design_opt

Bindings for protocols::design_opt namespace

class pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover

Bases: Mover

add_filter(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, : pyrosetta.rosetta.protocols.filters.Filter, sample_type: str, filter_delta: float) → None

C++: protocols::design_opt::GreedyOptMutationMover::add_filter(class std::shared_ptr<class protocols::filters::Filter>, const std::string, double) –> void

apply(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::design_opt::GreedyOptMutationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, : pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) → pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover

C++: protocols::design_opt::GreedyOptMutationMover::operator=(const class protocols::design_opt::GreedyOptMutationMover &) –> class protocols::design_opt::GreedyOptMutationMover &

calc_pfront_poses_filter_ranks(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) → None

C++: protocols::design_opt::GreedyOptMutationMover::calc_pfront_poses_filter_ranks() –> void

clear_cached_data(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) → None

C++: protocols::design_opt::GreedyOptMutationMover::clear_cached_data() –> 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.design_opt.GreedyOptMutationMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::design_opt::GreedyOptMutationMover::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>

delta_filters(*args, **kwargs)

Overloaded function.

1. delta_filters(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_DeltaFilter_t

C++: protocols::design_opt::GreedyOptMutationMover::delta_filters() const –> class utility::vector1<class std::shared_ptr<class protocols::simple_filters::DeltaFilter>, class std::allocator<class std::shared_ptr<class protocols::simple_filters::DeltaFilter> > >

2. delta_filters(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, d: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_DeltaFilter_t) -> None

C++: protocols::design_opt::GreedyOptMutationMover::delta_filters(const class utility::vector1<class std::shared_ptr<class protocols::simple_filters::DeltaFilter>, class std::allocator<class std::shared_ptr<class protocols::simple_filters::DeltaFilter> > >) –> void

diversify(*args, **kwargs)

Overloaded function.

1. diversify(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> bool

C++: protocols::design_opt::GreedyOptMutationMover::diversify() const –> bool

2. diversify(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, b: bool) -> None

C++: protocols::design_opt::GreedyOptMutationMover::diversify(const bool) –> void

downsample_pfront_poses(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) → None

C++: protocols::design_opt::GreedyOptMutationMover::downsample_pfront_poses() –> void

dump_pdb(*args, **kwargs)

Overloaded function.

1. dump_pdb(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> bool

C++: protocols::design_opt::GreedyOptMutationMover::dump_pdb() const –> bool

2. dump_pdb(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, dump_pdb: bool) -> None

C++: protocols::design_opt::GreedyOptMutationMover::dump_pdb(const bool) –> void

dump_scoring_table(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, filename: str, ref_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::design_opt::GreedyOptMutationMover::dump_scoring_table(std::string, const class core::pose::Pose &) const –> void

dump_table(*args, **kwargs)

Overloaded function.

1. dump_table(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> bool

C++: protocols::design_opt::GreedyOptMutationMover::dump_table() const –> bool

2. dump_table(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, dump_table: bool) -> None

C++: protocols::design_opt::GreedyOptMutationMover::dump_table(const bool) –> void

filter_deltas(*args, **kwargs)

Overloaded function.

1. filter_deltas(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::design_opt::GreedyOptMutationMover::filter_deltas() const –> class utility::vector1<double, class std::allocator<double> >

2. filter_deltas(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, filter_deltas: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::design_opt::GreedyOptMutationMover::filter_deltas(const class utility::vector1<double, class std::allocator<double> >) –> void

filter_pareto_opt_poses(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) → None

C++: protocols::design_opt::GreedyOptMutationMover::filter_pareto_opt_poses() –> void

filter_seqpos_pareto_opt_ptmuts(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) → None

C++: protocols::design_opt::GreedyOptMutationMover::filter_seqpos_pareto_opt_ptmuts() –> void

filters(*args, **kwargs)

Overloaded function.

1. filters(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t

C++: protocols::design_opt::GreedyOptMutationMover::filters() const –> class utility::vector1<class std::shared_ptr<class protocols::filters::Filter>, class std::allocator<class std::shared_ptr<class protocols::filters::Filter> > >

2. filters(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, filters: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t) -> None

C++: protocols::design_opt::GreedyOptMutationMover::filters(class utility::vector1<class std::shared_ptr<class protocols::filters::Filter>, class std::allocator<class std::shared_ptr<class protocols::filters::Filter> > >) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) → pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

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

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

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

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

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

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) → str

C++: protocols::design_opt::GreedyOptMutationMover::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

incl_nonopt(*args, **kwargs)

Overloaded function.

1. incl_nonopt(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> bool

C++: protocols::design_opt::GreedyOptMutationMover::incl_nonopt() const –> bool

2. incl_nonopt(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, b: bool) -> None

C++: protocols::design_opt::GreedyOptMutationMover::incl_nonopt(const bool) –> void

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

non-const accessor

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

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

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

static mover_name() → str

C++: protocols::design_opt::GreedyOptMutationMover::mover_name() –> std::string

static name() → str

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

parallel(*args, **kwargs)

Overloaded function.

1. parallel(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> bool

C++: protocols::design_opt::GreedyOptMutationMover::parallel() const –> bool

2. parallel(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, parallel: bool) -> None

C++: protocols::design_opt::GreedyOptMutationMover::parallel(const bool) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

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

pose_coords_are_same(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::design_opt::GreedyOptMutationMover::pose_coords_are_same(const class core::pose::Pose &, const class core::pose::Pose &) –> bool

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

Provide citations to the passed CitationCollectionList

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

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

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::design_opt::GreedyOptMutationMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

relax_mover(*args, **kwargs)

Overloaded function.

1. relax_mover(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::design_opt::GreedyOptMutationMover::relax_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

2. relax_mover(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, relax_mover: pyrosetta.rosetta.protocols.moves.Mover) -> None

C++: protocols::design_opt::GreedyOptMutationMover::relax_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

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

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

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

static root_node_for_greedy_opt(attlist1: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaRepeatableCTNode

C++: protocols::design_opt::GreedyOptMutationMover::root_node_for_greedy_opt(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaRepeatableCTNode>

rtmin(*args, **kwargs)

Overloaded function.

1. rtmin(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> bool

C++: protocols::design_opt::GreedyOptMutationMover::rtmin() const –> bool

2. rtmin(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, b: bool) -> None

C++: protocols::design_opt::GreedyOptMutationMover::rtmin(const bool) –> void

sample_types(*args, **kwargs)

Overloaded function.

1. sample_types(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::design_opt::GreedyOptMutationMover::sample_types() const –> class utility::vector1<std::string, class std::allocator<std::string > >

2. sample_types(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, sample_types: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: protocols::design_opt::GreedyOptMutationMover::sample_types(const class utility::vector1<std::string, class std::allocator<std::string > >) –> void

scorefxn(*args, **kwargs)

Overloaded function.

1. scorefxn(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

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

2. scorefxn(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::design_opt::GreedyOptMutationMover::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

shuffle_order(*args, **kwargs)

Overloaded function.

1. shuffle_order(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> bool

C++: protocols::design_opt::GreedyOptMutationMover::shuffle_order() const –> bool

2. shuffle_order(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, b: bool) -> None

C++: protocols::design_opt::GreedyOptMutationMover::shuffle_order(const bool) –> void

skip_best_check(*args, **kwargs)

Overloaded function.

1. skip_best_check(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> bool

C++: protocols::design_opt::GreedyOptMutationMover::skip_best_check() const –> bool

2. skip_best_check(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, skip_best_check: bool) -> None

C++: protocols::design_opt::GreedyOptMutationMover::skip_best_check(const bool) –> void

stop_before_condition(*args, **kwargs)

Overloaded function.

1. stop_before_condition(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> bool

C++: protocols::design_opt::GreedyOptMutationMover::stop_before_condition() const –> bool

2. stop_before_condition(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, stop_before_condition: bool) -> None

C++: protocols::design_opt::GreedyOptMutationMover::stop_before_condition(const bool) –> void

stopping_condition(*args, **kwargs)

Overloaded function.

1. stopping_condition(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, f: pyrosetta.rosetta.protocols.filters.Filter) -> None

C++: protocols::design_opt::GreedyOptMutationMover::stopping_condition(class std::shared_ptr<class protocols::filters::Filter>) –> void

2. stopping_condition(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover) -> pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::design_opt::GreedyOptMutationMover::stopping_condition() const –> class std::shared_ptr<class protocols::filters::Filter>

static subelement_ct_namer(tag_name: str) → str

C++: protocols::design_opt::GreedyOptMutationMover::subelement_ct_namer(std::string) –> std::string

static subsubelement_ct_namer(tag_name: str) → str

C++: protocols::design_opt::GreedyOptMutationMover::subsubelement_ct_namer(std::string) –> std::string

task_factory(*args, **kwargs)

Overloaded function.

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

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

2. task_factory(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::design_opt::GreedyOptMutationMover::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMoverCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMoverCreator, : pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMoverCreator) → pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMoverCreator

C++: protocols::design_opt::GreedyOptMutationMoverCreator::operator=(const class protocols::design_opt::GreedyOptMutationMoverCreator &) –> class protocols::design_opt::GreedyOptMutationMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMoverCreator) → str

C++: protocols::design_opt::GreedyOptMutationMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator, : pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator) → pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator

C++: protocols::design_opt::PointMutationCalculator::operator=(const class protocols::design_opt::PointMutationCalculator &) –> class protocols::design_opt::PointMutationCalculator &

calc_point_mut_filters(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator, start_pose: pyrosetta.rosetta.core.pose.Pose, seqpos_aa_vals_vec: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_utility_vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_std_allocator_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t) → None

C++: protocols::design_opt::PointMutationCalculator::calc_point_mut_filters(const class core::pose::Pose &, class utility::vector1<struct std::pair<unsigned long, class utility::vector1<struct std::pair<enum core::chemical::AA, class utility::vector1<double, class std::allocator<double> > >, class std::allocator<struct std::pair<enum core::chemical::AA, class utility::vector1<double, class std::allocator<double> > > > > >, class std::allocator<struct std::pair<unsigned long, class utility::vector1<struct std::pair<enum core::chemical::AA, class utility::vector1<double, class std::allocator<double> > >, class std::allocator<struct std::pair<enum core::chemical::AA, class utility::vector1<double, class std::allocator<double> > > > > > > > &) –> void

clone(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator) → pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator

C++: protocols::design_opt::PointMutationCalculator::clone() const –> class std::shared_ptr<class protocols::design_opt::PointMutationCalculator>

dump_pdb(*args, **kwargs)

Overloaded function.

1. dump_pdb(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator) -> bool

C++: protocols::design_opt::PointMutationCalculator::dump_pdb() const –> bool

2. dump_pdb(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator, dump_pdb: bool) -> None

C++: protocols::design_opt::PointMutationCalculator::dump_pdb(const bool) –> void

eval_filters(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator, pose: pyrosetta.rosetta.core.pose.Pose, filter_pass: bool, vals: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::design_opt::PointMutationCalculator::eval_filters(class core::pose::Pose &, bool &, class utility::vector1<double, class std::allocator<double> > &) –> void

filters(*args, **kwargs)

Overloaded function.

1. filters(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t

C++: protocols::design_opt::PointMutationCalculator::filters() const –> class utility::vector1<class std::shared_ptr<class protocols::filters::Filter>, class std::allocator<class std::shared_ptr<class protocols::filters::Filter> > >

2. filters(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator, filters: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t) -> None

C++: protocols::design_opt::PointMutationCalculator::filters(class utility::vector1<class std::shared_ptr<class protocols::filters::Filter>, class std::allocator<class std::shared_ptr<class protocols::filters::Filter> > >) –> void

mutate_and_relax(*args, **kwargs)

Overloaded function.

1. mutate_and_relax(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator, pose: pyrosetta.rosetta.core.pose.Pose, resi: int, target_aa: pyrosetta.rosetta.core.chemical.AA) -> None

C++: protocols::design_opt::PointMutationCalculator::mutate_and_relax(class core::pose::Pose &, const unsigned long &, const enum core::chemical::AA &) –> void

2. mutate_and_relax(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator, pose: pyrosetta.rosetta.core.pose.Pose, resi: int, target_aa: pyrosetta.rosetta.core.chemical.AA, green_packer: protocols::minimization_packing::GreenPacker) -> None

C++: protocols::design_opt::PointMutationCalculator::mutate_and_relax(class core::pose::Pose &, const unsigned long &, const enum core::chemical::AA &, class std::shared_ptr<class protocols::minimization_packing::GreenPacker>) –> void

parallel(*args, **kwargs)

Overloaded function.

1. parallel(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator, r: bool) -> None

C++: protocols::design_opt::PointMutationCalculator::parallel(const bool) –> void

2. parallel(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator) -> bool

C++: protocols::design_opt::PointMutationCalculator::parallel() const –> bool

relax_mover(*args, **kwargs)

Overloaded function.

1. relax_mover(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator) -> pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::design_opt::PointMutationCalculator::relax_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

2. relax_mover(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator, relax_mover: pyrosetta.rosetta.protocols.moves.Mover) -> None

C++: protocols::design_opt::PointMutationCalculator::relax_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

rtmin(*args, **kwargs)

Overloaded function.

