJobNodeID_>) –> void

process_deallocation_message(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, message: pyrosetta.rosetta.protocols.jd3.deallocation.DeallocationMessage) → None¶

A deallocation message first sent to the JobDistributor on this host originating from: a remote JobQueen. If a derived JobQueen has deallocation messages she needs to recieve, she should override derived_process_deallocation_message.

C++: protocols::jd3::standard::StandardJobQueen::process_deallocation_message(class std::shared_ptr<class protocols::jd3::deallocation::DeallocationMessage>) –> void

resource_definition_xsd(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen) → str¶: C++: protocols::jd3::standard::StandardJobQueen::resource_definition_xsd() const –> std::string

resource_manager(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen) → pyrosetta.rosetta.basic.resource_manager.ResourceManager¶

Accessor to the JQs resource_manager – only really needed for testing purposes.

C++: protocols::rosetta_scripts::RosettaScriptsJobQueen::resource_manager() –> class std::shared_ptr<class basic::resource_manager::ResourceManager>

result_outputter(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, spec: pyrosetta.rosetta.protocols.jd3.output.OutputSpecification) → pyrosetta.rosetta.protocols.jd3.output.ResultOutputter¶

Return the bag of of PoseOutputters (in the form of a MultipleOutputter) for the

Pose that has been requested and specified by a particular OutputSpecification;

This function guarantees that for each individual outputter-name (respecting the JD-provided filename suffix) that a separate set of PoseOutputters are returned so that multiple threads can potentially output at the same time.

You should not need to override this method.

C++: protocols::jd3::standard::StandardJobQueen::result_outputter(const class protocols::jd3::output::OutputSpecification &) –> class std::shared_ptr<class protocols::jd3::output::ResultOutputter>

update_job_dag(self: pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen, updater: pyrosetta.rosetta.protocols.jd3.JobDigraphUpdater) → None¶

The %StandardJobQueen’s implementation is to not update the JobDAG at all: the

most basic protocol defines a job DAG with only a single node.

Override this method if you have a need for updating the job dag during your protocol.

C++: protocols::jd3::standard::StandardJobQueen::update_job_dag(class protocols::jd3::JobDigraphUpdater &) –> void

class pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser¶

Bases: pybind11_object

Reading the xml file and generating the mover

Uses the Tag interface to the xml reader library in boost to parse an xml file that contains design protocol information.

SCOREFXNS provides a way to define scorefunctions as they are defined in the rosetta database, using the weights/patch convenctions. Several default scorefunctions are preset and can be used without defining them explicitly.

FILTERS defines a set of filters that can be used together with the dockdesign movers to prune out poses that don’t meet certain criteria

MOVERS defines the movers that will be used

PROTOCOLS is the only order-sensitive section where subsequent movers and filters are expected to be defined. These movers and filters were defined in the previous two sections. The order in which the protocols are specified by the user will be maintained by the DockDesign mover.

APPLY_TO_POSE – DEPRECATED/Removed. This section used to allow for applying certain movers to the pose prior to protocol start. This functionality has been removed. Anything other than an empty APPLY_TO_POSE section will raise an error.

xi:include statements can be placed anywhere to trigger read-in of another RosettaScripts XML file. Contents of the file replace the xi:include statement.

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

create_tag_from_xml(*args, **kwargs)¶

Overloaded function.

create_tag_from_xml(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, xml_fname: str, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.utility.tag.Tag

Create a tag from an XML file. Read from Script Vars options from a local options collection.

C++: protocols::rosetta_scripts::RosettaScriptsParser::create_tag_from_xml(const std::string &, const class utility::options::OptionCollection &) –> class std::shared_ptr<const class utility::tag::Tag>

create_tag_from_xml(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, xml_fname: str, script_vars: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.utility.tag.Tag

Create a tag from an XML file. Use Script Vars bariable to do any substitutions.: Script Var String: “xx=yy” for %xx% replacement in XML script.

C++: protocols::rosetta_scripts::RosettaScriptsParser::create_tag_from_xml(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> class std::shared_ptr<const class utility::tag::Tag>

create_tag_from_xml_string(*args, **kwargs)¶

Overloaded function.

create_tag_from_xml_string(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, xml_text: str, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.utility.tag.Tag

Create a tag from an XML string. Read from Script Vars options from a local options collection.

C++: protocols::rosetta_scripts::RosettaScriptsParser::create_tag_from_xml_string(const std::string &, const class utility::options::OptionCollection &) –> class std::shared_ptr<const class utility::tag::Tag>

create_tag_from_xml_string(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, xml_text: str, script_vars: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.utility.tag.Tag

Create a tag from an XML string. Use Script Vars bariable to do any substitutions.: Script Var String: “xx=yy” for %xx% replacement in XML script.

C++: protocols::rosetta_scripts::RosettaScriptsParser::create_tag_from_xml_string(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> class std::shared_ptr<const class utility::tag::Tag>

find_rosettascript_tag(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, rootTag: pyrosetta.rosetta.utility.tag.Tag, section_name: str, option_name: str, option_value: str) → pyrosetta.rosetta.utility.tag.Tag¶: C++: protocols::rosetta_scripts::RosettaScriptsParser::find_rosettascript_tag(class std::shared_ptr<const class utility::tag::Tag>, const std::string &, const std::string &, const std::string &) –> class std::shared_ptr<const class utility::tag::Tag>

generate_mover(*args, **kwargs)¶

Overloaded function.

generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, xml_fname: str) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol
generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, xml_fname: str, current_input_name: str) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol
generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, xml_fname: str, current_input_name: str, current_output_name: str) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol