aa_composition

Bindings for protocols::aa_composition namespace

class pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

add_residue_selector(self: pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Add a ResidueSelector to the constraint to use as a mask.

The constraint must already have been created with the create_constraint_from_file() function before this function is called.

C++: protocols::aa_composition::AddCompositionConstraintMover::add_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

apply(self: pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover, : pyrosetta.rosetta.core.pose.Pose) None

Actually apply the mover to a pose.

C++: protocols::aa_composition::AddCompositionConstraintMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover, : pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover) pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover

C++: protocols::aa_composition::AddCompositionConstraintMover::operator=(const class protocols::aa_composition::AddCompositionConstraintMover &) –> class protocols::aa_composition::AddCompositionConstraintMover &

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.aa_composition.AddCompositionConstraintMover) pyrosetta.rosetta.protocols.moves.Mover

Copy this object and return a pointer to the copy.

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

constraint(self: pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover) pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint

Get an owning pointer to the AACompositionConstraint object created by this mover.

NULL unless the create_constraint_from_file() function has been called.

C++: protocols::aa_composition::AddCompositionConstraintMover::constraint() const –> class std::shared_ptr<const class core::scoring::aa_composition_energy::AACompositionConstraint>

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>

create_constraint_from_file(self: pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover, filename: str) None

Create the AACompositionConstraint object and initialize it from a .comp file.

C++: protocols::aa_composition::AddCompositionConstraintMover::create_constraint_from_file(const std::string &) –> void

create_constraint_from_file_contents(self: pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover, filecontents: str) None

Create the AACompositionConstraint object from the data from a .comp file.

Allows external code to create the constraint object without having it read directly from disk.

C++: protocols::aa_composition::AddCompositionConstraintMover::create_constraint_from_file_contents(const std::string &) –> void

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

Create a new object of this type and return a pointer to it.

C++: protocols::aa_composition::AddCompositionConstraintMover::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.aa_composition.AddCompositionConstraintMover) str

C++: protocols::aa_composition::AddCompositionConstraintMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static mover_name() str

C++: protocols::aa_composition::AddCompositionConstraintMover::mover_name() –> std::string

static name() str

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

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

Parse RosettaScripts XML tag to set up the mover.

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

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

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

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

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

C++: protocols::aa_composition::AddCompositionConstraintMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

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

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

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

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

each use.

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMoverCreator, : pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMoverCreator) pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMoverCreator

C++: protocols::aa_composition::AddCompositionConstraintMoverCreator::operator=(const class protocols::aa_composition::AddCompositionConstraintMoverCreator &) –> class protocols::aa_composition::AddCompositionConstraintMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMoverCreator) str

C++: protocols::aa_composition::AddCompositionConstraintMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

This mover adds sequence constraints to the ends of each helix, requiring at least one positively-charged residue in the three C-terminal residues, and at least one negatively-charged resiude in the three N-terminal residues.

add_alanine_constraints(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) bool

Should this mover add constraints to the helix requiring a certain alanine fraction?

Default true.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::add_alanine_constraints() const –> bool

add_c_terminal_constraints(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) bool

Should this mover add constraints to the C-termini of helices requiring positive charges there?

Default true.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::add_c_terminal_constraints() const –> bool

add_hydrophobic_constraints(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) bool

Should this mover add constraints to the helix requiring at minimum fraction of hydrophobic residues?

Default true.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::add_hydrophobic_constraints() const –> bool

add_n_terminal_constraints(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) bool

Should this mover add constraints to the N-termini of helices requiring negative charges there?

Default true.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::add_n_terminal_constraints() const –> bool

add_overall_constraints(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) bool

Should this mover add constraints to the helix penalizing helix-disfavouring residue types?

Default true.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::add_overall_constraints() const –> bool

ala_constraint_over_strength(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) float

Get the penalty for having 1% more than the desired fractional content of alanine.

