symmetry

Bindings for protocols::minimization_packing::symmetry namespace

class pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover

Bases: pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover

This class is provided for historical support only The EnergyCutRotamerTrialsMover should handle symmetry transparently and is preferred.

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.symmetry.SymEnergyCutRotamerTrialsMover, : pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover) → pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover

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

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>

complex_type_generator_for_rotamer_trials_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.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.

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.symmetry.SymEnergyCutRotamerTrialsMover) → str

C++: protocols::minimization_packing::symmetry::SymEnergyCutRotamerTrialsMover::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

mover_name() → str

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

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, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, : pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::minimization_packing::RotamerTrialsMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

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

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) 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) -> str

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover

Bases: pyrosetta.rosetta.protocols.minimization_packing.MinMover

This class is kept only for backward compatibility – The regular MinMover should now handle symmetric poses transparently and is preferred.

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

2. 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.symmetry.SymMinMover, : pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover) → pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover

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

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

2. 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.symmetry.SymMinMover) → pyrosetta.rosetta.protocols.moves.Mover

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

complex_type_generator_for_min_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.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

2. 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.symmetry.SymMinMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::minimization_packing::symmetry::SymMinMover::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.

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.symmetry.SymMinMover) → str

C++: protocols::minimization_packing::symmetry::SymMinMover::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>

2. 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(class std::basic_string<char>) –> void

2. 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

2. 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

mover_name() → str

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

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

2. 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

2. 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 class std::basic_string<char> &, 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, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, : pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, : pyrosetta.rosetta.core.pose.Pose) → 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 &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

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

C++: protocols::minimization_packing::MinMover::parse_opts(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

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

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

2. 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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) 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

2. 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) -> str

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover

Bases: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover

This class is provided for backwards compatibility only The PackRotamersMover should work with symmetry transparently and is preferred.

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.symmetry.SymPackRotamersMover, : pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover) → pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover

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

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.symmetry.SymPackRotamersMover) → pyrosetta.rosetta.protocols.moves.Mover

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

complex_type_generator_for_pack_rotamers_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.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.symmetry.SymPackRotamersMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::minimization_packing::symmetry::SymPackRotamersMover::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.

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.symmetry.SymPackRotamersMover) → str

C++: protocols::minimization_packing::symmetry::SymPackRotamersMover::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

mover_name() → str

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

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

2. 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, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, : pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, : pyrosetta.rosetta.core.pose.Pose) → 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 &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

parse_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, : pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, : pyrosetta.rosetta.core.pose.Pose) → 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 &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

parse_task_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, : pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, : pyrosetta.rosetta.core.pose.Pose) → 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 &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

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

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

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) 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

2. 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

2. 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) -> str

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover

Bases: pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover

This class is provided for historical support only The RotamerTrialsMover should handle symmetry transparently and is preferred.

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.symmetry.SymRotamerTrialsMover, : pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover) → pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover

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

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>

complex_type_generator_for_rotamer_trials_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.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.

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.symmetry.SymRotamerTrialsMover) → str

C++: protocols::minimization_packing::symmetry::SymRotamerTrialsMover::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

mover_name() → str

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

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, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, : pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::minimization_packing::RotamerTrialsMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

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

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) 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) -> str

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void