minimization_packing

Bindings for protocols::minimization_packing namespace

class pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::minimization_packing::BoltzmannRotamerMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, : pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover

C++: protocols::minimization_packing::BoltzmannRotamerMover::operator=(const class protocols::minimization_packing::BoltzmannRotamerMover &) –> class protocols::minimization_packing::BoltzmannRotamerMover &

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.minimization_packing.BoltzmannRotamerMover) pyrosetta.rosetta.protocols.moves.Mover

clone this object

C++: protocols::minimization_packing::BoltzmannRotamerMover::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.minimization_packing.BoltzmannRotamerMover) pyrosetta.rosetta.protocols.moves.Mover

create this type of object

C++: protocols::minimization_packing::BoltzmannRotamerMover::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_bias_sampling(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) bool

C++: protocols::minimization_packing::BoltzmannRotamerMover::get_bias_sampling() const –> bool

get_bump_check(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) bool

C++: protocols::minimization_packing::BoltzmannRotamerMover::get_bump_check() const –> bool

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_ligand_resnum(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) int

C++: protocols::minimization_packing::BoltzmannRotamerMover::get_ligand_resnum() const –> unsigned long

get_ligand_weight(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) float

C++: protocols::minimization_packing::BoltzmannRotamerMover::get_ligand_weight() const –> double

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) str

C++: protocols::minimization_packing::BoltzmannRotamerMover::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_randomize_resnum(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) bool

C++: protocols::minimization_packing::BoltzmannRotamerMover::get_randomize_resnum() const –> bool

get_resnum(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) int

C++: protocols::minimization_packing::BoltzmannRotamerMover::get_resnum() const –> unsigned long

get_scorefxn(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::minimization_packing::BoltzmannRotamerMover::get_scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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

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

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

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

get_task(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) pyrosetta.rosetta.core.pack.task.PackerTask

C++: protocols::minimization_packing::BoltzmannRotamerMover::get_task() const –> class std::shared_ptr<class core::pack::task::PackerTask>

get_temperature(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover) float

C++: protocols::minimization_packing::BoltzmannRotamerMover::get_temperature() const –> double

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::minimization_packing::BoltzmannRotamerMover::mover_name() –> std::string

static name() str

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

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

C++: protocols::minimization_packing::BoltzmannRotamerMover::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::minimization_packing::BoltzmannRotamerMover::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

select_rotamer(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, boltzmann_factors: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_double_t, partition_function: float) int

C++: protocols::minimization_packing::BoltzmannRotamerMover::select_rotamer(const class utility::vector1<struct std::pair<unsigned long, double>, class std::allocator<struct std::pair<unsigned long, double> > > &, const double &) –> unsigned long

set_bias_sampling(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, bias_sampling: bool) None

C++: protocols::minimization_packing::BoltzmannRotamerMover::set_bias_sampling(bool) –> void

set_bump_check(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, bump_check: bool) None

C++: protocols::minimization_packing::BoltzmannRotamerMover::set_bump_check(bool) –> 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_ligand_resnum(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, ligand_resnum: int) None

C++: protocols::minimization_packing::BoltzmannRotamerMover::set_ligand_resnum(unsigned long) –> void

set_ligand_weight(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, ligand_weight: float) None

C++: protocols::minimization_packing::BoltzmannRotamerMover::set_ligand_weight(double) –> void

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

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

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

set_randomize_resnum(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, randomize_resnum: bool) None

C++: protocols::minimization_packing::BoltzmannRotamerMover::set_randomize_resnum(bool) –> void

set_resnum(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, resnum: int) None

C++: protocols::minimization_packing::BoltzmannRotamerMover::set_resnum(unsigned long) –> void

set_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::minimization_packing::BoltzmannRotamerMover::set_score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::minimization_packing::BoltzmannRotamerMover::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_task(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, task: pyrosetta.rosetta.core.pack.task.PackerTask) None

C++: protocols::minimization_packing::BoltzmannRotamerMover::set_task(class std::shared_ptr<class core::pack::task::PackerTask>) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::minimization_packing::BoltzmannRotamerMover::set_task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

set_temperature(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, temperature: float) None

C++: protocols::minimization_packing::BoltzmannRotamerMover::set_temperature(double) –> 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.minimization_packing.BoltzmannRotamerMover) -> None

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

C++: protocols::minimization_packing::BoltzmannRotamerMover::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.minimization_packing.BoltzmannRotamerMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator

C++: protocols::minimization_packing::BoltzmannRotamerMoverCreator::operator=(const class protocols::minimization_packing::BoltzmannRotamerMoverCreator &) –> class protocols::minimization_packing::BoltzmannRotamerMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator) str

C++: protocols::minimization_packing::BoltzmannRotamerMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator

Bases: pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator

assign(self: pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator, : pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator) pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator

C++: protocols::minimization_packing::ChainGroupDiscriminator::operator=(const class protocols::minimization_packing::ChainGroupDiscriminator &) –> class protocols::minimization_packing::ChainGroupDiscriminator &

clone(self: pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator) pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator

C++: protocols::minimization_packing::ChainGroupDiscriminator::clone() const –> class std::shared_ptr<class protocols::minimization_packing::GroupDiscriminator>

group_id(self: pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) int

C++: protocols::minimization_packing::ChainGroupDiscriminator::group_id(const class core::pose::Pose &, unsigned long) const –> unsigned long

class pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

A Mover to jointly optimize the geometry of a pair of disulfide-bonded residues.

apply(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Apply the mover

C++: protocols::minimization_packing::DisulfideOptimizationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover, : pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover) pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover

C++: protocols::minimization_packing::DisulfideOptimizationMover::operator=(const class protocols::minimization_packing::DisulfideOptimizationMover &) –> class protocols::minimization_packing::DisulfideOptimizationMover &

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.minimization_packing.DisulfideOptimizationMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::minimization_packing::DisulfideOptimizationMover::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.minimization_packing.DisulfideOptimizationMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover) str

C++: protocols::minimization_packing::DisulfideOptimizationMover::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 > > &

interaction_graph_threads(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover) int

Set threads to request for packing.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::minimization_packing::DisulfideOptimizationMover::interaction_graph_threads() const –> unsigned long

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::minimization_packing::DisulfideOptimizationMover::mover_name() –> std::string

static name() str

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

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

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

C++: protocols::minimization_packing::DisulfideOptimizationMover::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::minimization_packing::DisulfideOptimizationMover::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_final_optimization_n_iter(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover, final_optimization_n_iter: int) None