Penalties ramp quadratically.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::ala_constraint_over_strength() const –> const double &

ala_constraint_under_strength(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) float

Get the penalty for having 1% less than the desired fractional content of alanine.

Penalties ramp quadratically.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::ala_constraint_under_strength() const –> const double &

apply(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Apply the mover

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover, : pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::operator=(const class protocols::aa_composition::AddHelixSequenceConstraintsMover &) –> class protocols::aa_composition::AddHelixSequenceConstraintsMover &

c_terminal_constraint_strength(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) float

The weight given to the C-terminal constraints.

The mover applies a quadratic penalty for having fewer than the desired number of positive charges at the C-terminus of each helix. This is the penalty for having one fewer than the desired number. There is no penalty or bonus for having more than the desired number.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::c_terminal_constraint_strength() const –> const double &

c_terminus_size(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) int

The number of C-terminal residues in each helix, in which positive charges must be found.

Default 3.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::c_terminus_size() const –> unsigned long

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.aa_composition.AddHelixSequenceConstraintsMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::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>

desired_ala_fraction(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) float

Get the desired fractional content of alanine in each helix.

Penalties ramp quadratically.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::desired_ala_fraction() const –> const double &

desired_min_hydrophobic_fraction(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) float

Get the desired minimum hydrophobic fraction.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::desired_min_hydrophobic_fraction() const –> const double &

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

required in the context of the parser/scripting scheme

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::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.aa_composition.AddHelixSequenceConstraintsMover) str

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::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

has_residue_selector(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) bool

Has a residue selector been specified for this mover?

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::has_residue_selector() const –> bool

hydrophobic_constraint_strength(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) float
Get the strength of the hydrophobic constraint. (The penalty for having more than 1% less than the

desired minimum hydrophobic content.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::hydrophobic_constraint_strength() const –> const double &

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_c_terminal_charges(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) int

The number of positive charges required at the C-terminus of each helix.

Default 2.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::min_c_terminal_charges() const –> unsigned long

min_helix_length(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) int

Get the minimum number of residues in a helix for the helix to be considered.

Very short helices (e.g. one turn, five residues) have negligible helix macrodipoles, and can be disregarded. Defaults to 8.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::min_helix_length() const –> unsigned long

min_n_terminal_charges(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) int

The number of negative charges required at the N-terminus of each helix.

Default 2.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::min_n_terminal_charges() const –> unsigned long

static mover_name() str

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::mover_name() –> std::string

n_terminal_constraint_strength(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) float

The weight given to the N-terminal constraints.

The mover applies a quadratic penalty for having fewer than the desired number of negative charges at the N-terminus of each helix. This is the penalty for having one fewer than the desired number. There is no penalty or bonus for having more than the desired number.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::n_terminal_constraint_strength() const –> const double &

n_terminus_size(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) int

The number of N-terminal residues in each helix, in which negative charges must be found.

Default 3.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::n_terminus_size() const –> unsigned long

static name() str

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

overall_constraints_strength(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) float

Get the strength of the helix constraints that penalize helix-disfavouring residue types.

This is the penalty for having one more than the maximum count of the disfavoured residues. Past this, the penalty ramps quadratically.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::overall_constraints_strength() const –> const double &

overall_max_count(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) int

Max number of residues from the types to avoid list per helix.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::overall_max_count() const –> unsigned long

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

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

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

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

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

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

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

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

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

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

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

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

each use.

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

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

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

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

reset_mode(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) bool

Get whether old composition constraints should be deleted before applying this mover.

Default false (i.e. new composition constraints are appended to the old).

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::reset_mode() 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

residue_selector(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) pyrosetta.rosetta.core.select.residue_selector.ResidueSelector
An optional residue selector. If provided, only helices that have at least one residue in the selection have

constraints applied. If unused, all heliecs receive constraints.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_add_alanine_constraints(*args, **kwargs)

Overloaded function.

  1. set_add_alanine_constraints(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover, setting: bool) -> None

Set whether this mover should add constraints to the helix requiring a certain alanine fraction.

Default true.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_alanine_constraints(const bool) –> void

  1. set_add_alanine_constraints(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover, setting: bool, desired_ala_fraction: float, ala_constraint_under_strength: float, ala_constraint_over_strength: float) -> None

Set whether this mover should add constraints to the helix requiring a certain alanine fraction.

Default true.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_alanine_constraints(const bool, const double &, const double &, const double &) –> void

set_add_c_terminal_constraints(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover, setting: bool, min_charges: int, cterm_size: int, strength: float) None

Set whether this mover should add constraints to the C-termini of helices requiring positive charges there.

Default true.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_c_terminal_constraints(const bool, const unsigned long, const unsigned long, const double &) –> void

set_add_hydrophobic_constraints(*args, **kwargs)

Overloaded function.

  1. set_add_hydrophobic_constraints(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover, setting: bool) -> None

Set whether this mover should add constraints to the helix requiring at minimum fraction of hydrophobic residues.

Default true.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_hydrophobic_constraints(const bool) –> void

  1. set_add_hydrophobic_constraints(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover, setting: bool, desired_min_hydrophobic_fraction: float, hydrophobic_constraint_strength: float) -> None

Set whether this mover should add constraints to the helix requiring at minimum fraction of hydrophobic residues.

Default true.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_hydrophobic_constraints(const bool, const double &, const double &) –> void

set_add_n_terminal_constraints(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover, setting: bool, min_charges: int, nterm_size: int, strength: float) None

Set whether this mover should add constraints to the N-termini of helices requiring negative charges there.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_n_terminal_constraints(const bool, const unsigned long, const unsigned long, const double &) –> void

set_add_overall_constraints(*args, **kwargs)

Overloaded function.

  1. set_add_overall_constraints(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover, setting: bool) -> None

Set whether this mover should add constraints to the helix penalizing helix-disfavouring residue types.

Default true.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_overall_constraints(const bool) –> void

  1. set_add_overall_constraints(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover, setting: bool, types_to_avoid: str, overall_max_count: int, overall_constraints_strength: float) -> None

Set whether this mover should add constraints to the helix penalizing helix-disfavouring residue types.

Default true.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::set_add_overall_constraints(const bool, const std::string &, const unsigned long, const double &) –> 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_min_helix_length(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover, setting: int) None

Set the minimum number of residues in a helix for the helix to be considered.

Very short helices (e.g. one turn, five residues) have negligible helix macrodipoles, and can be disregarded. Defaults to 8.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::set_min_helix_length(const unsigned long) –> void

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

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

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

set_reset_mode(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover, setting: bool) None

Set whether old composition constraints should be deleted before applying this mover.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::set_reset_mode(const bool) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Set a residue selector if specified by the user

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) -> None

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

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::show(std::ostream &) const –> void

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

types_to_avoid(*args, **kwargs)

Overloaded function.

  1. types_to_avoid(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover) -> pyrosetta.rosetta.utility.vector1_std_string

Access the vector of types to avoid.

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::types_to_avoid() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

  1. types_to_avoid(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover, index: int) -> str

Access an element in the vector of types to avoid.

Note: no bounds checking!

C++: protocols::aa_composition::AddHelixSequenceConstraintsMover::types_to_avoid(const unsigned long) const –> const std::string &

class pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMoverCreator, : pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMoverCreator) pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMoverCreator

C++: protocols::aa_composition::AddHelixSequenceConstraintsMoverCreator::operator=(const class protocols::aa_composition::AddHelixSequenceConstraintsMoverCreator &) –> class protocols::aa_composition::AddHelixSequenceConstraintsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMoverCreator) str

C++: protocols::aa_composition::AddHelixSequenceConstraintsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

add_residue_selector(self: pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Add a ResidueSelector to the constraint to use as a mask.

The constraint must already have been created with the create_constraint_from_file() function before this function is called.

C++: protocols::aa_composition::AddMHCEpitopeConstraintMover::add_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

add_weight(self: pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover, cst_weight: float) None

Add an individual weight to the constraint.

The constraint must already have been created with the create_constraint_from_file() function before this function is called.

C++: protocols::aa_composition::AddMHCEpitopeConstraintMover::add_weight(double) –> void

apply(self: pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover, : pyrosetta.rosetta.core.pose.Pose) None

Actually apply the mover to a pose.

C++: protocols::aa_composition::AddMHCEpitopeConstraintMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover, : pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover) pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover

C++: protocols::aa_composition::AddMHCEpitopeConstraintMover::operator=(const class protocols::aa_composition::AddMHCEpitopeConstraintMover &) –> class protocols::aa_composition::AddMHCEpitopeConstraintMover &

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.aa_composition.AddMHCEpitopeConstraintMover) pyrosetta.rosetta.protocols.moves.Mover

Copy this object and return a pointer to the copy.

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

constraint(self: pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover) pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint

Get an owning pointer to the MHCEpitopeConstraint object created by this mover.

NULL unless the create_constraint_from_file() function has been called.

C++: protocols::aa_composition::AddMHCEpitopeConstraintMover::constraint() const –> class std::shared_ptr<const class core::scoring::mhc_epitope_energy::MHCEpitopeConstraint>

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>

create_constraint_from_file(self: pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover, filename: str) None

Create the MHCEpitopeConstraint object and initialize it from a .mhc file.

C++: protocols::aa_composition::AddMHCEpitopeConstraintMover::create_constraint_from_file(const std::string &) –> void

create_constraint_from_file_contents(self: pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover, filecontents: str) None

Create the MHCEpitopeConstraint object from the data from a .mhc file.

Allows external code to create the constraint object without having it read directly from disk.

C++: protocols::aa_composition::AddMHCEpitopeConstraintMover::create_constraint_from_file_contents(const std::string &) –> void

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

Create a new object of this type and return a pointer to it.

C++: protocols::aa_composition::AddMHCEpitopeConstraintMover::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.aa_composition.AddMHCEpitopeConstraintMover) str

C++: protocols::aa_composition::AddMHCEpitopeConstraintMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static mover_name() str

C++: protocols::aa_composition::AddMHCEpitopeConstraintMover::mover_name() –> std::string

static name() str

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

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

Parse RosettaScripts XML tag to set up the mover.

Can trigger a read from disk.

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

provide_citation_info(self: pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation for this mover.

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

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

C++: protocols::aa_composition::AddMHCEpitopeConstraintMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

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

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

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

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

each use.

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMoverCreator, : pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMoverCreator) pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMoverCreator

C++: protocols::aa_composition::AddMHCEpitopeConstraintMoverCreator::operator=(const class protocols::aa_composition::AddMHCEpitopeConstraintMoverCreator &) –> class protocols::aa_composition::AddMHCEpitopeConstraintMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMoverCreator) str

C++: protocols::aa_composition::AddMHCEpitopeConstraintMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

add_residue_selector(self: pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Add a ResidueSelector to the constraint to use as a mask.

The constraint must already have been created with the create_constraint_from_file() function before this function is called.

C++: protocols::aa_composition::AddNetChargeConstraintMover::add_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

apply(self: pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover, : pyrosetta.rosetta.core.pose.Pose) None

Actually apply the mover to a pose.

C++: protocols::aa_composition::AddNetChargeConstraintMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover, : pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover) pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover

C++: protocols::aa_composition::AddNetChargeConstraintMover::operator=(const class protocols::aa_composition::AddNetChargeConstraintMover &) –> class protocols::aa_composition::AddNetChargeConstraintMover &

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.aa_composition.AddNetChargeConstraintMover) pyrosetta.rosetta.protocols.moves.Mover

Copy this object and return a pointer to the copy.

