rosetta_scripts

Bindings for protocols::rosetta_scripts namespace

class pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper

Bases: pyrosetta.rosetta.protocols.moves.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_std_allocator_std_string_t

non-const accessor

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

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

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

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.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapperCreator

Bases: pyrosetta.rosetta.protocols.moves.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: pyrosetta.rosetta.protocols.moves.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_std_allocator_std_string_t

non-const accessor

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

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

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

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.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapperCreator

Bases: pyrosetta.rosetta.protocols.moves.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: pyrosetta.rosetta.protocols.moves.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_std_allocator_std_string_t

non-const accessor

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

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

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

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.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.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: pyrosetta.rosetta.protocols.moves.Mover, pyrosetta.rosetta.protocols.moves.ResId, pyrosetta.rosetta.protocols.jd2.JobOutputterObserver

class FilterReportTime

Bases: pybind11_builtins.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
class ParsedProtocolStep

Bases: pybind11_builtins.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

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.

  1. 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

  2. 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

  1. 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.

  1. 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

  1. 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 &

begin(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol) __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >

C++: protocols::rosetta_scripts::ParsedProtocol::begin() –> class __gnu_cxx::__normal_iterator<struct protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep *, class std::vector<struct protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, class std::allocator<struct protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >

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>

end(self: pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol) __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >

C++: protocols::rosetta_scripts::ParsedProtocol::end() –> class __gnu_cxx::__normal_iterator<struct protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep *, class std::vector<struct protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, class std::allocator<struct protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >

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.

  1. 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

  1. 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_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_std_allocator_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.

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

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

  1. 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.

  1. 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

  1. 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.

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

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

  1. 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.

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

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

  1. 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.

  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

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.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocolCreator

Bases: pyrosetta.rosetta.protocols.moves.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_builtins.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.

  1. 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

  1. 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_builtins.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: pyrosetta.rosetta.utility.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.

  1. 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>

  1. 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_builtins.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_builtins.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: pyrosetta.rosetta.utility.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.

  1. 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>

  1. 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_builtins.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
class pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen

Bases: pyrosetta.rosetta.protocols.jd3.standard.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_std_allocator_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_std_allocator_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_std_allocator_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_std_allocator_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_std_allocator_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_builtins.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.

  1. 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>

  1. 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.

  1. 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>

  1. 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.

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

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

  3. 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

Convenience function to construct a ParsedProtocol from a file

Reads in an RosettaScript from file, replaces script_vars if present,

Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects

C++: protocols::rosetta_scripts::RosettaScriptsParser::generate_mover(const std::string &, const std::string &, const std::string &) –> class std::shared_ptr<class protocols::rosetta_scripts::ParsedProtocol>

  1. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, xml_fname: str, script_vars: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  2. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, xml_fname: str, script_vars: pyrosetta.rosetta.utility.vector1_std_string, current_input_name: str) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  3. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, xml_fname: str, script_vars: pyrosetta.rosetta.utility.vector1_std_string, current_input_name: str, current_output_name: str) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

Convenience function to construct a ParsedProtocol from a file

Reads in an RosettaScript from file, replaces script_vars if present,

Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects

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

  1. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, options: pyrosetta.rosetta.utility.options.OptionCollection, current_input_name: str, current_output_name: str, resource_manager: pyrosetta.rosetta.basic.resource_manager.ResourceManager) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

Convenience function to construct a ParsedProtocol from a file

Reads in an RosettaScript from file, replaces script_vars if present,

Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects. Any Resources requested in the RESOURCES block will be retrieved from the ResourceManager and placed in the DataMap.

C++: protocols::rosetta_scripts::RosettaScriptsParser::generate_mover(const class utility::options::OptionCollection &, const std::string &, const std::string &, class std::shared_ptr<class basic::resource_manager::ResourceManager>) –> class std::shared_ptr<class protocols::rosetta_scripts::ParsedProtocol>

  1. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, options: pyrosetta.rosetta.utility.options.OptionCollection, xml_fname: str) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  2. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, options: pyrosetta.rosetta.utility.options.OptionCollection, xml_fname: str, current_input_name: str) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

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

  4. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, options: pyrosetta.rosetta.utility.options.OptionCollection, xml_fname: str, current_input_name: str, current_output_name: str, xml_objects: protocols::rosetta_scripts::XmlObjects) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  5. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, options: pyrosetta.rosetta.utility.options.OptionCollection, xml_fname: str, current_input_name: str, current_output_name: str, xml_objects: protocols::rosetta_scripts::XmlObjects, resource_manager: pyrosetta.rosetta.basic.resource_manager.ResourceManager) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

Convenience function to construct a ParsedProtocol from a file

Reads in an RosettaScript from file, replaces script_vars if present,

Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects

C++: protocols::rosetta_scripts::RosettaScriptsParser::generate_mover(const class utility::options::OptionCollection &, const std::string &, const std::string &, const std::string &, class std::shared_ptr<class protocols::rosetta_scripts::XmlObjects>, class std::shared_ptr<class basic::resource_manager::ResourceManager>) –> class std::shared_ptr<class protocols::rosetta_scripts::ParsedProtocol>

  1. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, options: pyrosetta.rosetta.utility.options.OptionCollection, current_input_name: str, current_output_name: str, resource_manager: pyrosetta.rosetta.basic.resource_manager.ResourceManager) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

Convenience function to construct a ParsedProtocol from a file

Reads in an RosettaScript from file, replaces script_vars if present,

Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects. Any Resources requested in the RESOURCES block will be retrieved from the ResourceManager and placed in the DataMap.

Places an OptionCollectionCOP into the datamap for local option parsing.

C++: protocols::rosetta_scripts::RosettaScriptsParser::generate_mover(class std::shared_ptr<const class utility::options::OptionCollection>, const std::string &, const std::string &, class std::shared_ptr<class basic::resource_manager::ResourceManager>) –> class std::shared_ptr<class protocols::rosetta_scripts::ParsedProtocol>

  1. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, options: pyrosetta.rosetta.utility.options.OptionCollection, xml_fname: str) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  2. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, options: pyrosetta.rosetta.utility.options.OptionCollection, xml_fname: str, current_input_name: str) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

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

  4. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, options: pyrosetta.rosetta.utility.options.OptionCollection, xml_fname: str, current_input_name: str, current_output_name: str, xml_objects: protocols::rosetta_scripts::XmlObjects) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  5. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, options: pyrosetta.rosetta.utility.options.OptionCollection, xml_fname: str, current_input_name: str, current_output_name: str, xml_objects: protocols::rosetta_scripts::XmlObjects, resource_manager: pyrosetta.rosetta.basic.resource_manager.ResourceManager) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

Convenience function to construct a ParsedProtocol from a file

Reads in an RosettaScript from file, replaces script_vars if present,

Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects

Places an OptionCollectionCOP into the datamap for local option parsing.