C++: protocols::minimization_packing::DisulfideOptimizationMover::set_final_optimization_n_iter(const unsigned long) –> void

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

setter for poses contained for rms

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

set_interaction_graph_threads(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover, setting: int) None

Set threads to request for packing.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::minimization_packing::DisulfideOptimizationMover::set_interaction_graph_threads(const unsigned long) –> 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_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::minimization_packing::DisulfideOptimizationMover::set_score_function(const class std::shared_ptr<const class core::scoring::ScoreFunction> &) –> void

set_selector(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: protocols::minimization_packing::DisulfideOptimizationMover::set_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> 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.minimization_packing.DisulfideOptimizationMover) -> None

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

C++: protocols::minimization_packing::DisulfideOptimizationMover::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.minimization_packing.DisulfideOptimizationMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator

C++: protocols::minimization_packing::DisulfideOptimizationMoverCreator::operator=(const class protocols::minimization_packing::DisulfideOptimizationMoverCreator &) –> class protocols::minimization_packing::DisulfideOptimizationMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator) str

C++: protocols::minimization_packing::DisulfideOptimizationMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover

Bases: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover

Wrapper for Rotamer Trials with Minimization, which modifies only rotamers whose energy changed by a given constant

apply(self: pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None

apply this mover to a pose

C++: protocols::minimization_packing::EnergyCutRotamerTrialsMinMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover, : pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover) pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover

C++: protocols::minimization_packing::EnergyCutRotamerTrialsMinMover::operator=(const class protocols::minimization_packing::EnergyCutRotamerTrialsMinMover &) –> class protocols::minimization_packing::EnergyCutRotamerTrialsMinMover &

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.minimization_packing.RotamerTrialsMinMover) pyrosetta.rosetta.protocols.moves.Mover

Return a copy of this mover instance (for RosettaScripts)

C++: protocols::minimization_packing::RotamerTrialsMinMover::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.minimization_packing.RotamerTrialsMinMover) pyrosetta.rosetta.protocols.moves.Mover

Return a new mover instance (for RosettaScripts)

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover) str

C++: protocols::minimization_packing::EnergyCutRotamerTrialsMinMover::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 > > &

init(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover) None

C++: protocols::minimization_packing::RotamerTrialsMinMover::init() –> void

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

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

static mover_name() str

C++: protocols::minimization_packing::RotamerTrialsMinMover::mover_name() –> std::string

static name() str

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

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

Parse XML for RosettaScripts

C++: protocols::minimization_packing::RotamerTrialsMinMover::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::minimization_packing::RotamerTrialsMinMover::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

score_function(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::minimization_packing::RotamerTrialsMinMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.minimization_packing.RotamerTrialsMinMover) -> None

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

C++: protocols::minimization_packing::RotamerTrialsMinMover::show(std::ostream &) const –> void

task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::minimization_packing::RotamerTrialsMinMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> 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.minimization_packing.EnergyCutRotamerTrialsMover

Bases: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover

apply(self: pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover, pose: pyrosetta.rosetta.core.pose.Pose) None

apply this mover to a pose

C++: protocols::minimization_packing::EnergyCutRotamerTrialsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover, : pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover) pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover

C++: protocols::minimization_packing::EnergyCutRotamerTrialsMover::operator=(const class protocols::minimization_packing::EnergyCutRotamerTrialsMover &) –> class protocols::minimization_packing::EnergyCutRotamerTrialsMover &

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.minimization_packing.RotamerTrialsMover) pyrosetta.rosetta.protocols.moves.Mover

clone this object

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

static complex_type_generator_for_rotamer_trials_mover(xsd: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator

C++: protocols::minimization_packing::RotamerTrialsMover::complex_type_generator_for_rotamer_trials_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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.minimization_packing.RotamerTrialsMover) pyrosetta.rosetta.protocols.moves.Mover

create this type of object

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover) str

C++: protocols::minimization_packing::EnergyCutRotamerTrialsMover::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::minimization_packing::RotamerTrialsMover::mover_name() –> std::string

static name() str

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

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

C++: protocols::minimization_packing::RotamerTrialsMover::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::minimization_packing::RotamerTrialsMover::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

score_function(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::minimization_packing::RotamerTrialsMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.minimization_packing.RotamerTrialsMover) -> None

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

C++: protocols::minimization_packing::RotamerTrialsMover::show(std::ostream &) const –> void

task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::minimization_packing::RotamerTrialsMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> 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.minimization_packing.GreenPacker

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.minimization_packing.GreenPacker, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::minimization_packing::GreenPacker::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.GreenPacker, : pyrosetta.rosetta.protocols.minimization_packing.GreenPacker) pyrosetta.rosetta.protocols.minimization_packing.GreenPacker

C++: protocols::minimization_packing::GreenPacker::operator=(const class protocols::minimization_packing::GreenPacker &) –> class protocols::minimization_packing::GreenPacker &

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

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

Generates a new Mover object freshly created with the default ctor.

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.GreenPacker) str

C++: protocols::minimization_packing::GreenPacker::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.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::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_group_discriminator(self: pyrosetta.rosetta.protocols.minimization_packing.GreenPacker, : pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator) None

C++: protocols::minimization_packing::GreenPacker::set_group_discriminator(class std::shared_ptr<class protocols::minimization_packing::GroupDiscriminator>) –> 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_reference_round_task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.GreenPacker, : pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::minimization_packing::GreenPacker::set_reference_round_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

set_scorefunction(self: pyrosetta.rosetta.protocols.minimization_packing.GreenPacker, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::minimization_packing::GreenPacker::set_scorefunction(const class core::scoring::ScoreFunction &) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.GreenPacker, : pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::minimization_packing::GreenPacker::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

  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.minimization_packing.GroupDiscriminator

Bases: pybind11_builtins.pybind11_object

Interface class used to break a pose down into a set of component “groups” where intra-group rotamer-pair energies are preserved between calls to the GreenPacker. E.g. in rigid-body docking between two proteins, chains 1 and 2 define groups 1 and 2. In rigid-body docking between two domains of the same chain, those residues upstream of jump 1 define group 1, and those downstream of jump 1 define group 2. In loop modelling, the static background is group 1, and the loop itself is group 0, since loop residues will have their bb dofs change regularly between repackings.

assign(self: pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator, : pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator) pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator

C++: protocols::minimization_packing::GroupDiscriminator::operator=(const class protocols::minimization_packing::GroupDiscriminator &) –> class protocols::minimization_packing::GroupDiscriminator &

clone(self: pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator) pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator

C++: protocols::minimization_packing::GroupDiscriminator::clone() const –> class std::shared_ptr<class protocols::minimization_packing::GroupDiscriminator>

group_id(self: pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) int

C++: protocols::minimization_packing::GroupDiscriminator::group_id(const class core::pose::Pose &, unsigned long) const –> unsigned long

class pyrosetta.rosetta.protocols.minimization_packing.MinMover

Bases: pyrosetta.rosetta.protocols.moves.MoveMapMover

A protocols::moves::Mover that minimizes a Pose to a local energy minimum by performing energy minimization of a ScoreFunction over the allowable degrees of freedom, defined by a MoveMap. The minimization type, minimization tolerance, and various other options can be also be set.

Common Methods:

MinMover.apply MinMover.movemap MinMover.score_function

abs_score_convergence_threshold(*args, **kwargs)

Overloaded function.

  1. abs_score_convergence_threshold(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, newval: float) -> None

C++: protocols::minimization_packing::MinMover::abs_score_convergence_threshold(double) –> void

  1. abs_score_convergence_threshold(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> float

C++: protocols::minimization_packing::MinMover::abs_score_convergence_threshold() const –> double

abs_score_diff_after_minimization(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) float

C++: protocols::minimization_packing::MinMover::abs_score_diff_after_minimization() const –> double

apply(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, pose: pyrosetta.rosetta.core.pose.Pose) None
Minimizes the DOFs of <pose_> specified in the MoveMap

using the ScoreFunction

example(s):

minmover.apply(pose)

See also:

MinMover MinMover.movemap MinMover.score_function

C++: protocols::minimization_packing::MinMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, : pyrosetta.rosetta.protocols.minimization_packing.MinMover) pyrosetta.rosetta.protocols.minimization_packing.MinMover

C++: protocols::minimization_packing::MinMover::operator=(const class protocols::minimization_packing::MinMover &) –> class protocols::minimization_packing::MinMover &

cartesian(*args, **kwargs)

Overloaded function.

  1. cartesian(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, newval: bool) -> None

C++: protocols::minimization_packing::MinMover::cartesian(bool) –> void

  1. cartesian(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> bool

C++: protocols::minimization_packing::MinMover::cartesian() const –> bool

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) pyrosetta.rosetta.protocols.moves.Mover

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

static complex_type_generator_for_min_mover(xsd: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator

C++: protocols::minimization_packing::MinMover::complex_type_generator_for_min_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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>

deriv_check(*args, **kwargs)

Overloaded function.

  1. deriv_check(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, deriv_check_in: bool) -> None

C++: protocols::minimization_packing::MinMover::deriv_check(bool) –> void

  1. deriv_check(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> bool

C++: protocols::minimization_packing::MinMover::deriv_check() const –> bool

explicitly_set_movemap(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) pyrosetta.rosetta.core.kinematics.MoveMap
Get the explicitly set movemap object, if present, nullptr if not

Will not create a default or look at the MoveMapFactory

C++: protocols::minimization_packing::MinMover::explicitly_set_movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

fresh_instance(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) str

C++: protocols::minimization_packing::MinMover::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 > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

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

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

max_iter(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, max_iter_in: int) None

C++: protocols::minimization_packing::MinMover::max_iter(unsigned long) –> void

min_options(*args, **kwargs)

Overloaded function.

  1. min_options(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> pyrosetta.rosetta.core.optimization.MinimizerOptions

allow non-const access to the internal minimizer options object

C++: protocols::minimization_packing::MinMover::min_options() –> class std::shared_ptr<class core::optimization::MinimizerOptions>

  1. min_options(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, min_options: pyrosetta.rosetta.core.optimization.MinimizerOptions) -> None

directly set the internal minimizer options object

C++: protocols::minimization_packing::MinMover::min_options(class std::shared_ptr<class core::optimization::MinimizerOptions>) –> void

min_type(*args, **kwargs)

Overloaded function.

  1. min_type(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, min_type_in: str) -> None

C++: protocols::minimization_packing::MinMover::min_type(std::string) –> void

  1. min_type(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> str

C++: protocols::minimization_packing::MinMover::min_type() const –> std::string

movemap(*args, **kwargs)

Overloaded function.

  1. movemap(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, movemap_in: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

Sets the MoveMap to <movemap_in>

determines which DOF to minimize

example(s):

minmover.movemap(movemap1)

See also:

MinMover MinMover.apply MinMover.score_function MoveMap

C++: protocols::minimization_packing::MinMover::movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

  1. movemap(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

Get the movemap for the pose

This is the preferred version to call.

C++: protocols::minimization_packing::MinMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap_factory(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, mmf: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) None
Sets the MoveMapFactory

The MoveMapFactory will be used to construct a MoveMap if an explicit one isn’t set

C++: protocols::minimization_packing::MinMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

static mover_name() str

C++: protocols::minimization_packing::MinMover::mover_name() –> std::string

static name() str

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

nb_list(*args, **kwargs)

Overloaded function.

  1. nb_list(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, nb_list_in: bool) -> None

core::optimization::MinimizerOptions::use_nblist(bool)

C++: protocols::minimization_packing::MinMover::nb_list(bool) –> void

  1. nb_list(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> bool

core::optimization::MinimizerOptions::use_nblist()

C++: protocols::minimization_packing::MinMover::nb_list() const –> bool

omega(*args, **kwargs)

Overloaded function.

  1. omega(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> bool

C++: protocols::minimization_packing::MinMover::omega() const –> bool

  1. omega(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, b: bool) -> None

C++: protocols::minimization_packing::MinMover::omega(const bool) –> void

parse_dof_task_type(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, tag_name: str, dof_type: pyrosetta.rosetta.core.id.DOF_Type, torsion_type: pyrosetta.rosetta.core.id.TorsionType, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::minimization_packing::MinMover::parse_dof_task_type(const std::string &, enum core::id::DOF_Type, enum core::id::TorsionType, class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_dof_tasks(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::minimization_packing::MinMover::parse_dof_tasks(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_movemap_factory(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::minimization_packing::MinMover::parse_movemap_factory(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

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

Called by protocols::moves::MoverFactory when constructing new protocols::moves::Movers. Takes care of the specific mover’s parsing.

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

parse_opts(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, : pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::minimization_packing::MinMover::parse_opts(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::minimization_packing::MinMover::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

score_diff_after_minimization(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) float

C++: protocols::minimization_packing::MinMover::score_diff_after_minimization() const –> double

score_function(*args, **kwargs)

Overloaded function.