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

constraint(self: pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover) pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint

Get an owning pointer to the NetChargeConstraint object created by this mover.

NULL unless the create_constraint_from_file() function has been called.

C++: protocols::aa_composition::AddNetChargeConstraintMover::constraint() const –> class std::shared_ptr<const class core::scoring::netcharge_energy::NetChargeConstraint>

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>

create_constraint_from_file(self: pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover, filename: str) None

Create the NetChargeConstraint object and initialize it from a .charge file.

C++: protocols::aa_composition::AddNetChargeConstraintMover::create_constraint_from_file(const std::string &) –> void

create_constraint_from_file_contents(self: pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover, filecontents: str) None

Create the NetChargeConstraint object from the data from a .charge file.

Allows external code to create the constraint object without having it read directly from disk.

C++: protocols::aa_composition::AddNetChargeConstraintMover::create_constraint_from_file_contents(const std::string &) –> void

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

Create a new object of this type and return a pointer to it.

C++: protocols::aa_composition::AddNetChargeConstraintMover::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.aa_composition.AddNetChargeConstraintMover) str

C++: protocols::aa_composition::AddNetChargeConstraintMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static mover_name() str

C++: protocols::aa_composition::AddNetChargeConstraintMover::mover_name() –> std::string

static name() str

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

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

Parse RosettaScripts XML tag to set up the mover.

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

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

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

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

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

C++: protocols::aa_composition::AddNetChargeConstraintMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

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

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

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

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

each use.

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMoverCreator, : pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMoverCreator) pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMoverCreator

C++: protocols::aa_composition::AddNetChargeConstraintMoverCreator::operator=(const class protocols::aa_composition::AddNetChargeConstraintMoverCreator &) –> class protocols::aa_composition::AddNetChargeConstraintMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMoverCreator) str

C++: protocols::aa_composition::AddNetChargeConstraintMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover, : pyrosetta.rosetta.core.pose.Pose) None

Actually apply the mover to a pose.

C++: protocols::aa_composition::ClearCompositionConstraintsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover, : pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover) pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover

C++: protocols::aa_composition::ClearCompositionConstraintsMover::operator=(const class protocols::aa_composition::ClearCompositionConstraintsMover &) –> class protocols::aa_composition::ClearCompositionConstraintsMover &

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.aa_composition.ClearCompositionConstraintsMover) pyrosetta.rosetta.protocols.moves.Mover

Copy this object and return a pointer to the copy.

C++: protocols::aa_composition::ClearCompositionConstraintsMover::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.aa_composition.ClearCompositionConstraintsMover) pyrosetta.rosetta.protocols.moves.Mover

Create a new object of this type and return a pointer to it.

C++: protocols::aa_composition::ClearCompositionConstraintsMover::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.aa_composition.ClearCompositionConstraintsMover) str

C++: protocols::aa_composition::ClearCompositionConstraintsMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static mover_name() str

C++: protocols::aa_composition::ClearCompositionConstraintsMover::mover_name() –> std::string

static name() str

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

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

Parse RosettaScripts XML tag to set up the mover.

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

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

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

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

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

C++: protocols::aa_composition::ClearCompositionConstraintsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

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

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

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

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

each use.

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMoverCreator, : pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMoverCreator) pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMoverCreator

C++: protocols::aa_composition::ClearCompositionConstraintsMoverCreator::operator=(const class protocols::aa_composition::ClearCompositionConstraintsMoverCreator &) –> class protocols::aa_composition::ClearCompositionConstraintsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMoverCreator) str

C++: protocols::aa_composition::ClearCompositionConstraintsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

pyrosetta.rosetta.protocols.aa_composition.find_helices_over_length(pose: pyrosetta.rosetta.core.pose.Pose, helices: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, min_length: int) None

Given a pose, run DSSP and populate the helices list.

Ignores helices shorter than min_length.

C++: protocols::aa_composition::find_helices_over_length(const class core::pose::Pose &, class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, const unsigned long) –> void