C++: protocols::rosetta_scripts::RosettaScriptsParser::generate_mover(class std::shared_ptr<const class utility::options::OptionCollection>, const std::string &, const std::string &, const std::string &, class std::shared_ptr<class protocols::rosetta_scripts::XmlObjects>, class std::shared_ptr<class basic::resource_manager::ResourceManager>) –> class std::shared_ptr<class protocols::rosetta_scripts::ParsedProtocol>

  1. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, mover: pyrosetta.rosetta.protocols.moves.Mover, new_input: bool, xml_file: str) -> None

  2. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, mover: pyrosetta.rosetta.protocols.moves.Mover, new_input: bool, xml_file: str, current_input_name: str) -> None

  3. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, mover: pyrosetta.rosetta.protocols.moves.Mover, new_input: bool, xml_file: str, current_input_name: str, current_output_name: str) -> None

  4. generate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, mover: pyrosetta.rosetta.protocols.moves.Mover, new_input: bool, xml_file: str, current_input_name: str, current_output_name: str, guarantee_new_mover: bool) -> None

Original, JD2-compatible mover generating function.

NOT accessible in PyRosetta. For general use and PyRosetta, use mover-returning generate_mover() functions. READS FROM GLOBAL OPTIONS.

C++: protocols::rosetta_scripts::RosettaScriptsParser::generate_mover(class std::shared_ptr<class protocols::moves::Mover> &, bool, const std::string &, const std::string &, const std::string &, bool) –> void

generate_mover_for_protocol(*args, **kwargs)

Overloaded function.

  1. generate_mover_for_protocol(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, protocol_tag: pyrosetta.rosetta.utility.tag.Tag, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  2. generate_mover_for_protocol(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, protocol_tag: pyrosetta.rosetta.utility.tag.Tag, options: pyrosetta.rosetta.utility.options.OptionCollection, current_input_name: str) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  3. generate_mover_for_protocol(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, protocol_tag: pyrosetta.rosetta.utility.tag.Tag, options: pyrosetta.rosetta.utility.options.OptionCollection, current_input_name: str, current_output_name: str) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  4. generate_mover_for_protocol(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, protocol_tag: pyrosetta.rosetta.utility.tag.Tag, options: pyrosetta.rosetta.utility.options.OptionCollection, current_input_name: str, current_output_name: str, xml_objects: protocols::rosetta_scripts::XmlObjects) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  5. generate_mover_for_protocol(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, protocol_tag: pyrosetta.rosetta.utility.tag.Tag, options: pyrosetta.rosetta.utility.options.OptionCollection, current_input_name: str, current_output_name: str, xml_objects: protocols::rosetta_scripts::XmlObjects, resource_manager: pyrosetta.rosetta.basic.resource_manager.ResourceManager) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

Create the ParsedProtocolMover for the protocol using a tag.

Load the datamap with the predefined object, then go through tags, generating object and the ParsedProtocol Mover. READS from LOCAL OptionCollection.

C++: protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(class std::shared_ptr<const class utility::tag::Tag>, const class utility::options::OptionCollection &, const std::string &, const std::string &, class std::shared_ptr<class protocols::rosetta_scripts::XmlObjects>, class std::shared_ptr<class basic::resource_manager::ResourceManager>) –> class std::shared_ptr<class protocols::rosetta_scripts::ParsedProtocol>

  1. generate_mover_for_protocol(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, protocol_tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  2. generate_mover_for_protocol(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, protocol_tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, options: pyrosetta.rosetta.utility.options.OptionCollection, xml_objects: protocols::rosetta_scripts::XmlObjects) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  3. generate_mover_for_protocol(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, protocol_tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, options: pyrosetta.rosetta.utility.options.OptionCollection, xml_objects: protocols::rosetta_scripts::XmlObjects, resource_manager: pyrosetta.rosetta.basic.resource_manager.ResourceManager) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

Create the ParsedProtocolMover for the protocol using a tag.

Uses the passed DataMap for passing to parse_my_tag. This function does the heavy lifting.

Does not add any predefined objects to the data map (though in-tag defined objects will be added.)

C++: protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class utility::options::OptionCollection &, class std::shared_ptr<class protocols::rosetta_scripts::XmlObjects>, class std::shared_ptr<class basic::resource_manager::ResourceManager>) –> class std::shared_ptr<class protocols::rosetta_scripts::ParsedProtocol>

  1. generate_mover_for_protocol(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, : pyrosetta.rosetta.core.pose.Pose, : bool, protocol_tag: pyrosetta.rosetta.utility.tag.Tag, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  2. generate_mover_for_protocol(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, : pyrosetta.rosetta.core.pose.Pose, : bool, protocol_tag: pyrosetta.rosetta.utility.tag.Tag, options: pyrosetta.rosetta.utility.options.OptionCollection, current_input_name: str) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  3. generate_mover_for_protocol(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, : pyrosetta.rosetta.core.pose.Pose, : bool, protocol_tag: pyrosetta.rosetta.utility.tag.Tag, options: pyrosetta.rosetta.utility.options.OptionCollection, current_input_name: str, current_output_name: str) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  4. generate_mover_for_protocol(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, : pyrosetta.rosetta.core.pose.Pose, : bool, protocol_tag: pyrosetta.rosetta.utility.tag.Tag, options: pyrosetta.rosetta.utility.options.OptionCollection, current_input_name: str, current_output_name: str, xml_objects: protocols::rosetta_scripts::XmlObjects) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

  5. generate_mover_for_protocol(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, : pyrosetta.rosetta.core.pose.Pose, : bool, protocol_tag: pyrosetta.rosetta.utility.tag.Tag, options: pyrosetta.rosetta.utility.options.OptionCollection, current_input_name: str, current_output_name: str, xml_objects: protocols::rosetta_scripts::XmlObjects, resource_manager: pyrosetta.rosetta.basic.resource_manager.ResourceManager) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

Create the ParsedProtocolMover for the protocol using a tag.

This interface is preserved for (PyRosetta) backwards compatibility only. The Pose and bool (modified_pose) parameters are now unused.

C++: protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(class core::pose::Pose &, bool &, class std::shared_ptr<const class utility::tag::Tag>, const class utility::options::OptionCollection &, const std::string &, const std::string &, class std::shared_ptr<class protocols::rosetta_scripts::XmlObjects>, class std::shared_ptr<class basic::resource_manager::ResourceManager>) –> class std::shared_ptr<class protocols::rosetta_scripts::ParsedProtocol>

generate_mover_xml_string(*args, **kwargs)

Overloaded function.

  1. generate_mover_xml_string(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, options: pyrosetta.rosetta.utility.options.OptionCollection, xml_text: str, current_input_name: str, current_output_name: str, xml_objects: protocols::rosetta_scripts::XmlObjects) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

Convenience function to construct a ParsedProtocol from a string

Reads in an RosettaScript from file, replaces script_vars if present,

Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects

C++: protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_xml_string(const class utility::options::OptionCollection &, const std::string &, const std::string &, const std::string &, class std::shared_ptr<class protocols::rosetta_scripts::XmlObjects>) –> class std::shared_ptr<class protocols::rosetta_scripts::ParsedProtocol>

  1. generate_mover_xml_string(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, options: pyrosetta.rosetta.utility.options.OptionCollection, xml_text: str, current_input_name: str, current_output_name: str, xml_objects: protocols::rosetta_scripts::XmlObjects) -> pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

Convenience function to construct a ParsedProtocol from a string

Reads in an RosettaScript from file, replaces script_vars if present,

Then returns the full ParsedProtocol See also protocols::rosetta_scripts::XmlObjects

Places an OptionCollectionCOP into the datamap for local option parsing.

C++: protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_xml_string(class std::shared_ptr<const class utility::options::OptionCollection>, const std::string &, const std::string &, const std::string &, class std::shared_ptr<class protocols::rosetta_scripts::XmlObjects>) –> class std::shared_ptr<class protocols::rosetta_scripts::ParsedProtocol>

import_tags(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, import_tag_names: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_std_less_std_pair_std_string_std_string_std_allocator_std_pair_std_string_std_string_t, my_tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::rosetta_scripts::RosettaScriptsParser::import_tags(class std::set<struct std::pair<std::string, std::string >, struct std::less<struct std::pair<std::string, std::string > >, class std::allocator<struct std::pair<std::string, std::string > > > &, class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) const –> void

initialize_data_map(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, data: pyrosetta.rosetta.basic.datacache.DataMap, options: pyrosetta.rosetta.utility.options.OptionCollection) None

Initialize the passed datamap with the standard set of pre-defined RosettaScripts objects

C++: protocols::rosetta_scripts::RosettaScriptsParser::initialize_data_map(class basic::datacache::DataMap &, const class utility::options::OptionCollection &) –> void

instantiate_filter(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, tag_ptr: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

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

instantiate_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, tag_ptr: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

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

instantiate_packer_palette(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, tag_ptr: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Instantiate a PackerPalette object.

Vikram K. Mulligan (vmullig.edu).

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

instantiate_taskoperation(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, tag_ptr: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

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

parse_apply_to_pose_tag(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, apply_tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

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

parse_import_tag(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, import_tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

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

parse_protocol_tag(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, protocol_tag: pyrosetta.rosetta.utility.tag.Tag, options: pyrosetta.rosetta.utility.options.OptionCollection) pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol

Create the ParsedProtocolMover for the protocol using a tag.

Creates mover via standard parsing machinery

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

parse_resources_tag(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, resources_tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, resource_manager: pyrosetta.rosetta.basic.resource_manager.ResourceManager) None

C++: protocols::rosetta_scripts::RosettaScriptsParser::parse_resources_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, class std::shared_ptr<class basic::resource_manager::ResourceManager>) const –> void

protocol_option_set(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, options: pyrosetta.rosetta.utility.options.OptionCollection) bool

Checks the LOCAL options collection to see if a protocol has been set.

C++: protocols::rosetta_scripts::RosettaScriptsParser::protocol_option_set(const class utility::options::OptionCollection &) const –> bool

read_in_and_recursively_replace_includes(*args, **kwargs)

Overloaded function.

  1. read_in_and_recursively_replace_includes(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, filename: str, substituted_contents: str, filenames_encountered: pyrosetta.rosetta.utility.vector1_std_string, recursion_level: int) -> None

  2. read_in_and_recursively_replace_includes(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, filename: str, substituted_contents: str, filenames_encountered: pyrosetta.rosetta.utility.vector1_std_string, recursion_level: int, do_not_recurse: bool) -> None

  3. read_in_and_recursively_replace_includes(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, filename: str, substituted_contents: str, filenames_encountered: pyrosetta.rosetta.utility.vector1_std_string, recursion_level: int, do_not_recurse: bool, xml_text_for_top_level: str) -> None

Actually read in the XML file. Called recursively to read in XML files that

this XML file includes. At the end of this operation, substituted_contents contains the contents of the XML file, with all xi:includes replaced with the contents of included XML files. Files are opened and closed here.

Note that filenames_encountered is passed by copy rather than by reference DELIBERATELY. This is so that it remains a list of parent files, so that only circular dependencies (attempts to include one’s own parent, grandparent, etc.) are detected. If xml_text_for_top_level is set the filename passed will not be read and instead xml_text_for_top_level will be used as though it was the contents of the first file.

Vikram K. Mulligan (vmullig.edu)

Rocco Moretti (rmorettiase.com)

C++: protocols::rosetta_scripts::RosettaScriptsParser::read_in_and_recursively_replace_includes(const std::string &, std::string &, class utility::vector1<std::string, class std::allocator<std::string > >, const unsigned long, const bool, const std::string &) const –> void

static register_factory_prototypes() None

C++: protocols::rosetta_scripts::RosettaScriptsParser::register_factory_prototypes() –> void

static rosetta_scripts_complex_type_naming_func(element_name: str) str

C++: protocols::rosetta_scripts::RosettaScriptsParser::rosetta_scripts_complex_type_naming_func(const std::string &) –> std::string

static rosetta_scripts_element_name() str

C++: protocols::rosetta_scripts::RosettaScriptsParser::rosetta_scripts_element_name() –> std::string

set_recursion_limit(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, options: pyrosetta.rosetta.utility.options.OptionCollection) None

C++: protocols::rosetta_scripts::RosettaScriptsParser::set_recursion_limit(const class utility::options::OptionCollection &) –> void

static substitute_variables_in_stream(in: pyrosetta.rosetta.std.istream, script_vars: pyrosetta.rosetta.utility.vector1_std_string, out: pyrosetta.rosetta.std.stringstream) None

Substitute xx==yy using the XML syntax %%xx%%. / script_vars is a list of strings of “xx==yy”.

C++: protocols::rosetta_scripts::RosettaScriptsParser::substitute_variables_in_stream(std::istream &, const class utility::vector1<std::string, class std::allocator<std::string > > &, class std::basic_stringstream<char> &) –> void

validate_input_script_against_xsd(self: pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser, fname: str, input_xml: pyrosetta.rosetta.std.stringstream) None

C++: protocols::rosetta_scripts::RosettaScriptsParser::validate_input_script_against_xsd(const std::string &, const class std::basic_stringstream<char> &) const –> void

static write_ROSETTASCRIPTS_complex_type(: utility::tag::XMLSchemaDefinition) None

C++: protocols::rosetta_scripts::RosettaScriptsParser::write_ROSETTASCRIPTS_complex_type(class utility::tag::XMLSchemaDefinition &) –> void

static xsd_for_rosetta_scripts() str

C++: protocols::rosetta_scripts::RosettaScriptsParser::xsd_for_rosetta_scripts() –> std::string

class pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

mover that can be used to save or restore a pose at an arbitrary point during a rosetta scripts protocol. other movers or filters can be set up to access poses saved by this mover during their apply calls.

apply(self: pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::rosetta_scripts::SavePoseMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover, : pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover) pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover

C++: protocols::rosetta_scripts::SavePoseMover::operator=(const class protocols::rosetta_scripts::SavePoseMover &) –> class protocols::rosetta_scripts::SavePoseMover &

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.SavePoseMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::rosetta_scripts::SavePoseMover::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.SavePoseMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::rosetta_scripts::SavePoseMover::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_cloned_saved_pose(self: pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover) pyrosetta.rosetta.core.pose.Pose

Returns a cloned PoseOP of reference_pose_

C++: protocols::rosetta_scripts::SavePoseMover::get_cloned_saved_pose() const –> 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.SavePoseMover) str

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

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static mover_name() str

C++: protocols::rosetta_scripts::SavePoseMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::rosetta_scripts::SavePoseMover::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::SavePoseMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

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

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

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

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

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

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMoverCreator, : pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMoverCreator) pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMoverCreator

C++: protocols::rosetta_scripts::SavePoseMoverCreator::operator=(const class protocols::rosetta_scripts::SavePoseMoverCreator &) –> class protocols::rosetta_scripts::SavePoseMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMoverCreator) str

C++: protocols::rosetta_scripts::SavePoseMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects, src: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects) pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects

C++: protocols::rosetta_scripts::XmlObjects::operator=(const class protocols::rosetta_scripts::XmlObjects &) –> class protocols::rosetta_scripts::XmlObjects &

static create_from_file(*args, **kwargs)

Overloaded function.

  1. create_from_file(filename: str) -> pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects

Parses an xml file and returns an XmlObjects

The ParsedProtocol (xml script mover) is available as “ParsedProtocol”

C++: protocols::rosetta_scripts::XmlObjects::create_from_file(const std::string &) –> class std::shared_ptr<const class protocols::rosetta_scripts::XmlObjects>

  1. create_from_file(filename: str, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects

Parses an xml file and returns an XmlObjects

The ParsedProtocol (xml script mover) is available as “ParsedProtocol”

The pose parameter is ignored, and exists oly for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::create_from_file(const std::string &, class core::pose::Pose &) –> class std::shared_ptr<const class protocols::rosetta_scripts::XmlObjects>

  1. create_from_file(filename: str, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects

Parses an xml file and returns an XmlObjects

The ParsedProtocol (xml script mover) is available as “ParsedProtocol”

C++: protocols::rosetta_scripts::XmlObjects::create_from_file(const std::string &, const class utility::options::OptionCollection &) –> class std::shared_ptr<const class protocols::rosetta_scripts::XmlObjects>

  1. create_from_file(filename: str, : pyrosetta.rosetta.core.pose.Pose, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects

Parses an xml file and returns an XmlObjects

The ParsedProtocol (xml script mover) is available as “ParsedProtocol”

The pose parameter is ignored, and exists oly for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::create_from_file(const std::string &, class core::pose::Pose &, const class utility::options::OptionCollection &) –> class std::shared_ptr<const class protocols::rosetta_scripts::XmlObjects>

static create_from_string(*args, **kwargs)

Overloaded function.

  1. create_from_string(xml_text: str) -> pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects

Parses an xml-formatted string and returns an XmlObjects

This function will wrap your script with <ROSETTASCRIPTS>

if needed and will add a <PROTOCOLS> section if needed. The ParsedProtocol (xml script mover) is available as “ParsedProtocol”.

C++: protocols::rosetta_scripts::XmlObjects::create_from_string(const std::string &) –> class std::shared_ptr<const class protocols::rosetta_scripts::XmlObjects>

  1. create_from_string(xml_text: str, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects

Parses an xml-formatted string and returns an XmlObjects

This function will wrap your script with <ROSETTASCRIPTS>

if needed and will add a <PROTOCOLS> section if needed. The ParsedProtocol (xml script mover) is available as “ParsedProtocol”. The pose parameter is ignored, and provided only for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::create_from_string(const std::string &, class core::pose::Pose &) –> class std::shared_ptr<const class protocols::rosetta_scripts::XmlObjects>

  1. create_from_string(xml_text: str, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects

Parses an xml-formatted string and returns an XmlObjects

This function will wrap your script with <ROSETTASCRIPTS>

if needed and will add a <PROTOCOLS> section if needed. The ParsedProtocol (xml script mover) is available as “ParsedProtocol”.