1. rtmin(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator, r: bool) -> None

C++: protocols::design_opt::PointMutationCalculator::rtmin(const bool) –> void

2. rtmin(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator) -> bool

C++: protocols::design_opt::PointMutationCalculator::rtmin() const –> bool

sample_types(*args, **kwargs)

Overloaded function.

1. sample_types(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator) -> pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::design_opt::PointMutationCalculator::sample_types() const –> class utility::vector1<std::string, class std::allocator<std::string > >

2. sample_types(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator, sample_types: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: protocols::design_opt::PointMutationCalculator::sample_types(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

scorefxn(*args, **kwargs)

Overloaded function.

1. scorefxn(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator) -> pyrosetta.rosetta.core.scoring.ScoreFunction

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

2. scorefxn(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::design_opt::PointMutationCalculator::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_design_shell(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator, dz_shell: float) → None

C++: protocols::design_opt::PointMutationCalculator::set_design_shell(double) –> void

set_repack_shell(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator, rp_shell: float) → None

C++: protocols::design_opt::PointMutationCalculator::set_repack_shell(double) –> void

task_factory(*args, **kwargs)

Overloaded function.

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

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

2. task_factory(self: pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::design_opt::PointMutationCalculator::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

class pyrosetta.rosetta.protocols.design_opt.Supercharge

Bases: Mover

Adds charged residues to a protein surface

There are two modes for supercharging. The first is called AvNAPSA developed by the David Liu lab at Harvard. In this approach, surface residues are defined by the Average # Neighbor Atoms Per Sidechain Atom (AvNAPSA value), with a cutoff of 150. I think 100 is a safer cutoff. Arg, Lys, Asp, Glu, Asn, Gln are the only residues allowed to mutated. Lys is always chosen for positive, Glu is always chosen for negative, unless the native is Asn, then Asp is chosen. Thus, the sequence is deterministic. If one desires a particular net charge, the residues would be sorted from low to high AvNAPSA value and mutated one at a time until the target charge is achieved - this ignores the ceiling of 150 or 100. The second approach uses the Rosetta score function to guide the surface mutagenesis. The user must specifiy if Arg, Lys, or Asp, Glu are desired, and what the reference weights are. Alternatively, the user can specify a target net charge, and the reference weights of the charged residues will be incremented/decremented until the net charge is reached.

AvNAPSA-mode, target charge 1. Define surface. sort NQ and RK/DE residues by AvNAPSA value (low to high) 2. Next residue in sorted list: Positive: mutate DENQ–>K, Negative: mutate RKQ–>E and N–>D 3. If net charge = target net charge, output pdb

AvNAPSA-mode, no target charge 1. Define surface by AvNAPSA value (<100 default) 2. For each NQ and DE/RK residue in the surface: Positive: mutate DENQ–>K, Negative: mutate RKQ–>E and N–>D 3. Output pdb

Rosetta-mode, target charge 1. Define surface. Neighbor by distance calculator (CB dist.), <16 neighbors default

or Define surface by AvNAPSA value (<100 default)

2. Set design task read user resfile, if provided dont_mutate gly, pro, cys dont_mutate h-bonded sidechains dont_mutate correct charge residues

3. Set reference energies for RK/DE, starting at user input values

4. pack rotamers mover

5. check net charge, increment/decrement reference energies (back to step 3.)

6. Once a pack rotamers run results in the correct net charge, output pdb

Rosetta-mode, no target charge 1. Define surface. Neighbor by distance calculator (CB dist.), <16 neighbors default

or Define surface by AvNAPSA value (<100 default)

2. Set design task read user resfile, if provided dont_mutate gly, pro, cys dont_mutate h-bonded sidechains dont_mutate correct charge residues

3. Set reference energies for RK/DE, using the user input values

4. pack rotamers mover

5. Output pdb

Note: either mode will read a user input resfile, but be sure to use ALLAA as the default, because NATAA default will make the surface residues undesignable. Either mode will make a second resfile with NATAA as default.

CAUTION: Supercharge does it’s own output.