  1. score_function(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Sets the ScoreFunction to <scorefxn_in>

determines which function to minimize

example(s):

minmover.score_function(scorefxn)

See also:

MinMover MinMover.apply MinMover.movemap ScoreFunction

C++: protocols::minimization_packing::MinMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

  1. score_function(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::minimization_packing::MinMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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

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

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

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

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

setter for poses contained for rms

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

set_movemap(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, movemap_in: pyrosetta.rosetta.core.kinematics.MoveMap) None

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

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

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

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

set_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.minimization_packing.MinMover) -> None

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

C++: protocols::minimization_packing::MinMover::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

tolerance(*args, **kwargs)

Overloaded function.

  1. tolerance(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover, tolerance_in: float) -> None

C++: protocols::minimization_packing::MinMover::tolerance(double) –> void

  1. tolerance(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> float

C++: protocols::minimization_packing::MinMover::tolerance() const –> double

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.minimization_packing.MinMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator

C++: protocols::minimization_packing::MinMoverCreator::operator=(const class protocols::minimization_packing::MinMoverCreator &) –> class protocols::minimization_packing::MinMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator) str

C++: protocols::minimization_packing::MinMoverCreator::keyname() const –> std::string

static mover_name() str

C++: protocols::minimization_packing::MinMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.minimization_packing.MinPackMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

a mover that packs and minimizes the side-chains. It uses a ScoreFunction for packing and either a PackerTask, or a TaskFactory that generates a PackerTask for instructions on what rotamer sets are allowed at each residue position during packing.

apply(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::minimization_packing::MinPackMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, : pyrosetta.rosetta.protocols.minimization_packing.MinPackMover) pyrosetta.rosetta.protocols.minimization_packing.MinPackMover

C++: protocols::minimization_packing::MinPackMover::operator=(const class protocols::minimization_packing::MinPackMover &) –> class protocols::minimization_packing::MinPackMover &

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.minimization_packing.MinPackMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::minimization_packing::MinPackMover::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.minimization_packing.MinPackMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover) str

C++: protocols::minimization_packing::MinPackMover::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 > > &

init(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover) None

C++: protocols::minimization_packing::MinPackMover::init() –> void

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

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

static mover_name() str

C++: protocols::minimization_packing::MinPackMover::mover_name() –> std::string

static name() str

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

off_rotamer_pack(*args, **kwargs)

Overloaded function.

  1. off_rotamer_pack(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, : bool) -> None

C++: protocols::minimization_packing::MinPackMover::off_rotamer_pack(bool) –> void

  1. off_rotamer_pack(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover) -> bool

C++: protocols::minimization_packing::MinPackMover::off_rotamer_pack() const –> bool

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

parse XML (specifically in the context of the parser/scripting scheme)

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

parse_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

parse “scorefxn” XML option (can be employed virtually by derived Packing movers)

C++: protocols::minimization_packing::MinPackMover::parse_score_function(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> void

parse_task_operations(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

parse “task_operations” XML option (can be employed virtually by derived Packing movers)

C++: protocols::minimization_packing::MinPackMover::parse_task_operations(class std::shared_ptr<const class utility::tag::Tag>, const 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::minimization_packing::MinPackMover::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

score_function(*args, **kwargs)

Overloaded function.

  1. score_function(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::minimization_packing::MinPackMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

  1. score_function(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::minimization_packing::MinPackMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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

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

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

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

set_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

task(*args, **kwargs)

Overloaded function.

  1. task(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

C++: protocols::minimization_packing::MinPackMover::task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

  1. task(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover) -> pyrosetta.rosetta.core.pack.task.PackerTask

C++: protocols::minimization_packing::MinPackMover::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

task_factory(*args, **kwargs)

Overloaded function.

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

C++: protocols::minimization_packing::MinPackMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

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

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

task_is_valid(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::minimization_packing::MinPackMover::task_is_valid(const class core::pose::Pose &) const –> bool

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.minimization_packing.MinPackMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator

C++: protocols::minimization_packing::MinPackMoverCreator::operator=(const class protocols::minimization_packing::MinPackMoverCreator &) –> class protocols::minimization_packing::MinPackMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator) str

C++: protocols::minimization_packing::MinPackMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer

Bases: pybind11_builtins.pybind11_object

aa(self: pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer) pyrosetta.rosetta.core.chemical.AA

C++: protocols::minimization_packing::MinimalRotamer::aa() const –> enum core::chemical::AA

same(self: pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer, : pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer) bool

C++: protocols::minimization_packing::MinimalRotamer::same(const class protocols::minimization_packing::MinimalRotamer &) const –> bool

same_residue_type(self: pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer, : pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer) bool

C++: protocols::minimization_packing::MinimalRotamer::same_residue_type(const class protocols::minimization_packing::MinimalRotamer &) const –> bool

class pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

A protocols::moves::Mover that packs the side-chains using a rotamer library It uses a ScoreFunction for packing and a PackerTask, or a TaskFactory that generates a PackerTask, for instructions on what rotamer sets are allowed at each residue position during packing

Common Methods:

PackRotamersMover.apply

please derive from PackRotamersMover instead of attempting to add protocol-specific stuff here!

apply(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) None
Performs side-chain packing based on the input PackerTask

using the input ScoreFunction

example(s):

packmover.apply(pose)

See Also:

PackerTask ScoreFunction

C++: protocols::minimization_packing::PackRotamersMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover

C++: protocols::minimization_packing::PackRotamersMover::operator=(const class protocols::minimization_packing::PackRotamersMover &) –> class protocols::minimization_packing::PackRotamersMover &

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.minimization_packing.PackRotamersMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

static complex_type_generator_for_pack_rotamers_mover(xsd: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator

C++: protocols::minimization_packing::PackRotamersMover::complex_type_generator_for_pack_rotamers_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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.minimization_packing.PackRotamersMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) str

C++: protocols::minimization_packing::PackRotamersMover::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 > > &

initialize_task_factory_with_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_std_allocator_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None

C++: protocols::minimization_packing::PackRotamersMover::initialize_task_factory_with_operations(const class std::list<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > > &) –> void

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

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

static mover_name() str

C++: protocols::minimization_packing::PackRotamersMover::mover_name() –> std::string

static name() str

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

nloop(*args, **kwargs)

Overloaded function.