C++: protocols::rosetta_scripts::XmlObjects::create_from_string(const std::string &, const class utility::options::OptionCollection &) –> class std::shared_ptr<const class protocols::rosetta_scripts::XmlObjects>

  1. create_from_string(xml_text: str, : pyrosetta.rosetta.core.pose.Pose, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects

Parses an xml-formatted string and returns an XmlObjects

This function will wrap your script with <ROSETTASCRIPTS>

if needed and will add a <PROTOCOLS> section if needed. The ParsedProtocol (xml script mover) is available as “ParsedProtocol”. The pose parameter is ignored, and exists only for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::create_from_string(const std::string &, class core::pose::Pose &, const class utility::options::OptionCollection &) –> class std::shared_ptr<const class protocols::rosetta_scripts::XmlObjects>

get_filter(self: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects, name: str) pyrosetta.rosetta.protocols.filters.Filter

Extract a Filter by name after using one of the create* methods

This returns a clone and cannot be used to modify the ParsedProtocol

C++: protocols::rosetta_scripts::XmlObjects::get_filter(const std::string &) const –> class std::shared_ptr<class protocols::filters::Filter>

get_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects, name: str) pyrosetta.rosetta.protocols.moves.Mover

Extract a Mover by name after using one of the create* methods

This returns a clone and cannot be used to modify the ParsedProtocol

C++: protocols::rosetta_scripts::XmlObjects::get_mover(const std::string &) const –> class std::shared_ptr<class protocols::moves::Mover>

get_residue_selector(self: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects, name: str) pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Extract a ResidueSelector by name after using one of the create* methods

This returns a clone and cannot be used to modify the ParsedProtocol

C++: protocols::rosetta_scripts::XmlObjects::get_residue_selector(const std::string &) const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_score_function(self: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects, name: str) pyrosetta.rosetta.core.scoring.ScoreFunction

Extract a ScoreFunction by name after using one of the create* methods

This returns a clone and cannot be used to modify the ParsedProtocol

C++: protocols::rosetta_scripts::XmlObjects::get_score_function(const std::string &) const –> class std::shared_ptr<class core::scoring::ScoreFunction>

get_simple_metric(self: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects, name: str) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Extract a SimpleMetric by name after using one of the create* methods

This returns a clone and cannot be used to modify the ParsedProtocol

C++: protocols::rosetta_scripts::XmlObjects::get_simple_metric(const std::string &) const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

get_task_operation(self: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects, name: str) pyrosetta.rosetta.core.pack.task.operation.TaskOperation

Extract a TaskOperation by name after using one of the create* methods

This returns a clone and cannot be used to modify the ParsedProtocol

C++: protocols::rosetta_scripts::XmlObjects::get_task_operation(const std::string &) const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

init_from_maps(self: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Initialization function from the DataMaps

C++: protocols::rosetta_scripts::XmlObjects::init_from_maps(class basic::datacache::DataMap &) –> void

list_filters(self: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects) pyrosetta.rosetta.utility.vector1_std_string

List all the Filters contained by name

C++: protocols::rosetta_scripts::XmlObjects::list_filters() const –> class utility::vector1<std::string, class std::allocator<std::string > >

list_movers(self: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects) pyrosetta.rosetta.utility.vector1_std_string

List all the Movers contained by name

C++: protocols::rosetta_scripts::XmlObjects::list_movers() const –> class utility::vector1<std::string, class std::allocator<std::string > >

list_residue_selectors(self: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects) pyrosetta.rosetta.utility.vector1_std_string

List all the ResidueSelectors contained by name

C++: protocols::rosetta_scripts::XmlObjects::list_residue_selectors() const –> class utility::vector1<std::string, class std::allocator<std::string > >

list_score_functions(self: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects) pyrosetta.rosetta.utility.vector1_std_string

List all the ScoreFunctions contained by name

C++: protocols::rosetta_scripts::XmlObjects::list_score_functions() const –> class utility::vector1<std::string, class std::allocator<std::string > >

list_simple_metrics(self: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects) pyrosetta.rosetta.utility.vector1_std_string

List all the SimpleMetrics contained by name

C++: protocols::rosetta_scripts::XmlObjects::list_simple_metrics() const –> class utility::vector1<std::string, class std::allocator<std::string > >

list_task_operations(self: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects) pyrosetta.rosetta.utility.vector1_std_string

List all the TaskOperations by name

C++: protocols::rosetta_scripts::XmlObjects::list_task_operations() const –> class utility::vector1<std::string, class std::allocator<std::string > >

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects) -> None

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

Generate string representation of XmlObjects for debugging purposes.

C++: protocols::rosetta_scripts::XmlObjects::show(std::ostream &) const –> void

static static_get_filter(*args, **kwargs)

Overloaded function.

  1. static_get_filter(xml_text: str) -> pyrosetta.rosetta.protocols.filters.Filter

Constructs a single Filter from xml

Pass this function a single Filter tag and it will

return to you that Filter. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call.

C++: protocols::rosetta_scripts::XmlObjects::static_get_filter(const std::string &) –> class std::shared_ptr<class protocols::filters::Filter>

  1. static_get_filter(xml_text: str, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.protocols.filters.Filter

Constructs a single Filter from xml

Pass this function a single Filter tag and it will

return to you that Filter. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call. The pose parameter is ignored, and exists only for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::static_get_filter(const std::string &, class core::pose::Pose &) –> class std::shared_ptr<class protocols::filters::Filter>

  1. static_get_filter(xml_text: str, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.protocols.filters.Filter

Constructs a single Filter from xml

Pass this function a single Filter tag and it will

return to you that Filter. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call.

C++: protocols::rosetta_scripts::XmlObjects::static_get_filter(const std::string &, const class utility::options::OptionCollection &) –> class std::shared_ptr<class protocols::filters::Filter>

  1. static_get_filter(xml_text: str, pose: pyrosetta.rosetta.core.pose.Pose, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.protocols.filters.Filter

Constructs a single Filter from xml

Pass this function a single Filter tag and it will

return to you that Filter. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call. The pose parameter is ignored, and exists only for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::static_get_filter(const std::string &, class core::pose::Pose &, const class utility::options::OptionCollection &) –> class std::shared_ptr<class protocols::filters::Filter>

static static_get_mover(*args, **kwargs)

Overloaded function.

  1. static_get_mover(xml_text: str) -> pyrosetta.rosetta.protocols.moves.Mover

Constructs a single Mover from xml

Pass this function a single Mover tag and it will

return to you that Mover. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call.

C++: protocols::rosetta_scripts::XmlObjects::static_get_mover(const std::string &) –> class std::shared_ptr<class protocols::moves::Mover>

  1. static_get_mover(xml_text: str, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.protocols.moves.Mover

Constructs a single Mover from xml

Pass this function a single Mover tag and it will

return to you that Mover. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call. The pose parameter is ignored, and exists only for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::static_get_mover(const std::string &, class core::pose::Pose &) –> class std::shared_ptr<class protocols::moves::Mover>

  1. static_get_mover(xml_text: str, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.protocols.moves.Mover

Constructs a single Mover from xml

Pass this function a single Mover tag and it will

return to you that Mover. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call.

