minimization_packing¶

symmetry

Bindings for protocols::minimization_packing namespace

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.

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

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

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, : 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 for RosettaScripts

C++: protocols::minimization_packing::RotamerTrialsMinMover::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::RotamerTrialsMinMover::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.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¶

////////////////////////////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.

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

C++: protocols::minimization_packing::RotamerTrialsMinMover::show(class std::basic_ostream<char> &) 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.

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

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

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.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.

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

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.

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

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

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>

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.

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

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

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.

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.

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>

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.

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

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.

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

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::MinMover::mover_name() –> std::string

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

nb_list(*args, **kwargs)¶

Overloaded function.

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

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.

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

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

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::MinMover::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.

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

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.

show(self: pyrosetta.rosetta.protocols.minimization_packing.MinMover) -> None
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.

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

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

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

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

type(*args, **kwargs)¶

Overloaded function.

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

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

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.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.

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

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

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

off_rotamer_pack(*args, **kwargs)¶

Overloaded function.

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

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

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, : 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::MinPackMover::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.MinPackMover, : 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::MinPackMover::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.MinPackMover, : 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::MinPackMover::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::MinPackMover::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(*args, **kwargs)¶

Overloaded function.

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

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¶

////////////////////////////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.

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

Outputs details about the Mover, including current settings.

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

task(*args, **kwargs)¶

Overloaded function.

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

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.

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

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.

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

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

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.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>

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.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.

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 > > &

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::PackRotamersMover::mover_name() –> std::string

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

nloop(*args, **kwargs)¶

Overloaded function.

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

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

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::PackRotamersMover::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.

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

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.

show(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> None
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.

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

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.

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

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.

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

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

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.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>

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.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.

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 > > &

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::PackRotamersMover::mover_name() –> std::string

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

nloop(*args, **kwargs)¶

Overloaded function.

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

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

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, : 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::PackRotamersMoverLazy::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::PackRotamersMover::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.

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

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.

show(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> None
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.

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

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.

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

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.

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

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

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.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.

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

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

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, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, movers: pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, pose: pyrosetta.rosetta.core.pose.Pose) → 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 &, 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

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.

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

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

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

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::minimization_packing::PertMinMover::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

residues(*args, **kwargs)¶

Overloaded function.

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>

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.

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

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

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.

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>

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¶

////////////////////////////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.

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

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

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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

uniform(*args, **kwargs)¶

Overloaded function.

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

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

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.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.

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

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, : 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::RepackSidechainsMover::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.RepackSidechainsMover, : 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::RepackSidechainsMover::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

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¶

////////////////////////////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_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¶: C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> void

show(*args, **kwargs)¶

Overloaded function.

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(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

type(*args, **kwargs)¶

Overloaded function.

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

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

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.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.

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

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, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, movers: pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, pose: pyrosetta.rosetta.core.pose.Pose) → 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 &, 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

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¶

////////////////////////////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.

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

Outputs details about the Mover, including current settings.

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

task(*args, **kwargs)¶

Overloaded function.

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

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.

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

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.

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

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

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.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.

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>

mover_name() → str¶: C++: protocols::minimization_packing::SaneMinMover::mover_name() –> std::string

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, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, movers: pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, pose: pyrosetta.rosetta.core.pose.Pose) → 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 &, 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::SaneMinMover::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.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¶

////////////////////////////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.

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(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

type(*args, **kwargs)¶

Overloaded function.

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

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

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.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.

bb(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, val: bool) -> None

C++: protocols::minimization_packing::TaskAwareMinMover::bb(bool) –> void

bb(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover) -> bool

C++: protocols::minimization_packing::TaskAwareMinMover::bb() const –> bool

chi(*args, **kwargs)¶

Overloaded function.

chi(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, val: bool) -> None

C++: protocols::minimization_packing::TaskAwareMinMover::chi(bool) –> void

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.

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.

jump(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, j: bool) -> None

C++: protocols::minimization_packing::TaskAwareMinMover::jump(const bool) –> void

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

mover_name() → str¶: C++: protocols::minimization_packing::TaskAwareMinMover::mover_name() –> std::string

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, : 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::TaskAwareMinMover::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_task_operations(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, : 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

C++: protocols::minimization_packing::TaskAwareMinMover::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::TaskAwareMinMover::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

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.

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(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

type(*args, **kwargs)¶

Overloaded function.

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

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

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

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