  1. nloop(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, nloop_in: int) -> None

C++: protocols::minimization_packing::PackRotamersMover::nloop(unsigned long) –> void

  1. nloop(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> int

C++: protocols::minimization_packing::PackRotamersMover::nloop() const –> unsigned long

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

parse XML (specifically in the context of the parser/scripting scheme)

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

parse_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

parse “scorefxn” XML option (can be employed virtually by derived Packing movers)

C++: protocols::minimization_packing::PackRotamersMover::parse_score_function(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> void

parse_task_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

parse “task_operations” XML option (can be employed virtually by derived Packing movers)

C++: protocols::minimization_packing::PackRotamersMover::parse_task_operations(class std::shared_ptr<const class utility::tag::Tag>, const 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::minimization_packing::PackRotamersMover::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

rotamer_sets(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets

Returns the RotamerSets object being used for packing

  • This is only valid after a call to setup or apply.

C++: protocols::minimization_packing::PackRotamersMover::rotamer_sets() const –> class std::shared_ptr<const class core::pack::rotamer_set::RotamerSets>

score_function(*args, **kwargs)

Overloaded function.

  1. score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Sets the ScoreFunction to <sf>

example(s):

packmover.score_function(scorefxn)

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::minimization_packing::PackRotamersMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

  1. score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

Returns the ScoreFunction

example(s):

packmover.score_function()

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::minimization_packing::PackRotamersMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

set_annealer_observer(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, observer: pyrosetta.rosetta.core.pack.annealer.AnnealerObserver) None

C++: protocols::minimization_packing::PackRotamersMover::set_annealer_observer(class std::shared_ptr<class core::pack::annealer::AnnealerObserver>) –> 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.minimization_packing.PackRotamersMover) -> None

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

C++: protocols::minimization_packing::PackRotamersMover::show(std::ostream &) const –> void

task(*args, **kwargs)

Overloaded function.

  1. task(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

Sets the PackerTask to <t>

example(s):

packmover.task(task_pack)

See Also:

PackRotamersMover PackRotamersMover.task_factory

C++: protocols::minimization_packing::PackRotamersMover::task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

  1. task(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.PackerTask

Returns the PackerTask

example(s):

packmover.task()

See Also:

PackRotamersMover PackRotamersMover.task_factory

C++: protocols::minimization_packing::PackRotamersMover::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

task_factory(*args, **kwargs)

Overloaded function.

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

Sets the TaskFactory to <tf>

example(s):

packmover.task_factory(task_design)

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::minimization_packing::PackRotamersMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

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

Returns the TaskFactory

example(s):

packmover.task_factory()

See Also:

PackRotamersMover PackRotamersMover.task

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

task_is_valid(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::minimization_packing::PackRotamersMover::task_is_valid(const class core::pose::Pose &) const –> bool

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.minimization_packing.PackRotamersMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator

C++: protocols::minimization_packing::PackRotamersMoverCreator::operator=(const class protocols::minimization_packing::PackRotamersMoverCreator &) –> class protocols::minimization_packing::PackRotamersMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator) str

C++: protocols::minimization_packing::PackRotamersMoverCreator::keyname() const –> std::string

static mover_name() str

C++: protocols::minimization_packing::PackRotamersMoverCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy

Bases: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover

a mover that packs the side-chains using a rotamer library in a lazy fashion.

apply(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) None
Performs side-chain packing based on the input PackerTask

using the input ScoreFunction

example(s):

packmover.apply(pose)

See Also:

PackerTask ScoreFunction

C++: protocols::minimization_packing::PackRotamersMover::apply(class core::pose::Pose &) –> void

apply_to_rotpack(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy, pose: pyrosetta.rosetta.core.pose.Pose, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) None

C++: protocols::minimization_packing::PackRotamersMoverLazy::apply_to_rotpack(class core::pose::Pose &, class utility::vector0<int, class std::allocator<int> >) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy, : pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy) pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy

C++: protocols::minimization_packing::PackRotamersMoverLazy::operator=(const class protocols::minimization_packing::PackRotamersMoverLazy &) –> class protocols::minimization_packing::PackRotamersMoverLazy &

call_setup(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::minimization_packing::PackRotamersMoverLazy::call_setup(class core::pose::Pose &) –> 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.minimization_packing.PackRotamersMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

static complex_type_generator_for_pack_rotamers_mover(xsd: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator

C++: protocols::minimization_packing::PackRotamersMover::complex_type_generator_for_pack_rotamers_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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.minimization_packing.PackRotamersMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) str

C++: protocols::minimization_packing::PackRotamersMover::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 > > &

initialize_task_factory_with_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_std_allocator_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None

C++: protocols::minimization_packing::PackRotamersMover::initialize_task_factory_with_operations(const class std::list<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > > &) –> void

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

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

static mover_name() str

C++: protocols::minimization_packing::PackRotamersMover::mover_name() –> std::string

static name() str

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

nloop(*args, **kwargs)

Overloaded function.

  1. nloop(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, nloop_in: int) -> None

C++: protocols::minimization_packing::PackRotamersMover::nloop(unsigned long) –> void

  1. nloop(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> int

C++: protocols::minimization_packing::PackRotamersMover::nloop() const –> unsigned long

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

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

parse_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

parse “scorefxn” XML option (can be employed virtually by derived Packing movers)

C++: protocols::minimization_packing::PackRotamersMover::parse_score_function(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> void

parse_task_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

parse “task_operations” XML option (can be employed virtually by derived Packing movers)

C++: protocols::minimization_packing::PackRotamersMover::parse_task_operations(class std::shared_ptr<const class utility::tag::Tag>, const 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::minimization_packing::PackRotamersMover::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

rotamer_sets(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets

Returns the RotamerSets object being used for packing

  • This is only valid after a call to setup or apply.

C++: protocols::minimization_packing::PackRotamersMover::rotamer_sets() const –> class std::shared_ptr<const class core::pack::rotamer_set::RotamerSets>

score_function(*args, **kwargs)

Overloaded function.

  1. score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Sets the ScoreFunction to <sf>

example(s):

packmover.score_function(scorefxn)

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::minimization_packing::PackRotamersMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

  1. score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

Returns the ScoreFunction

example(s):

packmover.score_function()

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::minimization_packing::PackRotamersMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

set_annealer_observer(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, observer: pyrosetta.rosetta.core.pack.annealer.AnnealerObserver) None

C++: protocols::minimization_packing::PackRotamersMover::set_annealer_observer(class std::shared_ptr<class core::pack::annealer::AnnealerObserver>) –> 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.minimization_packing.PackRotamersMover) -> None

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

C++: protocols::minimization_packing::PackRotamersMover::show(std::ostream &) const –> void

task(*args, **kwargs)

Overloaded function.