C++: protocols::rosetta_scripts::XmlObjects::static_get_mover(const std::string &, const class utility::options::OptionCollection &) –> class std::shared_ptr<class protocols::moves::Mover>

  1. static_get_mover(xml_text: str, : pyrosetta.rosetta.core.pose.Pose, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.protocols.moves.Mover

Constructs a single Mover from xml

Pass this function a single Mover tag and it will

return to you that Mover. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call. The pose parameter is ignored, and exists only for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::static_get_mover(const std::string &, class core::pose::Pose &, const class utility::options::OptionCollection &) –> class std::shared_ptr<class protocols::moves::Mover>

static static_get_residue_selector(*args, **kwargs)

Overloaded function.

  1. static_get_residue_selector(xml_text: str) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Constructs a single ResidueSelector from xml

Pass this function a single ResidueSelector tag and it will

return to you that ResidueSelector. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call.

C++: protocols::rosetta_scripts::XmlObjects::static_get_residue_selector(const std::string &) –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

  1. static_get_residue_selector(xml_text: str, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Constructs a single ResidueSelector from xml

Pass this function a single ResidueSelector tag and it will

return to you that ResidueSelector. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call. The pose parameter is ignored, and exists only for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::static_get_residue_selector(const std::string &, class core::pose::Pose &) –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

  1. static_get_residue_selector(xml_text: str, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Constructs a single ResidueSelector from xml

Pass this function a single ResidueSelector tag and it will

return to you that ResidueSelector. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call.

C++: protocols::rosetta_scripts::XmlObjects::static_get_residue_selector(const std::string &, const class utility::options::OptionCollection &) –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

  1. static_get_residue_selector(xml_text: str, : pyrosetta.rosetta.core.pose.Pose, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Constructs a single ResidueSelector from xml

Pass this function a single ResidueSelector tag and it will

return to you that ResidueSelector. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call. The pose parameter is ignored, and exists only for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::static_get_residue_selector(const std::string &, class core::pose::Pose &, const class utility::options::OptionCollection &) –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

static static_get_score_function(*args, **kwargs)

Overloaded function.

  1. static_get_score_function(xml_text: str) -> pyrosetta.rosetta.core.scoring.ScoreFunction

Constructs a single ScoreFunction from xml

Pass this function a single <ScoreFunction /> tag and it will

return to you that ScoreFunction

C++: protocols::rosetta_scripts::XmlObjects::static_get_score_function(const std::string &) –> class std::shared_ptr<class core::scoring::ScoreFunction>

  1. static_get_score_function(xml_text: str, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.ScoreFunction

Constructs a single ScoreFunction from xml

Pass this function a single <ScoreFunction /> tag and it will

return to you that ScoreFunction The pose parameter is ignored, and exists only for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::static_get_score_function(const std::string &, class core::pose::Pose &) –> class std::shared_ptr<class core::scoring::ScoreFunction>

  1. static_get_score_function(xml_text: str, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.core.scoring.ScoreFunction

Constructs a single ScoreFunction from xml

Pass this function a single <ScoreFunction /> tag and it will

return to you that ScoreFunction

C++: protocols::rosetta_scripts::XmlObjects::static_get_score_function(const std::string &, const class utility::options::OptionCollection &) –> class std::shared_ptr<class core::scoring::ScoreFunction>

  1. static_get_score_function(xml_text: str, : pyrosetta.rosetta.core.pose.Pose, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.core.scoring.ScoreFunction

Constructs a single ScoreFunction from xml

Pass this function a single <ScoreFunction /> tag and it will

return to you that ScoreFunction The pose parameter is ignored, and exists only for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::static_get_score_function(const std::string &, class core::pose::Pose &, const class utility::options::OptionCollection &) –> class std::shared_ptr<class core::scoring::ScoreFunction>

static static_get_simple_metric(*args, **kwargs)

Overloaded function.

  1. static_get_simple_metric(xml_text: str) -> pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Constructs a single SimpleMetric from xml

Pass this function a single SimpleMetric tag and it will

return to you that SimpleMetric. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call.

C++: protocols::rosetta_scripts::XmlObjects::static_get_simple_metric(const std::string &) –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

  1. static_get_simple_metric(xml_text: str, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Constructs a single SimpleMetric from xml

Pass this function a single SimpleMetric tag and it will

return to you that SimpleMetric. For C++ users, you may need The pose parameter is ignored, and exists only for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::static_get_simple_metric(const std::string &, class core::pose::Pose &) –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

  1. static_get_simple_metric(xml_text: str, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Constructs a single SimpleMetric from xml

Pass this function a single SimpleMetric tag and it will

return to you that SimpleMetric. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call.

C++: protocols::rosetta_scripts::XmlObjects::static_get_simple_metric(const std::string &, const class utility::options::OptionCollection &) –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

  1. static_get_simple_metric(xml_text: str, : pyrosetta.rosetta.core.pose.Pose, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Constructs a single SimpleMetric from xml

Pass this function a single SimpleMetric tag and it will

return to you that SimpleMetric. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call. The pose parameter is ignored, and exists only for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::static_get_simple_metric(const std::string &, class core::pose::Pose &, const class utility::options::OptionCollection &) –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

static static_get_task_operation(*args, **kwargs)

Overloaded function.

  1. static_get_task_operation(xml_text: str) -> pyrosetta.rosetta.core.pack.task.operation.TaskOperation

Constructs a single TaskOperation from xml

Pass this function a single TaskOperation tag and it will

return to you that TaskOperation. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call.

C++: protocols::rosetta_scripts::XmlObjects::static_get_task_operation(const std::string &) –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

  1. static_get_task_operation(xml_text: str, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.pack.task.operation.TaskOperation

Constructs a single TaskOperation from xml

Pass this function a single TaskOperation tag and it will

return to you that TaskOperation. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call. The pose parameter is ignored, and exists only for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::static_get_task_operation(const std::string &, class core::pose::Pose &) –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

  1. static_get_task_operation(xml_text: str, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.core.pack.task.operation.TaskOperation

Constructs a single TaskOperation from xml

Pass this function a single TaskOperation tag and it will

return to you that TaskOperation. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call.