AvNAPSA_negative(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: bool) → None

C++: protocols::design_opt::Supercharge::AvNAPSA_negative(bool) –> void

AvNAPSA_positive(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: bool) → None

C++: protocols::design_opt::Supercharge::AvNAPSA_positive(bool) –> void

AvNAPSA_values(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, pose: pyrosetta.rosetta.core.pose.Pose) → None

average number of neighboring atoms per sidechain atom

C++: protocols::design_opt::Supercharge::AvNAPSA_values(const class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::design_opt::Supercharge::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, : pyrosetta.rosetta.protocols.design_opt.Supercharge) → pyrosetta.rosetta.protocols.design_opt.Supercharge

C++: protocols::design_opt::Supercharge::operator=(const class protocols::design_opt::Supercharge &) –> class protocols::design_opt::Supercharge &

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>

compare_residue_energies_all(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: bool) → None

C++: protocols::design_opt::Supercharge::compare_residue_energies_all(bool) –> void

compare_residue_energies_mut(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: bool) → None

C++: protocols::design_opt::Supercharge::compare_residue_energies_mut(bool) –> void

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>

design_supercharge(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, starting_pose: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::design_opt::Supercharge::design_supercharge(const class core::pose::Pose &, class core::pose::Pose &) –> void

design_supercharge_AvNAPSA(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, starting_pose: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::design_opt::Supercharge::design_supercharge_AvNAPSA(const class core::pose::Pose &, class core::pose::Pose &) –> void

dont_mutate_correct_charge(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: bool) → None

C++: protocols::design_opt::Supercharge::dont_mutate_correct_charge(bool) –> void

dont_mutate_glyprocys(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: bool) → None

C++: protocols::design_opt::Supercharge::dont_mutate_glyprocys(bool) –> void

dont_mutate_hbonded_sidechains(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: bool) → None

C++: protocols::design_opt::Supercharge::dont_mutate_hbonded_sidechains(bool) –> void

energy_comparison(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, native: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::design_opt::Supercharge::energy_comparison(class core::pose::Pose &, class core::pose::Pose &) –> void

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

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

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

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

fpd

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

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

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

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

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

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

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.design_opt.Supercharge) → str

C++: protocols::design_opt::Supercharge::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_net_charge(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::design_opt::Supercharge::get_net_charge(const class core::pose::Pose &) –> int

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

include_arg(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: bool) → None

C++: protocols::design_opt::Supercharge::include_arg(bool) –> void

include_asp(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: bool) → None

C++: protocols::design_opt::Supercharge::include_asp(bool) –> void

include_glu(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: bool) → None

C++: protocols::design_opt::Supercharge::include_glu(bool) –> void

include_lys(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: bool) → None

C++: protocols::design_opt::Supercharge::include_lys(bool) –> void

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

non-const accessor

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

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

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

local_nstruct(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: int) → None

C++: protocols::design_opt::Supercharge::local_nstruct(unsigned long) –> void

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

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

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

pre_packminpack(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: bool) → None

C++: protocols::design_opt::Supercharge::pre_packminpack(bool) –> void

prepack_input_structure(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::design_opt::Supercharge::prepack_input_structure(class core::pose::Pose &) –> void

print_netcharge_and_mutations(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, starting_pose: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::design_opt::Supercharge::print_netcharge_and_mutations(const class core::pose::Pose &, const class core::pose::Pose &) –> void

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

Provide citations to the passed CitationCollectionList

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

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

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

refweight_arg(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: float) → None

C++: protocols::design_opt::Supercharge::refweight_arg(double) –> void

refweight_asp(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: float) → None

C++: protocols::design_opt::Supercharge::refweight_asp(double) –> void

refweight_glu(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: float) → None

C++: protocols::design_opt::Supercharge::refweight_glu(double) –> void

refweight_lys(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: float) → None

C++: protocols::design_opt::Supercharge::refweight_lys(double) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

set_reference_energies(self: pyrosetta.rosetta.protocols.design_opt.Supercharge) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::design_opt::Supercharge::set_reference_energies() –> class utility::vector1<double, class std::allocator<double> >

set_resfile(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::design_opt::Supercharge::set_resfile(const class core::pose::Pose &) –> void

set_resfile_AvNAPSA(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::design_opt::Supercharge::set_resfile_AvNAPSA(const class core::pose::Pose &) –> void

set_surface(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::design_opt::Supercharge::set_surface(const class core::pose::Pose &) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

surface_atom_cutoff(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: int) → None

if target_net_charge is specified, the AvNAPSA cutoff is ignored

C++: protocols::design_opt::Supercharge::surface_atom_cutoff(unsigned long) –> void

surface_residue_cutoff(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: int) → None

C++: protocols::design_opt::Supercharge::surface_residue_cutoff(unsigned long) –> void

target_net_charge(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: int) → None

C++: protocols::design_opt::Supercharge::target_net_charge(int) –> void

target_net_charge_active(self: pyrosetta.rosetta.protocols.design_opt.Supercharge, s: bool) → None

C++: protocols::design_opt::Supercharge::target_net_charge_active(bool) –> void

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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