  1. task(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

Sets the PackerTask to <t>

example(s):

packmover.task(task_pack)

See Also:

PackRotamersMover PackRotamersMover.task_factory

C++: protocols::minimization_packing::PackRotamersMover::task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

  1. task(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.PackerTask

Returns the PackerTask

example(s):

packmover.task()

See Also:

PackRotamersMover PackRotamersMover.task_factory

C++: protocols::minimization_packing::PackRotamersMover::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

task_factory(*args, **kwargs)

Overloaded function.

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

Sets the TaskFactory to <tf>

example(s):

packmover.task_factory(task_design)

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::minimization_packing::PackRotamersMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

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

Returns the TaskFactory

example(s):

packmover.task_factory()

See Also:

PackRotamersMover PackRotamersMover.task

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

task_is_valid(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::minimization_packing::PackRotamersMover::task_is_valid(const class core::pose::Pose &) const –> bool

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.minimization_packing.PackRotamersMoverLazyCreator

Bases: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator

assign(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazyCreator, : pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazyCreator) pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazyCreator

C++: protocols::minimization_packing::PackRotamersMoverLazyCreator::operator=(const class protocols::minimization_packing::PackRotamersMoverLazyCreator &) –> class protocols::minimization_packing::PackRotamersMoverLazyCreator &

create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator) str

C++: protocols::minimization_packing::PackRotamersMoverCreator::keyname() const –> std::string

static mover_name() str

C++: protocols::minimization_packing::PackRotamersMoverLazyCreator::mover_name() –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.minimization_packing.PertMinMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Random perturbation, followed by minimization

apply(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::minimization_packing::PertMinMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, : pyrosetta.rosetta.protocols.minimization_packing.PertMinMover) pyrosetta.rosetta.protocols.minimization_packing.PertMinMover

C++: protocols::minimization_packing::PertMinMover::operator=(const class protocols::minimization_packing::PertMinMover &) –> class protocols::minimization_packing::PertMinMover &

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.minimization_packing.PertMinMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::minimization_packing::PertMinMover::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.minimization_packing.PertMinMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover) str

C++: protocols::minimization_packing::PertMinMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

min(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::minimization_packing::PertMinMover::min(class core::pose::Pose &) const –> void

movemap(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover) pyrosetta.rosetta.core.select.movemap.MoveMapFactory

C++: protocols::minimization_packing::PertMinMover::movemap() const –> class std::shared_ptr<const class core::select::movemap::MoveMapFactory>

movemap_factory(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, setting: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) None

C++: protocols::minimization_packing::PertMinMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

static mover_name() str

C++: protocols::minimization_packing::PertMinMover::mover_name() –> std::string

static name() str

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

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

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

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

pert(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, pose: pyrosetta.rosetta.core.pose.Pose, resi: pyrosetta.rosetta.utility.vector1_bool) None

C++: protocols::minimization_packing::PertMinMover::pert(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

pert_size(*args, **kwargs)

Overloaded function.

  1. pert_size(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover) -> float

C++: protocols::minimization_packing::PertMinMover::pert_size() const –> double

  1. pert_size(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, setting: float) -> None

C++: protocols::minimization_packing::PertMinMover::pert_size(double) –> 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::minimization_packing::PertMinMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

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

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

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

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

each use.

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

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

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

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

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

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

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

residues(*args, **kwargs)

Overloaded function.

  1. residues(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::minimization_packing::PertMinMover::residues() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

  1. residues(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, setting: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::minimization_packing::PertMinMover::residues(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

sc_only(*args, **kwargs)

Overloaded function.

  1. sc_only(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover) -> bool

C++: protocols::minimization_packing::PertMinMover::sc_only() const –> bool

  1. sc_only(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, setting: bool) -> None

C++: protocols::minimization_packing::PertMinMover::sc_only(bool) –> void

scorefxn(*args, **kwargs)

Overloaded function.

  1. scorefxn(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

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

  1. scorefxn(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::minimization_packing::PertMinMover::scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.minimization_packing.PertMinMover) -> None

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

C++: protocols::minimization_packing::PertMinMover::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 &

uniform(*args, **kwargs)

Overloaded function.

  1. uniform(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover) -> bool

C++: protocols::minimization_packing::PertMinMover::uniform() const –> bool

  1. uniform(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, setting: bool) -> None

C++: protocols::minimization_packing::PertMinMover::uniform(bool) –> void

class pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator

C++: protocols::minimization_packing::PertMinMoverCreator::operator=(const class protocols::minimization_packing::PertMinMoverCreator &) –> class protocols::minimization_packing::PertMinMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator) str

C++: protocols::minimization_packing::PertMinMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

A protocols::moves::Mover that packs the side-chains (very similar to pack_missing_sidechains()

apply(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::minimization_packing::RepackSidechainsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover, : pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover) pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover

C++: protocols::minimization_packing::RepackSidechainsMover::operator=(const class protocols::minimization_packing::RepackSidechainsMover &) –> class protocols::minimization_packing::RepackSidechainsMover &

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.minimization_packing.RepackSidechainsMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::minimization_packing::RepackSidechainsMover::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.minimization_packing.RepackSidechainsMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover) str

C++: protocols::minimization_packing::RepackSidechainsMover::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.minimization_packing.RepackSidechainsMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

parse XML (specifically in the context of the parser/scripting scheme)

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

parse_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

parse “scorefxn” XML option (can be employed virtually by derived Packing movers)

C++: protocols::minimization_packing::RepackSidechainsMover::parse_score_function(class std::shared_ptr<const class utility::tag::Tag>, const 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

scorefxn(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover) pyrosetta.rosetta.core.scoring.ScoreFunction

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

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

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

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

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

set_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_scorefxn(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::minimization_packing::RepackSidechainsMover::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.minimization_packing.RepackSidechainsMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator

C++: protocols::minimization_packing::RepackSidechainsMoverCreator::operator=(const class protocols::minimization_packing::RepackSidechainsMoverCreator &) –> class protocols::minimization_packing::RepackSidechainsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator) str

C++: protocols::minimization_packing::RepackSidechainsMoverCreator::keyname() const –> std::string

static mover_name() str

C++: protocols::minimization_packing::RepackSidechainsMoverCreator::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.minimization_packing.RotamerTrialsMinMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None
Apply Rotamer-Trials with minimization to pose, using the score function

and tasks provided by the constructor

C++: protocols::minimization_packing::RotamerTrialsMinMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, : pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover) pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover

C++: protocols::minimization_packing::RotamerTrialsMinMover::operator=(const class protocols::minimization_packing::RotamerTrialsMinMover &) –> class protocols::minimization_packing::RotamerTrialsMinMover &

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.minimization_packing.RotamerTrialsMinMover) pyrosetta.rosetta.protocols.moves.Mover

Return a copy of this mover instance (for RosettaScripts)

C++: protocols::minimization_packing::RotamerTrialsMinMover::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.minimization_packing.RotamerTrialsMinMover) pyrosetta.rosetta.protocols.moves.Mover

Return a new mover instance (for RosettaScripts)

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover) str

C++: protocols::minimization_packing::RotamerTrialsMinMover::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 > > &

init(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover) None

C++: protocols::minimization_packing::RotamerTrialsMinMover::init() –> void

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

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

static mover_name() str

C++: protocols::minimization_packing::RotamerTrialsMinMover::mover_name() –> std::string

static name() str

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

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

Parse XML for RosettaScripts

C++: protocols::minimization_packing::RotamerTrialsMinMover::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::minimization_packing::RotamerTrialsMinMover::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

score_function(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::minimization_packing::RotamerTrialsMinMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.minimization_packing.RotamerTrialsMinMover) -> None

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

C++: protocols::minimization_packing::RotamerTrialsMinMover::show(std::ostream &) const –> void

task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::minimization_packing::RotamerTrialsMinMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> 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.minimization_packing.RotamerTrialsMinMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator

C++: protocols::minimization_packing::RotamerTrialsMinMoverCreator::operator=(const class protocols::minimization_packing::RotamerTrialsMinMoverCreator &) –> class protocols::minimization_packing::RotamerTrialsMinMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator) str

C++: protocols::minimization_packing::RotamerTrialsMinMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::minimization_packing::RotamerTrialsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, : pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover) pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover

C++: protocols::minimization_packing::RotamerTrialsMover::operator=(const class protocols::minimization_packing::RotamerTrialsMover &) –> class protocols::minimization_packing::RotamerTrialsMover &

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.minimization_packing.RotamerTrialsMover) pyrosetta.rosetta.protocols.moves.Mover

clone this object

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

static complex_type_generator_for_rotamer_trials_mover(xsd: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator

C++: protocols::minimization_packing::RotamerTrialsMover::complex_type_generator_for_rotamer_trials_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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.minimization_packing.RotamerTrialsMover) pyrosetta.rosetta.protocols.moves.Mover

create this type of object

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover) str

C++: protocols::minimization_packing::RotamerTrialsMover::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::minimization_packing::RotamerTrialsMover::mover_name() –> std::string

static name() str

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

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

C++: protocols::minimization_packing::RotamerTrialsMover::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::minimization_packing::RotamerTrialsMover::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

score_function(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::minimization_packing::RotamerTrialsMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.minimization_packing.RotamerTrialsMover) -> None

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

C++: protocols::minimization_packing::RotamerTrialsMover::show(std::ostream &) const –> void

task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None

C++: protocols::minimization_packing::RotamerTrialsMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> 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.minimization_packing.RotamerTrialsMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator

C++: protocols::minimization_packing::RotamerTrialsMoverCreator::operator=(const class protocols::minimization_packing::RotamerTrialsMoverCreator &) –> class protocols::minimization_packing::RotamerTrialsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator) str

C++: protocols::minimization_packing::RotamerTrialsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

a mover that replaces the repackable parts - sidechains, bases, etc. - based purely on geometric similarity to the starting structure. The purpose is to generate the best case output of a repacking calculation as a positive control for benchmarking and parameter fitting. Thus, the soft rep potential was originally derived as the score function that gave the best fit between repacked and rotamerized structures for a large test set.

apply(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::minimization_packing::RotamerizeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover, : pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover) pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover

C++: protocols::minimization_packing::RotamerizeMover::operator=(const class protocols::minimization_packing::RotamerizeMover &) –> class protocols::minimization_packing::RotamerizeMover &

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

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

Generates a new Mover object freshly created with the default ctor.

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover) str

C++: protocols::minimization_packing::RotamerizeMover::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.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::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

rotamer_sets(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover) pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets

C++: protocols::minimization_packing::RotamerizeMover::rotamer_sets() const –> class std::shared_ptr<const class core::pack::rotamer_set::RotamerSets>

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

task(*args, **kwargs)

Overloaded function.

  1. task(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

C++: protocols::minimization_packing::RotamerizeMover::task(class std::shared_ptr<class core::pack::task::PackerTask>) –> void

  1. task(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover) -> pyrosetta.rosetta.core.pack.task.PackerTask

C++: protocols::minimization_packing::RotamerizeMover::task() const –> class std::shared_ptr<class core::pack::task::PackerTask>

task_factory(*args, **kwargs)

Overloaded function.

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

C++: protocols::minimization_packing::RotamerizeMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

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

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

task_is_valid(self: pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::minimization_packing::RotamerizeMover::task_is_valid(const class core::pose::Pose &) const –> bool

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.minimization_packing.SaneMinMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

performing energy minimization of a ScoreFunction over the allowable degrees of freedom, defined by a MoveMap. Unlike the classic MinMover, the only method for setting Minimization options is via the MinimizerOptions class.

apply(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Minimizes the DOFs of pose specified in the MoveMap

C++: protocols::minimization_packing::SaneMinMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover, : pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover) pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover

C++: protocols::minimization_packing::SaneMinMover::operator=(const class protocols::minimization_packing::SaneMinMover &) –> class protocols::minimization_packing::SaneMinMover &

cartesian(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover) bool

C++: protocols::minimization_packing::SaneMinMover::cartesian() const –> bool

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::minimization_packing::SaneMinMover::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.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover) str

C++: protocols::minimization_packing::SaneMinMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

min_options(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover) pyrosetta.rosetta.core.optimization.MinimizerOptions

C++: protocols::minimization_packing::SaneMinMover::min_options() const –> class std::shared_ptr<class core::optimization::MinimizerOptions>

move_map(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover) pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::minimization_packing::SaneMinMover::move_map() const –> class std::shared_ptr<class core::kinematics::MoveMap>

static mover_name() str

C++: protocols::minimization_packing::SaneMinMover::mover_name() –> std::string

static name() str

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

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

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::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::minimization_packing::SaneMinMover::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

score_function(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::minimization_packing::SaneMinMover::score_function() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

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

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

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

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

set_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.minimization_packing.SaneMinMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator, : pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator) pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator

C++: protocols::minimization_packing::SaneMinMoverCreator::operator=(const class protocols::minimization_packing::SaneMinMoverCreator &) –> class protocols::minimization_packing::SaneMinMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator) str