C++: protocols::rosetta_scripts::XmlObjects::static_get_task_operation(const std::string &, const class utility::options::OptionCollection &) –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

  1. static_get_task_operation(xml_text: str, : pyrosetta.rosetta.core.pose.Pose, options: pyrosetta.rosetta.utility.options.OptionCollection) -> pyrosetta.rosetta.core.pack.task.operation.TaskOperation

Constructs a single TaskOperation from xml

Pass this function a single TaskOperation tag and it will

return to you that TaskOperation. For C++ users, you may need to use std::dynamic_pointer_cast< > after this call. The pose parameter is ignored, and exists only for backwards compatibility.

C++: protocols::rosetta_scripts::XmlObjects::static_get_task_operation(const std::string &, class core::pose::Pose &, const class utility::options::OptionCollection &) –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

pyrosetta.rosetta.protocols.rosetta_scripts.append_subelement_for_parse_movemap_factory_legacy(*args, **kwargs)

Overloaded function.

  1. append_subelement_for_parse_movemap_factory_legacy(xsd: utility::tag::XMLSchemaDefinition, subelements: utility::tag::XMLSchemaSimpleSubelementList) -> None

  2. append_subelement_for_parse_movemap_factory_legacy(xsd: utility::tag::XMLSchemaDefinition, subelements: utility::tag::XMLSchemaSimpleSubelementList, description: str) -> None

Adds a subelement to an input subelement list describing a MoveMap subtag

that will be used by the parse_movemap_legacy function.

C++: protocols::rosetta_scripts::append_subelement_for_parse_movemap_factory_legacy(class utility::tag::XMLSchemaDefinition &, class utility::tag::XMLSchemaSimpleSubelementList &, const std::string &) –> void

pyrosetta.rosetta.protocols.rosetta_scripts.attributes_for_parse_database_session(xsd: utility::tag::XMLSchemaDefinition, attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) None

C++: protocols::rosetta_scripts::attributes_for_parse_database_session(class utility::tag::XMLSchemaDefinition &, class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.rosetta_scripts.attributes_for_parse_residue_selector(*args, **kwargs)

Overloaded function.

  1. attributes_for_parse_residue_selector(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None

  2. attributes_for_parse_residue_selector(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, description: str) -> None

Appends the attributes read by parse_residue_selector

C++: protocols::rosetta_scripts::attributes_for_parse_residue_selector(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const std::string &) –> void

pyrosetta.rosetta.protocols.rosetta_scripts.attributes_for_parse_xyz_vector(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) None

C++: protocols::rosetta_scripts::attributes_for_parse_xyz_vector(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.rosetta_scripts.attributes_for_saved_reference_pose(*args, **kwargs)

Overloaded function.

  1. attributes_for_saved_reference_pose(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None

  2. attributes_for_saved_reference_pose(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, attribute_name: str) -> None

convenience function to access pointers to poses that will be stored

in the data map at an arbitrary point during an RS protocol Will look for tag in in_tag variable

C++: protocols::rosetta_scripts::attributes_for_saved_reference_pose(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const std::string &) –> void

pyrosetta.rosetta.protocols.rosetta_scripts.attributes_for_saved_reference_pose_w_description(*args, **kwargs)

Overloaded function.

  1. attributes_for_saved_reference_pose_w_description(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, description: str) -> None

  2. attributes_for_saved_reference_pose_w_description(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, description: str, attribute_name: str) -> None

convenience function to access pointers to poses that will be stored

in the data map at an arbitrary point during an RS protocol Will look for tag in in_tag variable

C++: protocols::rosetta_scripts::attributes_for_saved_reference_pose_w_description(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const std::string &, const std::string &) –> void

pyrosetta.rosetta.protocols.rosetta_scripts.find_nearest_disulfide(pose: pyrosetta.rosetta.core.pose.Pose, res: int) int

finds the nearest disulife to given residue on pose by searching both up and down stream to the given postion

C++: protocols::rosetta_scripts::find_nearest_disulfide(const class core::pose::Pose &, const unsigned long) –> unsigned long

pyrosetta.rosetta.protocols.rosetta_scripts.find_nearest_res(*args, **kwargs)

Overloaded function.

  1. find_nearest_res(source: pyrosetta.rosetta.core.pose.Pose, target: pyrosetta.rosetta.core.pose.Pose, res: int) -> int

  2. find_nearest_res(source: pyrosetta.rosetta.core.pose.Pose, target: pyrosetta.rosetta.core.pose.Pose, res: int, chain: int) -> int

find source residue that is nearest to res on source. If distance is greater than 2.0A, return 0. chain=0, search all chains, chain=1,2,3 etc. search only that chain

C++: protocols::rosetta_scripts::find_nearest_res(const class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, const unsigned long) –> unsigned long

  1. find_nearest_res(source: pyrosetta.rosetta.core.pose.Pose, target: pyrosetta.rosetta.core.pose.Pose, res: int, target_res: int, dist: float) -> None

  2. find_nearest_res(source: pyrosetta.rosetta.core.pose.Pose, target: pyrosetta.rosetta.core.pose.Pose, res: int, target_res: int, dist: float, chain: int) -> None

find nearest residue and also return the distance

C++: protocols::rosetta_scripts::find_nearest_res(const class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, unsigned long &, double &, const unsigned long) –> void

pyrosetta.rosetta.protocols.rosetta_scripts.legacy_saved_pose_or_input(*args, **kwargs)

Overloaded function.

  1. legacy_saved_pose_or_input(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, class_name: str) -> pyrosetta.rosetta.core.pose.Pose

  2. legacy_saved_pose_or_input(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, class_name: str, use_native: bool) -> pyrosetta.rosetta.core.pose.Pose

  3. legacy_saved_pose_or_input(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, class_name: str, use_native: bool, refname: str) -> pyrosetta.rosetta.core.pose.Pose

Retrieve the reference pose. If not given, fall back to the native pose (if asked for),

or the input pose as a last resort. Will print a warning message if the input pose is used.

The XSD is the same as for saved_reference_pose.

C++: protocols::rosetta_scripts::legacy_saved_pose_or_input(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const std::string &, bool, const std::string &) –> class std::shared_ptr<const class core::pose::Pose>

pyrosetta.rosetta.protocols.rosetta_scripts.parse_database_session(tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) pyrosetta.rosetta.utility.sql_database.session

C++: protocols::rosetta_scripts::parse_database_session(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> class std::shared_ptr<class utility::sql_database::session>

pyrosetta.rosetta.protocols.rosetta_scripts.parse_filter(filter_name: str, d: pyrosetta.rosetta.basic.datacache.DataMap) pyrosetta.rosetta.protocols.filters.Filter

Return the Filter with the given name. Raise a RosettaScriptsOptionError if not present

C++: protocols::rosetta_scripts::parse_filter(const std::string &, const class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::filters::Filter>

pyrosetta.rosetta.protocols.rosetta_scripts.parse_filter_or_null(filter_name: str, d: pyrosetta.rosetta.basic.datacache.DataMap) pyrosetta.rosetta.protocols.filters.Filter

Return the Filter with the given name. Return nullptr if not present.