C++: protocols::minimization_packing::SaneMinMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover

Bases: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover

apply(self: pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::minimization_packing::SetReturningPackRotamersMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover, : pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover) pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover

C++: protocols::minimization_packing::SetReturningPackRotamersMover::operator=(const class protocols::minimization_packing::SetReturningPackRotamersMover &) –> class protocols::minimization_packing::SetReturningPackRotamersMover &

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.minimization_packing.PackRotamersMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

static complex_type_generator_for_pack_rotamers_mover(xsd: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator

C++: protocols::minimization_packing::PackRotamersMover::complex_type_generator_for_pack_rotamers_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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.minimization_packing.PackRotamersMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover) str

C++: protocols::minimization_packing::SetReturningPackRotamersMover::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_repacked_poses(self: pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover, v: pyrosetta.rosetta.utility.vector1_core_pose_Pose) None

C++: protocols::minimization_packing::SetReturningPackRotamersMover::get_repacked_poses(class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &) –> void

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 > > &

initialize_task_factory_with_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_std_allocator_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None

C++: protocols::minimization_packing::PackRotamersMover::initialize_task_factory_with_operations(const class std::list<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > > &) –> void

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

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

static mover_name() str

C++: protocols::minimization_packing::PackRotamersMover::mover_name() –> std::string

static name() str

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

nloop(*args, **kwargs)

Overloaded function.

  1. nloop(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, nloop_in: int) -> None

C++: protocols::minimization_packing::PackRotamersMover::nloop(unsigned long) –> void

  1. nloop(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> int

C++: protocols::minimization_packing::PackRotamersMover::nloop() const –> unsigned long

output_repacked_poses(self: pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover, filename_prefix: str) None

C++: protocols::minimization_packing::SetReturningPackRotamersMover::output_repacked_poses(std::string) –> void

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

parse XML (specifically in the context of the parser/scripting scheme)

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

parse_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

parse “scorefxn” XML option (can be employed virtually by derived Packing movers)

C++: protocols::minimization_packing::PackRotamersMover::parse_score_function(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> void

parse_task_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

parse “task_operations” XML option (can be employed virtually by derived Packing movers)

C++: protocols::minimization_packing::PackRotamersMover::parse_task_operations(class std::shared_ptr<const class utility::tag::Tag>, const 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::minimization_packing::PackRotamersMover::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

rotamer_sets(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets

Returns the RotamerSets object being used for packing

  • This is only valid after a call to setup or apply.

C++: protocols::minimization_packing::PackRotamersMover::rotamer_sets() const –> class std::shared_ptr<const class core::pack::rotamer_set::RotamerSets>

score_function(*args, **kwargs)

Overloaded function.

  1. score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Sets the ScoreFunction to <sf>

example(s):

packmover.score_function(scorefxn)

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::minimization_packing::PackRotamersMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

  1. score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

Returns the ScoreFunction

example(s):

packmover.score_function()

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::minimization_packing::PackRotamersMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

set_annealer_observer(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, observer: pyrosetta.rosetta.core.pack.annealer.AnnealerObserver) None

C++: protocols::minimization_packing::PackRotamersMover::set_annealer_observer(class std::shared_ptr<class core::pack::annealer::AnnealerObserver>) –> 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.minimization_packing.PackRotamersMover) -> None

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

C++: protocols::minimization_packing::PackRotamersMover::show(std::ostream &) const –> void

task(*args, **kwargs)

Overloaded function.

  1. task(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

Sets the PackerTask to <t>

example(s):

packmover.task(task_pack)

See Also:

PackRotamersMover PackRotamersMover.task_factory

C++: protocols::minimization_packing::PackRotamersMover::task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

  1. task(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.PackerTask

Returns the PackerTask

example(s):

packmover.task()

See Also:

PackRotamersMover PackRotamersMover.task_factory

C++: protocols::minimization_packing::PackRotamersMover::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

task_factory(*args, **kwargs)

Overloaded function.

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

Sets the TaskFactory to <tf>

example(s):

packmover.task_factory(task_design)

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::minimization_packing::PackRotamersMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

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

Returns the TaskFactory

example(s):

packmover.task_factory()

See Also:

PackRotamersMover PackRotamersMover.task

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

task_is_valid(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::minimization_packing::PackRotamersMover::task_is_valid(const class core::pose::Pose &) const –> bool

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.minimization_packing.TaskAwareMinMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

this class wraps MinMover, but ensures that its MoveMap always contains up-to-date information about sidechain mobility. It takes its base movemap, allows sidechain freedom at any position mobile in a Factory-generated PackerTask, and passes the new movemap to MinMover. The MinMover’s MoveMap does not accumulate state over many calls to apply().

apply(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::minimization_packing::TaskAwareMinMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, : pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover) pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover

C++: protocols::minimization_packing::TaskAwareMinMover::operator=(const class protocols::minimization_packing::TaskAwareMinMover &) –> class protocols::minimization_packing::TaskAwareMinMover &

bb(*args, **kwargs)

Overloaded function.

  1. bb(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, val: bool) -> None

C++: protocols::minimization_packing::TaskAwareMinMover::bb(bool) –> void

  1. bb(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover) -> bool

C++: protocols::minimization_packing::TaskAwareMinMover::bb() const –> bool

chi(*args, **kwargs)

Overloaded function.

  1. chi(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, val: bool) -> None

C++: protocols::minimization_packing::TaskAwareMinMover::chi(bool) –> void

  1. chi(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover) -> bool

C++: protocols::minimization_packing::TaskAwareMinMover::chi() const –> bool

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::minimization_packing::TaskAwareMinMover::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.minimization_packing.TaskAwareMinMover) pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

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

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover) str

C++: protocols::minimization_packing::TaskAwareMinMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

jump(*args, **kwargs)

Overloaded function.

  1. jump(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, j: bool) -> None

C++: protocols::minimization_packing::TaskAwareMinMover::jump(const bool) –> void

  1. jump(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover) -> bool

C++: protocols::minimization_packing::TaskAwareMinMover::jump() const –> bool

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::minimization_packing::TaskAwareMinMover::mover_name() –> std::string

static name() str

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

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

parse XML (specifically in the context of the parser/scripting scheme)

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

parse_task_operations(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

parse “task_operations” XML option

C++: protocols::minimization_packing::TaskAwareMinMover::parse_task_operations(class std::shared_ptr<const class utility::tag::Tag>, const 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::minimization_packing::TaskAwareMinMover::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)