C++: protocols::rosetta_scripts::parse_filter_or_null(const std::string &, const class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::filters::Filter>

pyrosetta.rosetta.protocols.rosetta_scripts.parse_movemap_factory_legacy(*args, **kwargs)

Overloaded function.

  1. parse_movemap_factory_legacy(in_tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.core.select.movemap.MoveMapFactory

  2. parse_movemap_factory_legacy(in_tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, reset_movemap: bool) -> pyrosetta.rosetta.core.select.movemap.MoveMapFactory

  3. parse_movemap_factory_legacy(in_tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, reset_movemap: bool, mmf_to_modify: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) -> pyrosetta.rosetta.core.select.movemap.MoveMapFactory

Parse a MoveMap factory from tags using the old MoveMap specification syntax.

Will return nullptr if the tag doesn’t contain a MoveMap specification.

C++: protocols::rosetta_scripts::parse_movemap_factory_legacy(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const bool, class std::shared_ptr<class core::select::movemap::MoveMapFactory>) –> class std::shared_ptr<class core::select::movemap::MoveMapFactory>

pyrosetta.rosetta.protocols.rosetta_scripts.parse_mover(mover_name: str, d: pyrosetta.rosetta.basic.datacache.DataMap) pyrosetta.rosetta.protocols.moves.Mover

Return the Mover with the given name. Raise a RosettaScriptsOptionError if not present

C++: protocols::rosetta_scripts::parse_mover(const std::string &, const class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::moves::Mover>

pyrosetta.rosetta.protocols.rosetta_scripts.parse_mover_or_null(mover_name: str, d: pyrosetta.rosetta.basic.datacache.DataMap) pyrosetta.rosetta.protocols.moves.Mover

Return the Mover with the given name. Return nullptr if not present.

C++: protocols::rosetta_scripts::parse_mover_or_null(const std::string &, const class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::moves::Mover>

pyrosetta.rosetta.protocols.rosetta_scripts.parse_named_movemap_factory_legacy(*args, **kwargs)

Overloaded function.

  1. parse_named_movemap_factory_legacy(in_tag: pyrosetta.rosetta.utility.tag.Tag, name: str, data: pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.core.select.movemap.MoveMapFactory

  2. parse_named_movemap_factory_legacy(in_tag: pyrosetta.rosetta.utility.tag.Tag, name: str, data: pyrosetta.rosetta.basic.datacache.DataMap, reset_movemap: bool) -> pyrosetta.rosetta.core.select.movemap.MoveMapFactory

  3. parse_named_movemap_factory_legacy(in_tag: pyrosetta.rosetta.utility.tag.Tag, name: str, data: pyrosetta.rosetta.basic.datacache.DataMap, reset_movemap: bool, mmf_to_modify: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) -> pyrosetta.rosetta.core.select.movemap.MoveMapFactory

Parse a MoveMap factory from tags using the old MoveMap specification syntax.

Will look for a MoveMap entry with a particular name entry.

Will return nullptr if the tag doesn’t contain a MoveMap specification.

C++: protocols::rosetta_scripts::parse_named_movemap_factory_legacy(class std::shared_ptr<const class utility::tag::Tag>, const std::string &, class basic::datacache::DataMap &, const bool, class std::shared_ptr<class core::select::movemap::MoveMapFactory>) –> class std::shared_ptr<class core::select::movemap::MoveMapFactory>

pyrosetta.rosetta.protocols.rosetta_scripts.parse_xyz_vector(xyz_vector_tag: pyrosetta.rosetta.utility.tag.Tag) pyrosetta.rosetta.numeric.xyzVector_double_t

///////////////// XYZ Vector /////////////////////////

C++: protocols::rosetta_scripts::parse_xyz_vector(class std::shared_ptr<const class utility::tag::Tag>) –> class numeric::xyzVector<double>

pyrosetta.rosetta.protocols.rosetta_scripts.print_information(*args, **kwargs)

Overloaded function.

  1. print_information(component_name: str, outstream: pyrosetta.rosetta.std.stringstream) -> bool

Prints out XSD information about the XML-accessible options for a given RosettaScipts-accessible

mover, filter, task operation, residue selector, simple_metric, or packer palette.

Returns true for FAILURE to find the given component, false otherwise.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::rosetta_scripts::print_information(const std::string &, class std::basic_stringstream<char> &) –> bool

  1. print_information(component_names: pyrosetta.rosetta.utility.vector1_std_string) -> None

Prints out XSD information about the XML-accessible options for a given set of RosettaScipts-accessible

movers, filters, task operations, residue selectors, simple metrics, or packer palettes.

Calls the single string version.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::rosetta_scripts::print_information(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

pyrosetta.rosetta.protocols.rosetta_scripts.print_template_script() None

Prints out an empty template RosettaScript to the tracer.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::rosetta_scripts::print_template_script() –> void

pyrosetta.rosetta.protocols.rosetta_scripts.residue_packer_states(pose: pyrosetta.rosetta.core.pose.Pose, tf: pyrosetta.rosetta.core.pack.task.TaskFactory, designable: bool, packable: bool) pyrosetta.rosetta.utility.vector1_unsigned_long

returns a vector containing all the residues with a given packer state according to the TF

C++: protocols::rosetta_scripts::residue_packer_states(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::TaskFactory>, const bool, const bool) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.rosetta_scripts.save_schema(filename: str) None

Saves the XSD to the given file.

C++: protocols::rosetta_scripts::save_schema(const std::string &) –> void

pyrosetta.rosetta.protocols.rosetta_scripts.saved_reference_pose(*args, **kwargs)

Overloaded function.

  1. saved_reference_pose(in_tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.core.pose.Pose

  2. saved_reference_pose(in_tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap, tag_str: str) -> pyrosetta.rosetta.core.pose.Pose

///////////////// Reference Pose ///////////////////////

C++: protocols::rosetta_scripts::saved_reference_pose(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const std::string &) –> class std::shared_ptr<class core::pose::Pose>